Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011482.1 Corchorus capsularis cultivar CVL-1 contig11503, 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: 34338
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:5392 original size:28 final size:28
Alignment explanation
Indices: 5329--5408 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
5319 GTTTAATACC
* *
5329 CAAATTAGCCCCTTAACTATCCATTTTGAGA
1 CAAATTGGCCCCTTAACT-T--TTTTTGAGA
* *
5360 TAAATTGGCCCCTTAACTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTGAGA
5388 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
5409 AAAAACGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 27 0.61
30 1 0.02
31 16 0.36
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (28 bp):
CAAATTGGCCCCTTAACTTTTTTTGAGA
Found at i:6133 original size:29 final size:29
Alignment explanation
Indices: 6097--6154 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
6087 TCTCATTTTT
* *
6097 AAAAGTTAAAGGGTCAATTTGTCCCAAAA
1 AAAAGTTAAAGGGCCAATTTATCCCAAAA
*
6126 AAAAGTTAAAGGGCCAATTTATTCCAAAA
1 AAAAGTTAAAGGGCCAATTTATCCCAAAA
6155 TGAATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAAGTTAAAGGGCCAATTTATCCCAAAA
Found at i:6744 original size:11 final size:11
Alignment explanation
Indices: 6730--6767 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6720 ATTCATAACA
6730 AATTTATAATT
1 AATTTATAATT
6741 AATTTATAATT
1 AATTTATAATT
6752 -ATTTGATAATT
1 AATTT-ATAATT
*
6763 TATTT
1 AATTT
6768 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:6949 original size:2 final size:2
Alignment explanation
Indices: 6942--6969 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6932 TTAATAGTTC
6942 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
6970 TAAGCCAAAA
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:9730 original size:23 final size:21
Alignment explanation
Indices: 9680--9732 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
9670 TCAACTCGTG
9680 ATAT-TTTAATATTATTAAAA
1 ATATATTTAATATTATTAAAA
* *
9700 ATTTTATTTAATATTAATTATGAA
1 A-TATATTTAATATT-ATTA-AAA
9724 ATATATTTA
1 ATATATTTA
9733 TGAATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 2 0.08
22 9 0.35
23 11 0.42
24 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATATTTAATATTATTAAAA
Found at i:11068 original size:21 final size:21
Alignment explanation
Indices: 11029--11069 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11019 TTCCGTCCCA
*
11029 TCAAAAGCACCATCCATCTTT
1 TCAAAAGCACCAGCCATCTTT
* *
11050 TCAATAGCACCAGCGATCTT
1 TCAAAAGCACCAGCCATCTT
11070 AACTAAAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.27
Consensus pattern (21 bp):
TCAAAAGCACCAGCCATCTTT
Found at i:11384 original size:14 final size:14
Alignment explanation
Indices: 11365--11413 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
11355 TATATTATAG
11365 ATTTTATCTTTAAA
1 ATTTTATCTTTAAA
* * *
11379 ATTTTATATATAACT
1 ATTTTATCTTTAA-A
*
11394 ATTTTATCTTTAAC
1 ATTTTATCTTTAAA
11408 ATTTTA
1 ATTTTA
11414 CTATTTTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTATCTTTAAA
Found at i:11827 original size:86 final size:85
Alignment explanation
Indices: 11681--11839 Score: 210
Period size: 86 Copynumber: 1.9 Consensus size: 85
11671 AGACTCTTTG
* * * * * ** *
11681 ATCTCTTTATAACTATTTTATTTTTATCATTTTATTGTTTTAATTAAAAAAATTTGATATATTGG
1 ATCTCTTTATAACTATCTTATTTTTACCATTTTACTATTTTAACTAAAAAAATTAAATATATTAG
11746 AATTATTTTTAATTAAATCTA
66 AATT-TTTTTAATTAAATCTA
** *
11767 ATCTCTTTATAACTATCTTATTTTTACCATTTTACTATTTTAACTGCAAAACTTAAATATATTAG
1 ATCTCTTTATAACTATCTTATTTTTACCATTTTACTATTTTAACTAAAAAAATTAAATATATTAG
11832 AATTTTTT
66 AATTTTTT
11840 AAATATATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
85 4 0.06
86 58 0.94
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (85 bp):
ATCTCTTTATAACTATCTTATTTTTACCATTTTACTATTTTAACTAAAAAAATTAAATATATTAG
AATTTTTTTAATTAAATCTA
Found at i:11851 original size:13 final size:14
Alignment explanation
Indices: 11833--11868 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
11823 ATATATTAGA
11833 ATTTTTTAAAT-AT
1 ATTTTTTAAATGAT
11846 ATTTTTTAAATGAT
1 ATTTTTTAAATGAT
*
11860 ATTATTTAA
1 ATTTTTTAA
11869 CAGTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTTTTTAAATGAT
Found at i:11928 original size:46 final size:48
Alignment explanation
Indices: 11844--11935 Score: 111
Period size: 46 Copynumber: 2.0 Consensus size: 48
11834 TTTTTTAAAT
* *
11844 ATATTTTTTAAATGATATTATTTAACAGTTTTTATTTAAATAAATTTA
1 ATATTTTTTAAATGATATTATTTAACAGTTTTAATTTAAAAAAATTTA
*
11892 ATATTTTTATAAAT-AT-TT-TTTACCA-TTTTAATTTTAAAAAAATT
1 ATATTTTT-TAAATGATATTATTTAACAGTTTTAA-TTTAAAAAAATT
11936 GGAGACTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
45 5 0.13
46 17 0.44
47 2 0.05
48 10 0.26
49 5 0.13
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (48 bp):
ATATTTTTTAAATGATATTATTTAACAGTTTTAATTTAAAAAAATTTA
Found at i:16663 original size:21 final size:21
Alignment explanation
Indices: 16593--16662 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
16583 TCTTTGCATT
*
16593 CGAGCACGCTCTATTTCATGA
1 CGAGCACGCTCTGTTTCATGA
*
16614 CGAGCACGCTCTGCTTCATGA
1 CGAGCACGCTCTGTTTCATGA
*
16635 CGAGCACTCTCTGTTTCATGA
1 CGAGCACGCTCTGTTTCATGA
16656 CGAGCAC
1 CGAGCAC
16663 TTTCCTCTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (21 bp):
CGAGCACGCTCTGTTTCATGA
Found at i:18883 original size:33 final size:32
Alignment explanation
Indices: 18846--19078 Score: 117
Period size: 33 Copynumber: 7.3 Consensus size: 32
18836 TAGAAATCCT
18846 CTGATTTACAGCAACATCTTCTCTGCCATTTTG
1 CTGATTTACAGCAA-ATCTTCTCTGCCATTTTG
* * ** *
18879 CTGATTTATAG--AAT-TAACTCTAGAAATTCT-
1 CTGATTTACAGCAAATCT-TCTCT-GCCATTTTG
* *
18909 CTGATTTGCAGCAATATCTTCTCTTCCATTTTG
1 CTGATTTACAGCAA-ATCTTCTCTGCCATTTTG
* * ** *
18942 CTGATTTACAG--AATTTTCCCTCGAAATTCT-
1 CTGATTTACAGCAAATCTTCTCT-GCCATTTTG
* *
18972 CTGATTTGCAGCAACATCTTCTCTTCCATTTTG
1 CTGATTTACAGCAA-ATCTTCTCTGCCATTTTG
* * ** **
19005 CTGATTTACAG--AATTTTCCCTCGAAATCCT-
1 CTGATTTACAGCAAATCTTCTCT-GCCATTTTG
* * *
19035 CTAATTTGCAGCAACATCTTCTCTTCCATTTTG
1 CTGATTTACAGCAA-ATCTTCTCTGCCATTTTG
19068 CTGATTTACAG
1 CTGATTTACAG
19079 AATTTTCCCT
Statistics
Matches: 138, Mismatches: 45, Indels: 34
0.64 0.21 0.16
Matches are distributed among these distances:
29 1 0.01
30 48 0.35
31 15 0.11
32 14 0.10
33 59 0.43
34 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (32 bp):
CTGATTTACAGCAAATCTTCTCTGCCATTTTG
Found at i:18885 original size:63 final size:63
Alignment explanation
Indices: 18802--19105 Score: 455
Period size: 63 Copynumber: 4.8 Consensus size: 63
18792 TGAAGAATCA
* * * * * * *
18802 TCTCTGCCATTTTGTTGATTTGCAGAATTATCTCTAGAAATCCTCTGATTTACAGCAACATCT
1 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTGATTTGCAGCAACATCT
* * ** * * * *
18865 TCTCTGCCATTTTGCTGATTTATAGAATTAACTCTAGAAATTCTCTGATTTGCAGCAATATCT
1 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTGATTTGCAGCAACATCT
*
18928 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATTCTCTGATTTGCAGCAACATCT
1 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTGATTTGCAGCAACATCT
*
18991 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTAATTTGCAGCAACATCT
1 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTGATTTGCAGCAACATCT
19054 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTGATTTG
1 TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTGATTTG
19106 ACAGAATTTT
Statistics
Matches: 224, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 224 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (63 bp):
TCTCTTCCATTTTGCTGATTTACAGAATTTTCCCTCGAAATCCTCTGATTTGCAGCAACATCT
Found at i:18978 original size:30 final size:30
Alignment explanation
Indices: 18942--19135 Score: 126
Period size: 31 Copynumber: 6.2 Consensus size: 30
18932 TTCCATTTTG
*
18942 CTGATTTACAGAATTTTCCCTCGAAATTCT
1 CTGATTTACAGAATTTTCCCTCGAAATCCT
* * * * **
18972 CTGATTTGCAGCAACATCTTCTCTTC--CATTTT
1 CTGATTTACAG--A-ATTTTC-CCTCGAAATCCT
19004 GCTGATTTACAGAATTTTCCCTCGAAATCCT
1 -CTGATTTACAGAATTTTCCCTCGAAATCCT
* * * * * **
19035 CTAATTTGCAGCAACATCTTCTCTTC--CATTTT
1 CTGATTTACAG--A-ATTTTC-CCTCGAAATCCT
19067 GCTGATTTACAGAATTTTCCCTCGAAATCCT
1 -CTGATTTACAGAATTTTCCCTCGAAATCCT
*
19098 CTGATTTGACAGAATTTTCCCTCAAAATCCT
1 CTGATTT-ACAGAATTTTCCCTCGAAATCCT
19129 CTGATTT
1 CTGATTT
19136 GCAGCAACAT
Statistics
Matches: 123, Mismatches: 26, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
29 6 0.05
30 36 0.29
31 37 0.30
32 9 0.07
33 29 0.24
34 6 0.05
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (30 bp):
CTGATTTACAGAATTTTCCCTCGAAATCCT
Found at i:19173 original size:94 final size:93
Alignment explanation
Indices: 19005--19178 Score: 296
Period size: 94 Copynumber: 1.9 Consensus size: 93
18995 TTCCATTTTG
*
19005 CTGATTTACAGAATTTTCCCTCGAAATCCTCTAATTTGCAGCAACATCTTCTCTTCCATTTTGCT
1 CTGATTTACAGAATTTTCCCTCAAAATCCTCTAATTTGCAGCAACATCTTCTCTTCCATTTTGCT
19070 GATTTACAGAATTTTCCCTCGAAATCCT
66 GATTTACAGAATTTTCCCTCGAAATCCT
*
19098 CTGATTTGACAGAATTTTCCCTCAAAATCCTCTGATTTGCAGCAACATCTTCTCTGT-CATTTTG
1 CTGATTT-ACAGAATTTTCCCTCAAAATCCTCTAATTTGCAGCAACATCTTCTCT-TCCATTTTG
*
19162 CTGGTTTACAGAATTTT
64 CTGATTTACAGAATTTT
19179 GTTTAGATTT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
93 7 0.09
94 68 0.89
95 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (93 bp):
CTGATTTACAGAATTTTCCCTCAAAATCCTCTAATTTGCAGCAACATCTTCTCTTCCATTTTGCT
GATTTACAGAATTTTCCCTCGAAATCCT
Found at i:22029 original size:14 final size:15
Alignment explanation
Indices: 22006--22034 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21996 AGAGAAGGTC
22006 GAAGGAAGAAGAAGA
1 GAAGGAAGAAGAAGA
22021 GAAGG-AGAAGAAGA
1 GAAGGAAGAAGAAGA
22035 AAAAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
GAAGGAAGAAGAAGA
Found at i:22829 original size:35 final size:35
Alignment explanation
Indices: 22786--23232 Score: 546
Period size: 35 Copynumber: 12.7 Consensus size: 35
22776 CAGTAATAAG
22786 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
* * *
22821 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
* *
22856 CAACTTAATTTAGGGTAATTAAGTAATTCGGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
* * *
22891 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
* * *
22926 AAGCAACTTAATTCATGGTAATTAAGTGAGTCAGTAAT
1 ---CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
* *
22964 CAACTTAATTCAGGGTAATTAAGTAAATCGGTAAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGT-AAT
* *
23000 -AACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
*
23034 CAACTTAATTCAGGGTAATTAAGTAATTCGGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
* * *
23069 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
*
23104 CAACTTAATTTAGGGTAATTAAGTAATTCAGTAAGT
1 CAACTTAATTCAGGGTAATTAAGTAATTCAGTAA-T
* *
23140 -AACTTAATTCAGGGTAATTAAGTGAGTT-AATAAT
1 CAACTTAATTCAGGGTAATTAAGT-AATTCAGTAAT
* * *
23174 CAACTTAATTTAGGG-AAGTTAAGTAGTTCAATAAGT
1 CAACTTAATTCAGGGTAA-TTAAGTAATTCAGTAA-T
23210 -AACTTAATTCAGGG-AAGTTAAGT
1 CAACTTAATTCAGGGTAA-TTAAGT
23233 TTAGTAAGAA
Statistics
Matches: 363, Mismatches: 38, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
34 10 0.03
35 312 0.86
36 8 0.02
38 33 0.09
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (35 bp):
CAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
Found at i:23085 original size:178 final size:176
Alignment explanation
Indices: 22782--23232 Score: 648
Period size: 178 Copynumber: 2.6 Consensus size: 176
22772 GAATCAGTAA
* *
22782 TAAG-CAACTTAATTCAGGGTAATTAAGTAATTCAGTAATTAACTTAATTCAGGGTAATTAAGTG
1 TAAGTCAACTTAATTCAGGGTAATTAAGTAAATCAGTAAATAACTTAATTCAGGGTAATTAAGTG
*
22846 AGTCAGTAATCAACTTAATTTAGGGTAATTAAGTAATTCGGTAATTAACTTAATTCAGGGTAATT
66 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAATTCGGTAATTAACTTAATTCAGGGTAATT
* *
22911 AAGTGAGTCAGTAATAAGCAACTTAATTCATGGTAATTAAGTGAGTCAG
131 AAGTGAGTCAGTAAT---CAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
22960 TAA-TCAACTTAATTCAGGGTAATTAAGTAAATCGGTAAATAACTTAATTCAGGGTAATTAAGTG
1 TAAGTCAACTTAATTCAGGGTAATTAAGTAAATCAGTAAATAACTTAATTCAGGGTAATTAAGTG
23024 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAATTCGGTAATTAACTTAATTCAGGGTAATT
66 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAATTCGGTAATTAACTTAATTCAGGGTAATT
* *
23089 AAGTGAGTCAGTAATCAACTTAATTTAGGGTAATTAAGTAATTCAG
131 AAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * * * *
23135 TAAGT-AACTTAATTCAGGGTAATTAAGTGAGTTAAT-AATCAACTTAATTTAGGG-AAGTTAAG
1 TAAGTCAACTTAATTCAGGGTAATTAAGTAAATCAGTAAAT-AACTTAATTCAGGGTAA-TTAAG
*
23197 T-AGTTCAATAAGT-AACTTAATTCAGGG-AAGTTAAGT
64 TGAG-TCAGTAA-TCAACTTAATTCAGGGTAA-TTAAGT
23233 TTAGTAAGAA
Statistics
Matches: 251, Mismatches: 15, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
174 9 0.04
175 101 0.40
176 2 0.01
178 139 0.55
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (176 bp):
TAAGTCAACTTAATTCAGGGTAATTAAGTAAATCAGTAAATAACTTAATTCAGGGTAATTAAGTG
AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAATTCGGTAATTAACTTAATTCAGGGTAATT
AAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
Found at i:25932 original size:639 final size:638
Alignment explanation
Indices: 24678--25956 Score: 2369
Period size: 639 Copynumber: 2.0 Consensus size: 638
24668 CCATGCAAAC
*
24678 CAATGTATGAGGACACAATCACATCCCTATCAACAACATGCCCCTCGCCTTGCACTACCTCGAGC
1 CAATGTATGAGGACACAATCACATCCCTATCAACAACATGCCCCTCACCTTGCACTACCTCGAGC
*
24743 AATGACTTATGACCAACCCACTAATCGGTCCAAAATTTAGTCCCACTACCATCCCCTAGTCTCCA
66 AATGACTTATGACCAACCCACCAATCGGTCCAAAATTTAGTCCCACTACCATCCCCTAGTCTCCA
*
24808 ACGGGTGCCACGCTGAATACAATCCCTAGTTTGCAATAACCCATGCCAAGTAGAGGAACATCTCT
131 ACGGGTGCCACGCTGAATACAATCCCTAGTTTGCAATAACCCATGCCAAGTAGAGGAACATCTCC
*
24873 AGTATTTAAGGAGTCAACAAAAAGTTTTCCTTTTAAATACTTCTTCTGAAAAACTTAAGTGCATA
196 AGTATTTAAGGAGTCAACAAAAAGTTTTCCCTTTAAATACTTCTTCTGAAAAACTTAAGTGCATA
24938 AGTTCTAGACTCGAGTTTGTAACTTCCAACCTGTCTTGGCTAAAGTGCTAAATTCAAACTTCTTT
261 AGTTCTAGACTCGAGTTTGTAACTTCCAACCTGTCTTGGCTAAAGTGCTAAATTCAAACTTCTTT
* *
25003 CTTTTTTCAAACCTAAGCCACCATTACCTTTAGCTCGACAAACCCAATCGCAAACAACCAAAAGA
326 CTTTTTTCAAACCCAAGCCACCATTACCTTTAGCTCGACAAACCCAATCCCAAACAACCAAAAGA
25068 CCATGGGATTTATCTGCCTCCCCATTCCAAAGAAAATTCATGTTGCACTGATCAAGTCTATTACA
391 CCATGGGATTTATCTGCCTCCCCATTCCAAAGAAAATTCATGTTGCACTGATCAAGTCTATTACA
*
25133 CACTGCCACAAGTAACATAGTAGATTGCATAGTATAAGTCAGCAGGGAGCTCAAAGTTGACTGGA
456 CACCGCCACAAGTAACATAGTAGATTGCATAGTATAAGTCAGCAGGGAGCTCAAAGTTGACTGGA
*
25198 TCAACGTCTTTCTACCAGCATAACTCAAAACCTTGCCTTTCCAACTAGCCAATTTACCAAGAAAT
521 TCAACGCCTTTCTACCAGCATAACTCAAAACCTTGCCTTTCCAACTAGCCAATTTACCAAGAAAT
25263 CTATCAATCACATGCTTATACGTATTCTTCGTAACTCGGCCATGAACAATTGG
586 CTATCAATCACATGCTTATACGTATTCTTCGTAACTCGGCCATGAACAATTGG
* * *
25316 CAATGTATGAGGACACAGTCACATCCCTATCAACGACATGCCCCTCACCTTGCAGTACCTCGAGC
1 CAATGTATGAGGACACAATCACATCCCTATCAACAACATGCCCCTCACCTTGCACTACCTCGAGC
* *
25381 AATGGCTTATGACCAACCCACCAATCGGTCCAAAATTTGGTCCCACTACCATCCCCTAGTCTCCA
66 AATGACTTATGACCAACCCACCAATCGGTCCAAAATTTAGTCCCACTACCATCCCCTAGTCTCCA
*
25446 ACGGGTGCCACGCTGAATACAATCCCTAGTTTGCAATAACCCATGCTAAGTAGAGGAACATCTCC
131 ACGGGTGCCACGCTGAATACAATCCCTAGTTTGCAATAACCCATGCCAAGTAGAGGAACATCTCC
25511 AGTATTTAAGGAGTCAACAAAAAGTTTTCCCTTTAAATACTTCTTCTGAAAAACTTAAGTGCATA
196 AGTATTTAAGGAGTCAACAAAAAGTTTTCCCTTTAAATACTTCTTCTGAAAAACTTAAGTGCATA
*
25576 AGTTCTAGACTCGAGTTTGTAACTTCCAGCCTGTCTTGGCTAATAGTGCTAAATTCAAACTTCTT
261 AGTTCTAGACTCGAGTTTGTAACTTCCAACCTGTCTTGGCTAA-AGTGCTAAATTCAAACTTCTT
*
25641 TCTTTTTTCAAACCCAAGCCACCATTACCTTTAGCTCGACAAACCCAATCCCAAGCAACCAAAAG
325 TCTTTTTTCAAACCCAAGCCACCATTACCTTTAGCTCGACAAACCCAATCCCAAACAACCAAAAG
*
25706 ACCATGGGATTTATCTGCCTCCCTATTCCAAAGAAAATTCATGTTGCACTGATCAAGTCTATTAC
390 ACCATGGGATTTATCTGCCTCCCCATTCCAAAGAAAATTCATGTTGCACTGATCAAGTCTATTAC
* *
25771 ACACCGCCACAGGTAATATAGTAGATTGCATAGTATAAGTCAGCAGGGAGCTCAAAGTTGACTGG
455 ACACCGCCACAAGTAACATAGTAGATTGCATAGTATAAGTCAGCAGGGAGCTCAAAGTTGACTGG
25836 ATCAACGCCTTTCTACCAGCATAACTCAAAACCTTGCCTTTCCAACTAGCCAATTTACCAAGAAA
520 ATCAACGCCTTTCTACCAGCATAACTCAAAACCTTGCCTTTCCAACTAGCCAATTTACCAAGAAA
*
25901 TCTATCAATCACATGCTTATACGTATTCTTCGTAACTCGGTCATGAACAATTGG
585 TCTATCAATCACATGCTTATACGTATTCTTCGTAACTCGGCCATGAACAATTGG
25955 CA
1 CA
25957 CTCCTAAATA
Statistics
Matches: 620, Mismatches: 20, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
638 292 0.47
639 328 0.53
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (638 bp):
CAATGTATGAGGACACAATCACATCCCTATCAACAACATGCCCCTCACCTTGCACTACCTCGAGC
AATGACTTATGACCAACCCACCAATCGGTCCAAAATTTAGTCCCACTACCATCCCCTAGTCTCCA
ACGGGTGCCACGCTGAATACAATCCCTAGTTTGCAATAACCCATGCCAAGTAGAGGAACATCTCC
AGTATTTAAGGAGTCAACAAAAAGTTTTCCCTTTAAATACTTCTTCTGAAAAACTTAAGTGCATA
AGTTCTAGACTCGAGTTTGTAACTTCCAACCTGTCTTGGCTAAAGTGCTAAATTCAAACTTCTTT
CTTTTTTCAAACCCAAGCCACCATTACCTTTAGCTCGACAAACCCAATCCCAAACAACCAAAAGA
CCATGGGATTTATCTGCCTCCCCATTCCAAAGAAAATTCATGTTGCACTGATCAAGTCTATTACA
CACCGCCACAAGTAACATAGTAGATTGCATAGTATAAGTCAGCAGGGAGCTCAAAGTTGACTGGA
TCAACGCCTTTCTACCAGCATAACTCAAAACCTTGCCTTTCCAACTAGCCAATTTACCAAGAAAT
CTATCAATCACATGCTTATACGTATTCTTCGTAACTCGGCCATGAACAATTGG
Found at i:33038 original size:62 final size:62
Alignment explanation
Indices: 32941--33071 Score: 201
Period size: 62 Copynumber: 2.1 Consensus size: 62
32931 TTACAACTTA
* * * *
32941 GGGGGGCTAAAGCTAAATTTATCCAATTTTGTTAAGACTTGTGTAAGATATAG-GGGAGGTTT
1 GGGGGGCTAAAGCAAAATTTATCCAATTTTATTAAGACTTATGTAAGATAT-GCAGGAGGTTT
33003 GGGGGGCTAAAGCAAAATTTATCCAATTTTATTAAGACTTATGTAAGATATGCAGGAGGTTT
1 GGGGGGCTAAAGCAAAATTTATCCAATTTTATTAAGACTTATGTAAGATATGCAGGAGGTTT
33065 GGAGGGG
1 GG-GGGG
33072 GGGGGGGGCG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
61 1 0.02
62 58 0.92
63 4 0.06
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.31
Consensus pattern (62 bp):
GGGGGGCTAAAGCAAAATTTATCCAATTTTATTAAGACTTATGTAAGATATGCAGGAGGTTT
Found at i:33805 original size:2 final size:2
Alignment explanation
Indices: 33800--33824 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33790 TATATATATA
33800 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
33825 TGTATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:33835 original size:2 final size:2
Alignment explanation
Indices: 33830--33869 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33820 TGTGTTGTAT
33830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33870 AAGTAATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.