Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012383.1 Corchorus olitorius cultivar O-4 contig12416, 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: 53953
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1977 original size:22 final size:23
Alignment explanation
Indices: 1938--1980 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
1928 AATCCTAATC
1938 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
1961 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
1981 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:7020 original size:22 final size:23
Alignment explanation
Indices: 6981--7023 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
6971 AATCCTAATC
6981 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
7004 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
7024 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:8950 original size:42 final size:43
Alignment explanation
Indices: 8899--8992 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
8889 AGTGTATTAC
* * * *
8899 CTAA-ATTCTA-CTCCATCTTTAGGTAATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
8940 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
8985 CTAATATT
1 CTAATATT
8993 AATTGTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 35 0.78
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:10988 original size:28 final size:26
Alignment explanation
Indices: 10955--11011 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 26
10945 GGTAAAAATA
10955 AAATAATTATAAAATATTGAATTTAATT
1 AAATAA-TA-AAAATATTGAATTTAATT
10983 --A-AATAAAAATATTGAATTTAATT
1 AAATAATAAAAATATTGAATTTAATT
11006 AAATAA
1 AAATAA
11012 AAATAGAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
23 18 0.69
24 2 0.08
25 3 0.12
26 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
AAATAATAAAAATATTGAATTTAATT
Found at i:10993 original size:23 final size:23
Alignment explanation
Indices: 10965--11016 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
10955 AAATAATTAT
10965 AAAATATTGAATTTAATTAAATA
1 AAAATATTGAATTTAATTAAATA
10988 AAAATATTGAATTTAATTAAATA
1 AAAATATTGAATTTAATTAAATA
11011 AAAATA
1 AAAATA
11017 GAGGTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
AAAATATTGAATTTAATTAAATA
Found at i:11025 original size:23 final size:23
Alignment explanation
Indices: 10973--11036 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
10963 ATAAAATATT
**
10973 GAATTTAATTAAATAAAAATATT
1 GAATTTAATTAAATAAAAATAGA
10996 GAATTTAATTAAATAAAAATAGA
1 GAATTTAATTAAATAAAAATAGA
**
11019 GGTTTTAA-TAGAATAAAA
1 GAATTTAATTA-AATAAAA
11037 CTATATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
GAATTTAATTAAATAAAAATAGA
Found at i:12543 original size:12 final size:12
Alignment explanation
Indices: 12528--12552 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12518 TTTTTTTTAC
12528 TTCTTTTTTCTT
1 TTCTTTTTTCTT
12540 TTCTTTTTTCTT
1 TTCTTTTTTCTT
12552 T
1 T
12553 GGCTAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:13876 original size:31 final size:30
Alignment explanation
Indices: 13841--13911 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 30
13831 TACTCAGAAG
13841 GTCCCTCTACTTTCACAAAAA-AATCAATTTC
1 GTCCCTCTACTTT-A-AAAAAGAATCAATTTC
*
13872 GTCCCTCTAC--TAAAAAAGGATCAATTTC
1 GTCCCTCTACTTTAAAAAAGAATCAATTTC
*
13900 GTCCCTTTACTT
1 GTCCCTCTACTT
13912 GGCACTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 5 0.14
28 19 0.54
29 1 0.03
31 10 0.29
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (30 bp):
GTCCCTCTACTTTAAAAAAGAATCAATTTC
Found at i:16208 original size:2 final size:2
Alignment explanation
Indices: 16201--16226 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16191 TAAATTACTG
16201 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
16227 TTATTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19740 original size:59 final size:59
Alignment explanation
Indices: 19641--19785 Score: 236
Period size: 59 Copynumber: 2.5 Consensus size: 59
19631 AGTTATTGGG
* * *
19641 CTCTTCTTGAGACCCCATTGTTAGTGTGAGTAATGGTACATATCCTTTATTCTTTCTGC
1 CTCTTCTTGAGCCCCCATTGTTAGAGTGAGTAATGATACATATCCTTTATTCTTTCTGC
* *
19700 CTCTTATTGAGCCCCCATTGTTAGAGTGAGTGATGATACATATCCTTTATTCTTTCTGC
1 CTCTTCTTGAGCCCCCATTGTTAGAGTGAGTAATGATACATATCCTTTATTCTTTCTGC
*
19759 CTCTTCTTGAGCCTCCATTGTTAGAGT
1 CTCTTCTTGAGCCCCCATTGTTAGAGT
19786 AATGGTGTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (59 bp):
CTCTTCTTGAGCCCCCATTGTTAGAGTGAGTAATGATACATATCCTTTATTCTTTCTGC
Found at i:22551 original size:23 final size:23
Alignment explanation
Indices: 22505--22551 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
22495 AGCTTCAGAG
** *
22505 AAATTTGTTAAAAACATTCCTTA
1 AAATTTGTTAAAAACAGGCATTA
22528 AAATTTGTTAAAAACAGGCATTA
1 AAATTTGTTAAAAACAGGCATTA
22551 A
1 A
22552 TTTCTAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (23 bp):
AAATTTGTTAAAAACAGGCATTA
Found at i:24949 original size:24 final size:26
Alignment explanation
Indices: 24903--24952 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
24893 TTGGGTCAAA
24903 TTCCTTTTAATCCATGCATTTGGGCTCT
1 TTCCTTTTAATCCATG-A-TTGGGCTCT
24931 TTCCTTTTAATCCA-G-TTGGGCT
1 TTCCTTTTAATCCATGATTGGGCT
24953 TTGAGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.32
27 1 0.05
28 14 0.64
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (26 bp):
TTCCTTTTAATCCATGATTGGGCTCT
Found at i:29002 original size:54 final size:55
Alignment explanation
Indices: 28938--29043 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 55
28928 AAAAATACCC
* * * * *
28938 TTTCGGTCAAAGGGTCGGTTTT-GTCTTTTTTGCCTTTAAGTTTAGTATTTTCACA
1 TTTCGGTCAAAGGGTC-ATTTTCGCCTTTTTCGCATCTAAGTTTAGTATTTTCACA
*
28993 TTTC-GTCAAAGGGTCATTTTCGCCTTTTTCGCATCTAAGTTTAGTGTTTTC
1 TTTCGGTCAAAGGGTCATTTTCGCCTTTTTCGCATCTAAGTTTAGTATTTTC
29044 TATTTCCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
53 4 0.09
54 36 0.82
55 4 0.09
ACGTcount: A:0.16, C:0.17, G:0.19, T:0.48
Consensus pattern (55 bp):
TTTCGGTCAAAGGGTCATTTTCGCCTTTTTCGCATCTAAGTTTAGTATTTTCACA
Found at i:29133 original size:67 final size:66
Alignment explanation
Indices: 28993--29406 Score: 314
Period size: 67 Copynumber: 6.2 Consensus size: 66
28983 TATTTTCACA
* *
28993 TTTC-GTCAAAGGGTCATTTTCGCCTTTTTCGCATCTAAGTTTAGTGTTTTCTATTTCCAAAAAT
1 TTTCGGTCGAAGGGTCATTTTCGTC-TTTTCGCATCTAAGTTTA--GTTTTCTATTTCCAAAAAT
29057 ACCC
63 ACCC
*
29061 TTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATCTAAGTTTCA-TTTTCACATTTCCAAAAATA
1 TTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATCTAAGTTT-AGTTTTC-TATTTCCAAAAATA
29125 CCC
64 CCC
* * *
29128 TTTCGGTCGAAGGGTCATTTTCATCTTCTT-GCACCTAAGTTTAGTACTTTCTTTTTCCAAAAAT
1 TTTCGGTCGAAGGGTCATTTTCGTCTT-TTCGCATCTAAGTTTAGT--TTTCTATTTCCAAAAAT
*
29192 GCCC
63 ACCC
* ** * * *
29196 TTTCGGTCGAAGGGTCAATTTCAACTTTTC-CATGTCTAAG-TTAGTTTACT-TTTCCTAGAATA
1 TTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCA--TCTAAGTTTAGTTTTCTATTTCCAAAAATA
29258 CCC
64 CCC
* * * * * * * *
29261 TTTCGATCAAAAGGGTCA-ATTCTGTCATACTT-GCAT-TCGAGTTTACTTTT-GATTTCCAAGA
1 TTTCGGTC-GAAGGGTCATTTTC-GTC-T-TTTCGCATCT-AAGTTTAGTTTTCTATTTCCAAAA
29322 ATACCC
61 ATACCC
* * * * * * * *
29328 TTTCGGT-GAAAGGGTCAGTTTCGTCATTTTCGCATTTTAGTTTACTCTACT-GTT-CAAAAATG
1 TTTCGGTCG-AAGGGTCATTTTCGTC-TTTTCGCATCTAAGTTTAGTTTTCTATTTCCAAAAATA
29390 CCC
64 CCC
*
29393 TTTCGGTCAAAGGG
1 TTTCGGTCGAAGGG
29407 CGAACTTTGT
Statistics
Matches: 284, Mismatches: 38, Indels: 51
0.76 0.10 0.14
Matches are distributed among these distances:
65 46 0.16
66 50 0.18
67 89 0.31
68 71 0.25
69 28 0.10
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (66 bp):
TTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATCTAAGTTTAGTTTTCTATTTCCAAAAATACC
C
Found at i:29294 original size:135 final size:134
Alignment explanation
Indices: 28993--29349 Score: 324
Period size: 135 Copynumber: 2.7 Consensus size: 134
28983 TATTTTCACA
* ** * **
28993 TTTCG-TCAAAGGGTCATTTTCGCCTTTTTCGCATCTAAGTTTAGTGTTTTCTATTTCCAAAAAT
1 TTTCGATCAAAGGGTCATTTTC-ACTACTT-GCACCTAAGTTTAGTACTTTCTATTTCCAAAAAT
* ** *
29057 ACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATCTAAGTTTCATTTTCACATTTCCAAAA
64 ACCCTTTCGGTCGAAGGGTCAATTTCAACTTTTCGCATCTAAGTTTCAGTTTCACATTTCCAAAA
29122 ATACCC
129 ATACCC
* * * * *
29128 TTTCGGTCGAAGGGTCATTTTCATCTTCTTGCACCTAAGTTTAGTACTTTCTTTTTCCAAAAATG
1 TTTCGATCAAAGGGTCATTTTCA-CTACTTGCACCTAAGTTTAGTACTTTCTATTTCCAAAAATA
* * *
29193 CCCTTTCGGTCGAAGGGTCAATTTCAACTTTTC-CATGTCTAAG-TT-AGTTT-ACTTTTCCTAG
65 CCCTTTCGGTCGAAGGGTCAATTTCAACTTTTCGCA--TCTAAGTTTCAGTTTCACATTTCCAAA
29254 AATACCC
128 AATACCC
* *
29261 TTTCGATCAAAAGGGTCAATTCTGTCA-TACTTGCA-TTCGAG-TT--TACTTT-TGATTTCCAA
1 TTTCGATC-AAAGGGTC-ATT-T-TCACTACTTGCACCT-AAGTTTAGTACTTTCT-ATTTCCAA
* *
29320 GAATACCCTTTCGGT-GAAAGGGTCAGTTTC
60 AAATACCCTTTCGGTCG-AAGGGTCAATTTC
29350 GTCATTTTCG
Statistics
Matches: 187, Mismatches: 24, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
131 2 0.01
132 38 0.20
133 22 0.12
134 16 0.09
135 79 0.42
136 27 0.14
137 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (134 bp):
TTTCGATCAAAGGGTCATTTTCACTACTTGCACCTAAGTTTAGTACTTTCTATTTCCAAAAATAC
CCTTTCGGTCGAAGGGTCAATTTCAACTTTTCGCATCTAAGTTTCAGTTTCACATTTCCAAAAAT
ACCC
Found at i:31029 original size:101 final size:101
Alignment explanation
Indices: 30783--30997 Score: 394
Period size: 101 Copynumber: 2.1 Consensus size: 101
30773 AAATACTATA
*
30783 TGAGAAATTATTATGTGGGACTGATCCATCACGTCATCAATGGGATCAACCACTAATATGATGAC
1 TGAGAAATTATTATGTGGGACTGATCCATCACGTCATCAATGTGATCAACCACTAATATGATGAC
* *
30848 AACTCAACAATTTTCTAAAGTCCTATCTCAATAATG
66 AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
*
30884 TGAGAAATTATCATGTGGGACTGATCCATCACGTCATCAATGTGATCAACCACTAATATGATGAC
1 TGAGAAATTATTATGTGGGACTGATCCATCACGTCATCAATGTGATCAACCACTAATATGATGAC
30949 AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
66 AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
30985 TGAGAAATTATTA
1 TGAGAAATTATTA
30998 GATGGAACTG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 109 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (101 bp):
TGAGAAATTATTATGTGGGACTGATCCATCACGTCATCAATGTGATCAACCACTAATATGATGAC
AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
Found at i:31036 original size:101 final size:101
Alignment explanation
Indices: 30783--31039 Score: 358
Period size: 101 Copynumber: 2.5 Consensus size: 101
30773 AAATACTATA
* * * *
30783 TGAGAAATTATTATGTGGGACTGATCCATCACGTCATCAATGGGATCAACCACTAATATGATGAC
1 TGAGAAATTATCATGTGGAACTGATCCATCACGTCAGCAATGTGATCAACCACTAATATGATGAC
* *
30848 AACTCAACAATTTTCTAAAGTCCTATCTCAATAATG
66 AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
* *
30884 TGAGAAATTATCATGTGGGACTGATCCATCACGTCATCAATGTGATCAACCACTAATATGATGAC
1 TGAGAAATTATCATGTGGAACTGATCCATCACGTCAGCAATGTGATCAACCACTAATATGATGAC
30949 AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
66 AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
* * * *
30985 TGAGAAATTATTA-GATGGAACTG-TCCCTCCATGTCAGCCATGTGA-CTAACCACTA
1 TGAGAAATTATCATG-TGGAACTGATCCAT-CACGTCAGCAATGTGATC-AACCACTA
31040 GAACTGTGCC
Statistics
Matches: 143, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
100 6 0.04
101 137 0.96
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (101 bp):
TGAGAAATTATCATGTGGAACTGATCCATCACGTCAGCAATGTGATCAACCACTAATATGATGAC
AACTCAACAATTTTCTAAAGGCCTATCCCAATAATG
Found at i:32457 original size:30 final size:29
Alignment explanation
Indices: 32416--32483 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
32406 GACAACTTCT
*
32416 CCCCTGAATTTTCAAATTCTGGACAATTTAA
1 CCCCTG-ATTTTCAAATTCAGGACAATTT-A
*
32447 CCTCTGATTTTCAAATTCAGGACAATTTA
1 CCCCTGATTTTCAAATTCAGGACAATTTA
32476 CCCCTGAT
1 CCCCTGAT
32484 GTAGGGACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 8 0.24
30 21 0.62
31 5 0.15
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (29 bp):
CCCCTGATTTTCAAATTCAGGACAATTTA
Found at i:35239 original size:191 final size:190
Alignment explanation
Indices: 34915--35274 Score: 657
Period size: 191 Copynumber: 1.9 Consensus size: 190
34905 GTGCTAGCTA
34915 TTCTACATGGTCTTCGATTTGCCCATAGTCGTGGCATTACTTCCTACATTGTAGAGAGTGATTCA
1 TTCTACATGGTCTTCGATTTGCCCATAGTCGTGGCATTACTTCCTACATTGTAGAGAGTGATTCA
* *
34980 TTGATGGCCATACTTCTCCTGTGAAGTTCAGAACCGCTCATGTGGGAAGGTAGCAGCTTGATTCT
66 TTCATGGCCATACTTCTCCTGCGAAGTTCAGAACCGCTCATGTGGGAAGGTAGCAGCTTGATTCT
*
35045 TGACTTGAAGCTCGGAAGGTGGCTTCTCATTTTGCTTCTGAACTTCTCATTTCTGTTTCCT
131 TGACTTGAAGCTCGG-AGGTGGCTTCTCATTTTCCTTCTGAACTTCTCATTTCTGTTTCCT
*
35106 TTCTACATGGTCTTTGATTTGCCCATAGTCGTGGCATTACTTCCTACATTGTAGAGAGTGATTCA
1 TTCTACATGGTCTTCGATTTGCCCATAGTCGTGGCATTACTTCCTACATTGTAGAGAGTGATTCA
35171 TTCATGGCCATACTTCTCCTGCGAAGTTCAGAACCGCTCATGTGGGAAGGTAGCAGCTTGATTCT
66 TTCATGGCCATACTTCTCCTGCGAAGTTCAGAACCGCTCATGTGGGAAGGTAGCAGCTTGATTCT
* *
35236 TGACTTGAGGCTCTGAGGTGGCTTCTCATTTTCCTTCTG
131 TGACTTGAAGCTCGGAGGTGGCTTCTCATTTTCCTTCTG
35275 TTTCCTTTAT
Statistics
Matches: 163, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
190 23 0.14
191 140 0.86
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (190 bp):
TTCTACATGGTCTTCGATTTGCCCATAGTCGTGGCATTACTTCCTACATTGTAGAGAGTGATTCA
TTCATGGCCATACTTCTCCTGCGAAGTTCAGAACCGCTCATGTGGGAAGGTAGCAGCTTGATTCT
TGACTTGAAGCTCGGAGGTGGCTTCTCATTTTCCTTCTGAACTTCTCATTTCTGTTTCCT
Found at i:44614 original size:178 final size:178
Alignment explanation
Indices: 44334--44762 Score: 497
Period size: 178 Copynumber: 2.4 Consensus size: 178
44324 TTGAAAAATC
** * * * * ** *
44334 AAATTTAAATTTCGAGTCCTTCATGAAAGTCGCAGATCATGGAACAACCTTTTAACA-AGCACTT
1 AAATTTAGCTTTCGAATCCTTCATGAAAGTTGTAGATAATAAAACAACCTTTTAAGAGA-CACTT
* * *
44398 GAATCACCTCAATCGGACATCTGGAGCAAAAATTATGTAATATTAAGTGG-ATCGCCCATTCTCG
65 GAATCACCTCAATCAGACATCTGGAGCAAAAATTATGTAATATTAAGTGGAAT-GCCCATTCCCA
* *
44462 CTAACCAAAACAACTAAAATTTT-GGAAGCATTTTTTATACCCGAATCATT
129 CTAACCAAAACAACT-AAATTTTCGGAAGCATTTTTGATACCCGAAACATT
* **
44512 AAATTTAGCTTTCGAATCCTGT-ATGGAAGTTGTAGATAATAAAACAACCTTTTAAGAGACGGTT
1 AAATTTAGCTTTCGAATCCT-TCATGAAAGTTGTAGATAATAAAACAACCTTTTAAGAGACACTT
* * * *
44576 GAATCACCTCAATCAGACATTTGGAGCAAAAGTTATGTAATATTAAGTGGAATGTCCATTCCCAT
65 GAATCACCTCAATCAGACATCTGGAGCAAAAATTATGTAATATTAAGTGGAATGCCCATTCCCAC
* * * **
44641 TAACCGAAACAACTAATTTTTCGGAAGTATTTTTGATACTTGAAACATT
130 TAACCAAAACAACTAAATTTTCGGAAGCATTTTTGATACCCGAAACATT
* * * * ** *
44690 AAATTTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATCATGGAACAACCTTTTAATAGACACTTG
1 AAATTTAGCTTTCGAATCCTTCATGAAAGTTGTAGATAATAAAACAACCTTTTAAGAGACACTTG
44755 AATCACCT
66 AATCACCT
44763 TGATCGGATA
Statistics
Matches: 210, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
177 7 0.03
178 199 0.95
179 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (178 bp):
AAATTTAGCTTTCGAATCCTTCATGAAAGTTGTAGATAATAAAACAACCTTTTAAGAGACACTTG
AATCACCTCAATCAGACATCTGGAGCAAAAATTATGTAATATTAAGTGGAATGCCCATTCCCACT
AACCAAAACAACTAAATTTTCGGAAGCATTTTTGATACCCGAAACATT
Done.