Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012245.1 Corchorus olitorius cultivar O-4 contig12278, 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: 6175
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Found at i:1244 original size:54 final size:54
Alignment explanation
Indices: 1148--1262 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 54
1138 CTGATTAACC
* * *
1148 GGATCGCTTGAAGATAAGCCTAAATCCCTGAAAACTTCCTTGACTAACCGTACT
1 GGATCACTTGAAGATAAACCTAAATCCCTGAAAACTTCCTTGACTAACCGCACT
* * * * * *
1202 GGATCACTTGAAGATAAACTTAAA-CCACTGTAAATTTTCTTGATTGACCGCACT
1 GGATCACTTGAAGATAAACCTAAATCC-CTGAAAACTTCCTTGACTAACCGCACT
1256 GGATCAC
1 GGATCAC
1263 CTTTAGGAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (54 bp):
GGATCACTTGAAGATAAACCTAAATCCCTGAAAACTTCCTTGACTAACCGCACT
Found at i:1283 original size:37 final size:37
Alignment explanation
Indices: 1233--1309 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
1223 AAACCACTGT
1233 AAATTTTCTTGATTGACCGCACTGGATCACCTTTAGG
1 AAATTTTCTTGATTGACCGCACTGGATCACCTTTAGG
* *
1270 AAATTTTCTTGATTGACCGCACTTGATCACTTTTAGG
1 AAATTTTCTTGATTGACCGCACTGGATCACCTTTAGG
1307 AAA
1 AAA
1310 CTTAAACCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (37 bp):
AAATTTTCTTGATTGACCGCACTGGATCACCTTTAGG
Found at i:1333 original size:49 final size:51
Alignment explanation
Indices: 1277--1401 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
1267 AGGAAATTTT
* * * *
1277 CTTGATTGACCGCACTTGATCACTTT-TAG-GAAACTTAAACCACTGTAAA
1 CTTGATTGATCGCACTAGATCACTTTGAAGAAAAACTTAAACCACTGTAAA
*
1326 CTTGATTGATCGCAATAGATCACTTTGAAGAAAAACTTAAACCACTGTAAA
1 CTTGATTGATCGCACTAGATCACTTTGAAGAAAAACTTAAACCACTGTAAA
*
1377 CTTAATTGATCGCACTAGATCACTT
1 CTTGATTGATCGCACTAGATCACTT
1402 GAAACCACCA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 23 0.34
50 2 0.03
51 42 0.63
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (51 bp):
CTTGATTGATCGCACTAGATCACTTTGAAGAAAAACTTAAACCACTGTAAA
Found at i:1472 original size:16 final size:16
Alignment explanation
Indices: 1451--1501 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1441 ACTTGAAGTA
*
1451 AATTGAAGCATTGGAG
1 AATTGAAGAATTGGAG
1467 AATTGAAGAATTGGA-
1 AATTGAAGAATTGGAG
* *
1482 ACATTGAATAATTGAAG
1 A-ATTGAAGAATTGGAG
1499 AAT
1 AAT
1502 GGAGCATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.24, T:0.27
Consensus pattern (16 bp):
AATTGAAGAATTGGAG
Found at i:1486 original size:24 final size:24
Alignment explanation
Indices: 1451--1512 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
1441 ACTTGAAGTA
*
1451 AATT-GAAGCATTGGAGAATTGAAG
1 AATTGGAA-CATTGAAGAATTGAAG
*
1475 AATTGGAACATTGAATAATTGAAG
1 AATTGGAACATTGAAGAATTGAAG
*
1499 AA-TGGAGCATTGAA
1 AATTGGAACATTGAA
1513 TACCCCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.32
24 20 0.59
25 3 0.09
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (24 bp):
AATTGGAACATTGAAGAATTGAAG
Found at i:1611 original size:35 final size:35
Alignment explanation
Indices: 1564--1995 Score: 447
Period size: 35 Copynumber: 12.3 Consensus size: 35
1554 TAGGTCAACT
* *
1564 TGAAGAAAGATCGCCCTGAATCAATTGAAGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* * * *
1599 TGAAGAATGATCGCCCTGGTTCGATTGAAATTAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* *
1634 TGAAGAAAGATTGCCCTGGATCAATTGAAGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* *
1669 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* * *
1704 TGAAGAATGATTGCCCTGGATCAGTTGAAACT-AAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAA-TAAAC
** *
1739 TGAAGAAAGATCGCCCTGGATCAATTGAGGTAAAT
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* * * *
1774 TGAAGAAAGACCGCCCTGGGTCAAGTAAAATAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* * * * * *
1809 TGAAGAACGACCACCCTCGATCATTCTGACATAAAC
1 TGAAGAAAGATCGCCCTGGATCAAT-TGAAATAAAC
* * * *
1845 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* * *
1880 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
* *
1915 TGAAGAATGATCGCCCTGGATCATCTTGAAA-ACAAC
1 TGAAGAAAGATCGCCCTGGATCA-ATTGAAATA-AAC
* * * *
1951 TGAAGAAAGACCACCCTAGG-TCAACTGAAATAAAT
1 TGAAGAAAGATCGCCCT-GGATCAATTGAAATAAAC
1986 TGAAGAAAGA
1 TGAAGAAAGA
1996 CTGATCGGTC
Statistics
Matches: 334, Mismatches: 56, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
34 1 0.00
35 276 0.83
36 55 0.16
37 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (35 bp):
TGAAGAAAGATCGCCCTGGATCAATTGAAATAAAC
Found at i:1692 original size:105 final size:105
Alignment explanation
Indices: 1564--1996 Score: 492
Period size: 105 Copynumber: 4.1 Consensus size: 105
1554 TAGGTCAACT
* * * *
1564 TGAAGAAAGATCGCCCTGAATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGTTCGA-TTGAA
1 TGAAGAAAGACCGCCCTGGATCAATTGAAATAAACTGAAGAATGATCGCCCTGGATC-ATTTGAA
*
1628 ATTAACTGAAGAAAGATTGCCCTGGATCAATTGAAGTAAAC
65 ATTAACTGAAGAAAGATCGCCCTGGATCAATTGAAGTAAAC
* * * * *
1669 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATTGCCCTGGATCAGTTGAAA
1 TGAAGAAAGACCGCCCTGGATCAATTGAAATAAACTGAAGAATGATCGCCCTGGATCATTTGAAA
* * *
1734 CTAACTGAAGAAAGATCGCCCTGGATCAATTGAGGTAAAT
66 TTAACTGAAGAAAGATCGCCCTGGATCAATTGAAGTAAAC
* * * * * * * *
1774 TGAAGAAAGACCGCCCTGGGTCAAGTAAAATAAACTGAAGAACGACCACCCTCGATCATTCTGAC
1 TGAAGAAAGACCGCCCTGGATCAATTGAAATAAACTGAAGAATGATCGCCCTGGATCATT-TGAA
* * * * * *
1839 ATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
65 ATTAACTGAAGAAAGATCGCCCTGGATCAATTGAAGTAAAC
* *
1880 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAATGATCGCCCTGGATCATCTTGAA
1 TGAAGAAAGACCGCCCTGGATCAATTGAAATAAACTGAAGAATGATCGCCCTGGATCAT-TTGAA
** * * * * *
1945 AACAACTGAAGAAAGACCACCCTAGG-TCAACTGAAATAAAT
65 ATTAACTGAAGAAAGATCGCCCT-GGATCAATTGAAGTAAAC
1986 TGAAGAAAGAC
1 TGAAGAAAGAC
1997 TGATCGGTCG
Statistics
Matches: 284, Mismatches: 40, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
104 1 0.00
105 143 0.50
106 137 0.48
107 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (105 bp):
TGAAGAAAGACCGCCCTGGATCAATTGAAATAAACTGAAGAATGATCGCCCTGGATCATTTGAAA
TTAACTGAAGAAAGATCGCCCTGGATCAATTGAAGTAAAC
Found at i:2133 original size:78 final size:77
Alignment explanation
Indices: 1997--2143 Score: 258
Period size: 78 Copynumber: 1.9 Consensus size: 77
1987 GAAGAAAGAC
*
1997 TGATCGGTCGTCAGCAATCATAAAAATAATTCTCCACAAAATCCTAACTAAAGCAGATAGGGCAA
1 TGATCGGTCGTCAGCAATCATAAAAATAATTCCCCACAAAATCCTAACTAAAGCAGATAGGGCAA
2062 GTAGAGGTCGAT
66 GTAGAGGTCGAT
* *
2074 TGATCGGTCGTCAGCAATCATAAAAAATAATTCCCCACAAAATCCTAACTATAGTAGATAGGGCA
1 TGATCGGTCGTCAGCAATCAT-AAAAATAATTCCCCACAAAATCCTAACTAAAGCAGATAGGGCA
2139 AGTAG
65 AGTAG
2144 GGCCCGATCC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
77 21 0.32
78 45 0.68
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (77 bp):
TGATCGGTCGTCAGCAATCATAAAAATAATTCCCCACAAAATCCTAACTAAAGCAGATAGGGCAA
GTAGAGGTCGAT
Found at i:3689 original size:29 final size:30
Alignment explanation
Indices: 3652--3711 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
3642 AATTCTTTCC
* *
3652 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
3681 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
3712 CATGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:4278 original size:26 final size:26
Alignment explanation
Indices: 4210--4280 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
4200 AAGTGGACTT
4210 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATG-CCCTGAATGTG
* ** * *
4237 CAAATGACCAGGATGCCCTTAGTGT-
1 AAAATGACCAAAATGCCCTGAATGTG
4262 AAGAATGACCAAAATGCCC
1 AA-AATGACCAAAATGCCC
4281 CCTAGGTGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 1 0.03
26 22 0.63
27 12 0.34
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCTGAATGTG
Found at i:4625 original size:89 final size:88
Alignment explanation
Indices: 4515--4720 Score: 245
Period size: 89 Copynumber: 2.3 Consensus size: 88
4505 GAAGAAATAC
* ** * *
4515 TGCACCGCAGAAACTTAATTCACCGAATCGTCCTCAACTGTTTGAAAATGTGCTGCACCGAGCTC
1 TGCACCGCATAAACTT-ATTCACCGAATCACCCTCAACTATTTGAAAATGTGCTCCACCGAGCTC
*
4580 ACCGAATTCCAATCTTTGAAGA-GA
65 ACCGAATTCCAAT-ATTGAAGATGA
* * * *
4604 TGCACCGCATTAACTTGATTCACTGAATCACCCTGATCTATTTGAAAATGTGCTCCACCGAGCTC
1 TGCACCGCATAAACTT-ATTCACCGAATCACCCTCAACTATTTGAAAATGTGCTCCACCGAGCTC
*
4669 ACCGAATTCCAATATTGAAGATGC
65 ACCGAATTCCAATATTGAAGATGA
* *
4693 TACACCG-AGTCAACTTATTCACCGAATC
1 TGCACCGCA-TAAACTTATTCACCGAATC
4721 CCACTTGAAG
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
88 19 0.19
89 81 0.81
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (88 bp):
TGCACCGCATAAACTTATTCACCGAATCACCCTCAACTATTTGAAAATGTGCTCCACCGAGCTCA
CCGAATTCCAATATTGAAGATGA
Found at i:4733 original size:42 final size:42
Alignment explanation
Indices: 4683--4882 Score: 296
Period size: 42 Copynumber: 4.8 Consensus size: 42
4673 AATTCCAATA
* * * *
4683 TTGAAGATGCTACACCGAGTCAACTTATTCACCGAATCCCAC
1 TTGAAGATGCTACCCCGAGTCATCTGATTCACCGAATCCCGC
*
4725 TTGAAGATGCTACACCGAGTCATCTGATTCACCGAATCCCGC
1 TTGAAGATGCTACCCCGAGTCATCTGATTCACCGAATCCCGC
* * * *
4767 TTGAAGATGATACCCCGAGTCATCTAATTCACCAAATCCTGC
1 TTGAAGATGCTACCCCGAGTCATCTGATTCACCGAATCCCGC
*
4809 TTGAAGATGCTACCCCGAGTCATCTGATTAACCGAAT--CGC
1 TTGAAGATGCTACCCCGAGTCATCTGATTCACCGAATCCCGC
4849 TTGAAGATGCTACCCCGAGTCATCTGATTCACCG
1 TTGAAGATGCTACCCCGAGTCATCTGATTCACCG
4883 TCGCTTGAAG
Statistics
Matches: 144, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 35 0.24
42 109 0.76
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (42 bp):
TTGAAGATGCTACCCCGAGTCATCTGATTCACCGAATCCCGC
Found at i:5015 original size:37 final size:38
Alignment explanation
Indices: 4965--5042 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 38
4955 AAACCACTGT
4965 AAATTTTCTTGATTGACCGCAC-TGGATCACCTTTAGG
1 AAATTTTCTTGATTGACCGCACTTGGATCACCTTTAGG
*
5002 AAATTTTCTTGATTGACCGCACTTGGATCACTTTTAGG
1 AAATTTTCTTGATTGACCGCACTTGGATCACCTTTAGG
5040 AAA
1 AAA
5043 CTTAAACCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 22 0.56
38 17 0.44
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (38 bp):
AAATTTTCTTGATTGACCGCACTTGGATCACCTTTAGG
Found at i:5102 original size:51 final size:49
Alignment explanation
Indices: 5009--5134 Score: 144
Period size: 51 Copynumber: 2.5 Consensus size: 49
4999 AGGAAATTTT
* * * * * * *
5009 CTTGATTGACCGCACTTGGATCACTTTTAGGAAACTTAAACCAGTGTAAA
1 CTTGATTGATCGCA-ATAGATCACTTTAAGAAAACTTAAACCACTATAAA
*
5059 CTTGATTGATCGCAGTAGATCACTTTGAAGAAAATCTTAAACCACTATAAA
1 CTTGATTGATCGCAATAGATCACTTT-AAGAAAA-CTTAAACCACTATAAA
*
5110 CTTAATTGATCGCAATAGATCACTT
1 CTTGATTGATCGCAATAGATCACTT
5135 GAAACCACCA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 10 0.15
50 18 0.28
51 37 0.57
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (49 bp):
CTTGATTGATCGCAATAGATCACTTTAAGAAAACTTAAACCACTATAAA
Found at i:5205 original size:16 final size:16
Alignment explanation
Indices: 5184--5234 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5174 AGTTGAAGTA
*
5184 AATTGAAGTATTGGAG
1 AATTGAAGAATTGGAG
5200 AATTGAAGAATTGGA-
1 AATTGAAGAATTGGAG
* *
5215 ACATTGAATAATTGAAG
1 A-ATTGAAGAATTGGAG
5232 AAT
1 AAT
5235 GGAGCATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (16 bp):
AATTGAAGAATTGGAG
Found at i:5220 original size:24 final size:23
Alignment explanation
Indices: 5193--5245 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
5183 AAATTGAAGT
*
5193 ATTGGAGAATTGAAGAATTGGAAC
1 ATTGAAGAATTGAAGAA-TGGAAC
* *
5217 ATTGAATAATTGAAGAATGGAGC
1 ATTGAAGAATTGAAGAATGGAAC
5240 ATTGAA
1 ATTGAA
5246 TACCCCCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.26
Consensus pattern (23 bp):
ATTGAAGAATTGAAGAATGGAAC
Found at i:5242 original size:23 final size:24
Alignment explanation
Indices: 5200--5247 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
5190 AGTATTGGAG
5200 AATTGAAGAATTGGAACATTGAAT
1 AATTGAAGAATTGGAACATTGAAT
*
5224 AATTGAAGAA-TGGAGCATTGAAT
1 AATTGAAGAATTGGAACATTGAAT
5247 A
1 A
5248 CCCCCAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (24 bp):
AATTGAAGAATTGGAACATTGAAT
Found at i:5344 original size:35 final size:35
Alignment explanation
Indices: 5297--6114 Score: 393
Period size: 35 Copynumber: 23.2 Consensus size: 35
5287 TAGGTCAACT
* * * *
5297 TGAAGAAAGATCGCCTTGAATCAATTGAAGTAGAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* * * *
5332 TGAAGAATGATCGCCCTGGTTCGATTGAAATTAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* ****
5367 TGAAGAAAGAT-TTTTTGGATCAATTGAAGTAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
5401 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
*
5436 TGAAAAATGATCGCCCTGGATCAATTGAAGTAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* * * *
5471 TGAAGAATGATTGCCTTGGATCAGTTGAAACT-AAC
1 TGAAGAATGATCGCCCTGGATCAATTG-AAGTAAAC
* * **
5506 TGAAGAAAGATCGCCCTGGATCAATTGAGGTAATT
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* * * **
5541 TGAAGAAAG-TCCGCCTTGGGTCAACTAAAAG-AAAC
1 TGAAGAATGAT-CGCCCTGGATCAA-TTGAAGTAAAC
* * ** * * * * **
5576 TCAAGAACGGCCACCCTCGATCATTCTTACTTAAAC
1 TGAAGAATGATCGCCCTGGATCAAT-TGAAGTAAAC
* * * * * *
5612 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* * * * *
5647 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* * * * *
5682 TAAAGAACGACCACCCCGGATC-ATTCGGACA-TAAAC
1 TGAAGAATGATCGCCCTGGATCAATT--GA-AGTAAAC
* * * * *
5718 TGAAGAAAAGACCACCCTGGATCAACTGAAATAAAC
1 TGAAG-AATGATCGCCCTGGATCAATTGAAGTAAAC
** * * * *
5754 TGAAGAAAAACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* * * * *
5789 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
* * * *
5824 TAAAGAACGACCACCCTGGATC-ATTCGGACA-TAAAC
1 TGAAGAATGATCGCCCTGGATCAATT--GA-AGTAAAC
* * * * * *
5860 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAG-AATGATCGCCCTGGATCAATTGAAGTAAAC
* * * * * *
5896 TGAAAAATGACCACCCTCGATCATTCTGACA-TAAAT
1 TGAAGAATGATCGCCCTGGATCAAT-TGA-AGTAAAC
* * * * * *
5932 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAG-AATGATCGCCCTGGATCAATTGAAGTAAAC
* * * * *
5968 TGAAGAAAGACCGCCCTAGG-TCTACTGAAATAAAC
1 TGAAGAATGATCGCCCT-GGATCAATTGAAGTAAAC
*
6003 TGAAG-ATGATCGCCCTGGATCAACTTGAA-AACAAC
1 TGAAGAATGATCGCCCTGGATCAA-TTGAAGTA-AAC
* * * * * *
6038 TGAAGAAAGACCACCCTTGG-TCAACTGAAATAAAT
1 TGAAGAATGATCGCCC-TGGATCAATTGAAGTAAAC
* * * * * *
6073 TGAAGAAAGACCGCGCTGGGTCAACTGAAATAAAC
1 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
6108 TGAAGAA
1 TGAAGAA
6115 CGACCACCCT
Statistics
Matches: 632, Mismatches: 119, Indels: 64
0.78 0.15 0.08
Matches are distributed among these distances:
33 2 0.00
34 49 0.08
35 416 0.66
36 110 0.17
37 51 0.08
38 4 0.01
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (35 bp):
TGAAGAATGATCGCCCTGGATCAATTGAAGTAAAC
Found at i:5371 original size:70 final size:69
Alignment explanation
Indices: 5297--6114 Score: 435
Period size: 70 Copynumber: 11.6 Consensus size: 69
5287 TAGGTCAACT
* * * *
5297 TGAAGAAAGATCGCCTTGAATCAATTGAAGTAGACTGAAGAATGATCGCCCTGGTTCGATTGAAA
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATC-ATTGAAA
5362 TTAAC
65 TTAAC
**** *
5367 TGAAGAAAGAT-TTTTTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATCAATTGAAG
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATC-ATTGAAA
*
5431 TAAAC
65 TTAAC
* *
5436 TGAA-AAATGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATTGCCTTGGATCAGTTGAA
1 TGAAGAAA-GATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATCA-TTGAA
*
5500 ACTAAC
64 ATTAAC
* ** * * * * *
5506 TGAAGAAAGATCGCCCTGGATCAATTGAGGTAATTTGAAGAAAG-TCCGCCTTGGGTCAACTAAA
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGAT-CGCCCTGGATC-ATTGAA
**
5570 AGAAAC
64 ATTAAC
* * ** * * * * ** * * * * *
5576 TCAAGAACGGCCACCCTCGATCATTCTTACTTAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
1 TGAAGAAAGATCGCCCTGGATCAAT-TGAAGTAAACTGAAGAATGATCGCCCTGGATC-ATTGAA
*
5641 ATAAAC
64 ATTAAC
* * * * * * * * * *
5647 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTAAAGAACGACCACCCCGGATCATTCGGAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATCATT--GAA
*
5712 ATAAAC
64 ATTAAC
* * * * ** * * *
5718 TGAAGAAAAGACCACCCTGGATCAACTGAAATAAACTGAAGAAAAACCGCCCTGGGTCAACTGAA
1 TGAAG-AAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATC-ATTGAA
*
5783 ATAAAC
64 ATTAAC
* * * * * * * * *
5789 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTAAAGAACGACCACCCTGGATCATTCGGAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATCATT--GAA
*
5854 ATAAAC
64 ATTAAC
* * * * * * * * *
5860 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAAAATGACCACCCTCGATCATTCTGA
1 TGAAG-AAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATCA-T-TGA
* * *
5925 CATAAAT
63 AATTAAC
* * * * * * * *
5932 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTAGG-TCTACTGA
1 TGAAG-AAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCT-GGATC-ATTGA
*
5996 AATAAAC
63 AATTAAC
* * * * * *
6003 TGAAG-ATGATCGCCCTGGATCAACTTGAA-AACAACTGAAGAAAGACCACCCTTGG-TCAACTG
1 TGAAGAAAGATCGCCCTGGATCAA-TTGAAGTA-AACTGAAGAATGATCGCCC-TGGATC-ATTG
* *
6065 AAATAAAT
62 AAATTAAC
* * * * *
6073 TGAAGAAAGACCGCGCTGGGTCAACTGAAATAAACTGAAGAA
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAA
6115 CGACCACCCT
Statistics
Matches: 615, Mismatches: 109, Indels: 48
0.80 0.14 0.06
Matches are distributed among these distances:
68 3 0.00
69 77 0.13
70 254 0.41
71 123 0.20
72 152 0.25
73 5 0.01
74 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (69 bp):
TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAGAATGATCGCCCTGGATCATTGAAAT
TAAC
Found at i:5576 original size:105 final size:104
Alignment explanation
Indices: 5297--5798 Score: 297
Period size: 106 Copynumber: 4.8 Consensus size: 104
5287 TAGGTCAACT
* * * * * * *
5297 TGAAGAAAGATCGCCTTGAATCAATTGAAGTAGACTGAAGAATGATCGCCCTGGTTCGATTGAAA
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAAAATGATCGCCCTGGATC-AATAAAA
* ** *
5362 -TTAACTGAAGAAAGATTTTTTGGATCAATTGAAGTAAAC
65 GTAAACTGAAGAAAGATTCCTTGGATCAATTGAACTAAAC
* **
5401 TGAAGAATGATCGCCCTGGATCAATTGAAGTAAACTGAAAAATGATCGCCCTGGATCAATTGAAG
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAAAATGATCGCCCTGGATCAATAAAAG
* *
5466 TAAACTGAAGAATGATTGCCTTGGATCAGTTGAAACT-AAC
66 TAAACTGAAGAAAGATT-CCTTGGATCAATTG-AACTAAAC
* ** * *
5506 TGAAGAAAGATCGCCCTGGATCAATTGAGGTAATTTGAAGAAA-G-TCCGCCTTGGGTCAACTAA
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAA-AAATGAT-CGCCCTGGATCAA-TAA
* * *** * * **
5569 AAG-AAACTCAAGAACGGCCACCCTCGATC-ATTCTTACTTAAAC
63 AAGTAAACTGAAGAA-AGATTCCTTGGATCAATT-GAAC-TAAAC
* * * * * * * *
5612 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAA-GACCGCCCTGGGTCAACTGAA
1 TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAA-AAATGATCGCCCTGGATCAA-TAAA
* * ** ** *
5676 A-TAAACTAAAGAACGACCACCCCGGATC-ATTCGGACATAAAC
64 AGTAAACTGAAGAAAGA-TTCCTTGGATCAATT-GAAC-TAAAC
* * * * * * * *
5718 TGAAGAAAAGACCACCCTGGATCAACTGAAATAAACTGAAGAAA-AACCGCCCTGGGTCAACTGA
1 TGAAG-AAAGATCGCCCTGGATCAATTGAAGTAAACTGAA-AAATGATCGCCCTGGATCAA-TAA
5782 AA-TAAACTGAAGAAAGA
63 AAGTAAACTGAAGAAAGA
5799 CCGCCCTGGG
Statistics
Matches: 328, Mismatches: 56, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
103 4 0.01
104 71 0.22
105 80 0.24
106 102 0.31
107 71 0.22
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (104 bp):
TGAAGAAAGATCGCCCTGGATCAATTGAAGTAAACTGAAAAATGATCGCCCTGGATCAATAAAAG
TAAACTGAAGAAAGATTCCTTGGATCAATTGAACTAAAC
Found at i:5651 original size:106 final size:106
Alignment explanation
Indices: 5396--6175 Score: 768
Period size: 106 Copynumber: 7.3 Consensus size: 106
5386 TCAATTGAAG
* * * * * * * *
5396 TAAACTGAAGAATGATCGCCCTGGATCAATTGAAGTAAACTGAA-AAATGATCGCCCTGGATCAA
1 TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAA-GACCGCCCTGGGTCAA
* * * *** * * * *
5460 TTGAAGTAAACTGAAGAATGATTGCCTTGGATCAGT-TGAAA
65 CTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACA
* * * * ** ** * *
5501 CT-AACTGAAGAAAGATCGCCCTGGATCAATTGAGGTAATTTGAAGAAAGTCCGCCTTGGGTCAA
1 -TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * * *
5565 CTAAAAGAAACTCAAGAACGGCCACCCTCGATCATTCTTACT
65 CTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACA
5607 TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
1 TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
* *
5672 TGAAATAAACTAAAGAACGACCACCC-CGGATCATTCGGACA
66 TGAAATAAACTGAAGAACGACCACCCTC-GATCATTCTGACA
* *
5713 TAAACTGAAGAAAAGACCACCCTGGATCAACTGAAATAAACTGAAGAAAAACCGCCCTGGGTCAA
1 TAAACTGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * * *
5778 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCA-ACTGAAA
65 CTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACA
* * * * * * *
5819 TAAACTAAAGAACGACCACCCTGGATCATTCGGACATAAACTGAAGAAAAGACCACCCTGGGTCA
1 TAAACTGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAACTGAAG-AAAGACCGCCCTGGGTCA
* *
5884 ACTGAAATAAACTGAAAAATGACCACCCTCGATCATTCTGACA
64 ACTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACA
* * *
5927 TAAATTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTAGGTCTA
1 TAAACTGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * *
5992 CTGAAATAAACTGAAG-ATGATCGCCCTGGATCA-ACTTGA-A
65 CTGAAATAAACTGAAGAACGACCACCCTCGATCATTC-TGACA
* * * *
6032 AACAACTGAAGAAAGACCACCCTTGGTCAACTGAAATAAATTGAAGAAAGACCGCGCTGGGTCAA
1 TA-AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* *
6097 CTGAAATAAACTGAAGAACGACCACCCTCAATCATTCCGA-A
65 CTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACA
** *
6138 CTGGACTGAAGAACGACCACCCTGGGTCAACTTGAAAT
1 -TAAACTGAAGAAAGACCACCCTGGGTCAAC-TGAAAT
Statistics
Matches: 559, Mismatches: 99, Indels: 31
0.81 0.14 0.04
Matches are distributed among these distances:
105 160 0.29
106 192 0.34
107 164 0.29
108 27 0.05
109 16 0.03
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (106 bp):
TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
TGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACA
Found at i:5774 original size:142 final size:143
Alignment explanation
Indices: 5607--6175 Score: 737
Period size: 142 Copynumber: 4.0 Consensus size: 143
5597 CATTCTTACT
5607 TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
1 TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
5672 TGAAATAAACTAAAGAACGACCACCC-CGGATCATTCGGACATAAACTGAAGAAAAGACCACCCT
66 TGAAATAAACTAAAGAACGACCACCCTCGGATCATTCGGACATAAACTGAAG-AAAGACCACCCT
5736 GGATCAAC-TGAAA
130 GGATCAACTTGAAA
* *
5749 TAAACTGAAGAAAAACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
1 TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
5814 TGAAATAAACTAAAGAACGACCACCCT-GGATCATTCGGACATAAACTGAAGAAAAGACCACCCT
66 TGAAATAAACTAAAGAACGACCACCCTCGGATCATTCGGACATAAACTGAAG-AAAGACCACCCT
*
5878 GGGTCAAC-TGAAA
130 GGATCAACTTGAAA
* * * * * *
5891 TAAACTGAA-AAATGACCACCCTCGATCATTCTGACATAAATTGAAGAAAAGACCACCCTGGGTC
1 TAAACTGAAGAAA-GACCACCCTGGGTCA-ACTGAAATAAACTGAAG-AAAGACCGCCCTGGGTC
* * * * * * * * * *
5955 AACTGAAATAAACTGAAGAAAGACCGCCCTAGG-TC-TACTGAAATAAACTGAAG-ATGATCGCC
63 AACTGAAATAAACTAAAGAACGACCACCCTCGGATCATTCGGACATAAACTGAAGAAAGACCACC
6017 CTGGATCAACTTGAAA
128 CTGGATCAACTTGAAA
* * *
6033 -ACAACTGAAGAAAGACCACCCTTGGTCAACTGAAATAAATTGAAGAAAGACCGCGCTGGGTCAA
1 TA-AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * ** *
6097 CTGAAATAAACTGAAGAACGACCACCCTC-AATCATTCCGA-ACTGGACTGAAGAACGACCACCC
65 CTGAAATAAACTAAAGAACGACCACCCTCGGATCATTCGGACA-TAAACTGAAGAAAGACCACCC
*
6160 TGGGTCAACTTGAAA
129 TGGATCAACTTGAAA
6175 T
1 T
Statistics
Matches: 375, Mismatches: 39, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
140 46 0.12
141 46 0.12
142 204 0.54
143 32 0.09
144 45 0.12
145 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (143 bp):
TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
TGAAATAAACTAAAGAACGACCACCCTCGGATCATTCGGACATAAACTGAAGAAAGACCACCCTG
GATCAACTTGAAA
Found at i:5920 original size:214 final size:211
Alignment explanation
Indices: 5607--6175 Score: 781
Period size: 214 Copynumber: 2.7 Consensus size: 211
5597 CATTCTTACT
5607 TAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
1 TAAACTGAAGAAAGACCACCCT-GGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
*
5672 TGAAATAAACT-AAAGAACGACCACCC-CGGATCATTCGGACATAAACTGAAGAAAAGACCACCC
65 TGAAATAAACTGAAA-AACGACCACCCTC-GATCATTCCGACATAAACTGAAGAAAAGACCACCC
* *
5735 TGGATCAACTGAAATAAACTGAAGAAAAACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGAC
128 TGGGTCAACTGAAATAAACTGAAGAAAAACCGCCCTAGGTCAACTGAAATAAACTGAAG-AAGAC
*
5800 CGCCCTGGGTCAAC-TGAAA
192 CGCCCTGGATCAACTTGAAA
* * * * * *
5819 TAAACTAAAGAACGACCACCCTGGATCATTCGGACATAAACTGAAGAAAAGACCACCCTGGGTCA
1 TAAACTGAAGAAAGACCACCCTGG-TCA-ACTGAAATAAACTGAAG-AAAGACCGCCCTGGGTCA
* * *
5884 ACTGAAATAAACTGAAAAATGACCACCCTCGATCATTCTGACATAAATTGAAGAAAAGACCACCC
63 ACTGAAATAAACTGAAAAACGACCACCCTCGATCATTCCGACATAAACTGAAGAAAAGACCACCC
* * * *
5949 TGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTAGGTCTACTGAAATAAACTGAAGATGATC
128 TGGGTCAACTGAAATAAACTGAAGAAAAACCGCCCTAGGTCAACTGAAATAAACTGAAGAAGACC
6014 GCCCTGGATCAACTTGAAA
193 GCCCTGGATCAACTTGAAA
* *
6033 -ACAACTGAAGAAAGACCACCCTTGGTCAACTGAAATAAATTGAAGAAAGACCGCGCTGGGTCAA
1 TA-AACTGAAGAAAGACCACCC-TGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * ** *
6097 CTGAAATAAACTGAAGAACGACCACCCTCAATCATTCCGA-ACTGGACTGAAG-AACGACCACCC
64 CTGAAATAAACTGAAAAACGACCACCCTCGATCATTCCGACA-TAAACTGAAGAAAAGACCACCC
6160 TGGGTCAACTTGAAAT
128 TGGGTCAAC-TGAAAT
Statistics
Matches: 315, Mismatches: 32, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
211 22 0.07
212 89 0.28
213 44 0.14
214 153 0.49
215 7 0.02
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (211 bp):
TAAACTGAAGAAAGACCACCCTGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACT
GAAATAAACTGAAAAACGACCACCCTCGATCATTCCGACATAAACTGAAGAAAAGACCACCCTGG
GTCAACTGAAATAAACTGAAGAAAAACCGCCCTAGGTCAACTGAAATAAACTGAAGAAGACCGCC
CTGGATCAACTTGAAA
Done.