Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010420.1 Corchorus capsularis cultivar CVL-1 contig10441, 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: 18232
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Found at i:926 original size:23 final size:23
Alignment explanation
Indices: 900--954 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
890 GTCTTTGTAT
* *
900 ATATACATATCATAAATA-ATTTC
1 ATATACATAT-AAAAAAACATTTC
923 ATATACTAATATAAAAAAACATTTC
1 ATATAC--ATATAAAAAAACATTTC
948 ATATACA
1 ATATACA
955 CACAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 7 0.26
24 5 0.19
25 15 0.56
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATACATATAAAAAAACATTTC
Found at i:1710 original size:30 final size:30
Alignment explanation
Indices: 1675--1745 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 30
1665 AAATTTTTTT
1675 ATTTTATTTTGAGATTTTCACACCACTGTC
1 ATTTTATTTTGAGATTTTCACACCACTGTC
* *
1705 ATTTTATTTTGAGATTTTCACTCCATTGTC
1 ATTTTATTTTGAGATTTTCACACCACTGTC
1735 ATTTTCATTTT
1 ATTTT-ATTTT
1746 CTAAAACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 33 0.87
31 5 0.13
ACGTcount: A:0.21, C:0.17, G:0.08, T:0.54
Consensus pattern (30 bp):
ATTTTATTTTGAGATTTTCACACCACTGTC
Found at i:3389 original size:100 final size:103
Alignment explanation
Indices: 3182--3437 Score: 326
Period size: 100 Copynumber: 2.5 Consensus size: 103
3172 TAAAACAAAT
*
3182 TAATTTCACTAAGTTTAGCCCC-AATTACAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATT--AA-TTTATTTTTATTTTAAGGGTAAATTCCAAAATT
3246 AATAATTTATCGTTATAGAGTTTTAGAAATAAAATACAAAAC
63 AATAA-TTATCGTTATAGAGTTTTAGAAATAAAATACAAAAC
*
3288 TAATTTCACTAAGTTTAGCCCCAAATTAA-TT-TTTTTATTTTAAGGGTAAATTCCATAATTAAT
1 TAATTTCACTAAGTTTAGCCCCAAATTAATTTATTTTTATTTTAAGGGTAAATTCCAAAATTAAT
* * * *
3351 AA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATTATCGTTATAGAGTTTTAGAAATAAAATACAAAAC
* * *
3388 TAA-TTCACCAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATT--AATT-TATTTTTATTTTAAGGGT
3438 TAGAAAAATT
Statistics
Matches: 135, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
98 8 0.06
99 13 0.10
100 36 0.27
101 1 0.01
102 32 0.24
103 17 0.13
105 2 0.01
106 22 0.16
107 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (103 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAATTTATTTTTATTTTAAGGGTAAATTCCAAAATTAAT
AATTATCGTTATAGAGTTTTAGAAATAAAATACAAAAC
Found at i:6848 original size:21 final size:20
Alignment explanation
Indices: 6818--6856 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6808 AATATCATGG
6818 AAGACATGAAGAGACAATTCT
1 AAGACATGAA-AGACAATTCT
* *
6839 AAGACGTGAATGACAATT
1 AAGACATGAAAGACAATT
6857 AATAATGGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (20 bp):
AAGACATGAAAGACAATTCT
Found at i:8921 original size:36 final size:36
Alignment explanation
Indices: 8848--8921 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
8838 AAATAAATAA
* *
8848 TAAATATTTATTTAATAATTATTTAATAATTATAAT
1 TAAATATTTATTTAATAAATATTTAATAATTACAAT
* **
8884 TAAATTTTTATTTAATTAAATATTTCCTAATT-CAAT
1 TAAATATTTATTTAA-TAAATATTTAATAATTACAAT
8920 TA
1 TA
8922 TTAATAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 19 0.59
37 13 0.41
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (36 bp):
TAAATATTTATTTAATAAATATTTAATAATTACAAT
Found at i:10929 original size:22 final size:22
Alignment explanation
Indices: 10904--11405 Score: 211
Period size: 22 Copynumber: 23.0 Consensus size: 22
10894 ATTTCTTATG
*
10904 ACCTCTTTATGAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
*
10926 ACCT-TCCTATGAAATTTTAATA
1 ACCTCT-CTATGAAATTTTGATA
* * * *
10948 ACGAT-ACTATAAAATTTTGAGA
1 AC-CTCTCTATGAAATTTTGATA
* * **
10970 ACCTTTTTAT-AAATTTCTTTTA
1 ACCTCTCTATGAAATTT-TGATA
* *
10992 A-CTTTCTTATGAAA-TTTGTTA
1 ACCTCTC-TATGAAATTTTGATA
* * *
11013 ACCTCCCTAAGGAATTTTGA-A
1 ACCTCTCTATGAAATTTTGATA
* *
11034 GACATCACTATGAAATTTTGATA
1 -ACCTCTCTATGAAATTTTGATA
* * *
11057 ACTTCCCAATGAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* * * *
11079 ACCAACACTATGAGATGTTGATA
1 ACC-TCTCTATGAAATTTTGATA
* *
11102 ACCT-TCGTATGATATATTGATA
1 ACCTCTC-TATGAAATTTTGATA
* * * *
11124 ACCACGT-TATGAAAATTTAAAA
1 ACCTC-TCTATGAAATTTTGATA
11146 ACCTC-CATATG-AATTGTT-AGTA
1 ACCTCTC-TATGAAATT-TTGA-TA
* * * *
11168 ATCACACTCTGAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* * * * *
11190 ATCACACTATGGAATTGTGATA
1 ACCTCTCTATGAAATTTTGATA
*
11212 ACCTCACTATGAAATTTTGATAA
1 ACCTCTCTATGAAATTTTGAT-A
* *
11235 ACAT-TCCTATAAAATTTTGATAA
1 ACCTCT-CTATGAAATTTTGAT-A
* *
11258 ACCTCCCTATAAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* *
11280 ACTTC-CTTATGAAATCTTGATA
1 ACCTCTC-TATGAAATTTTGATA
*
11302 A-----CTA-CAAATTTTGATA
1 ACCTCTCTATGAAATTTTGATA
* **
11318 ACCTCCCTATGATTTTTTGATA
1 ACCTCTCTATGAAATTTTGATA
11340 ACCTCAT-TATGAAATTTTGATA
1 ACCTC-TCTATGAAATTTTGATA
11362 ACC-CTCTTATGAAATTTTGA-A
1 ACCTCTC-TATGAAATTTTGATA
* **
11383 AACTAAACTATGAAATTTTGATA
1 ACCT-CTCTATGAAATTTTGATA
11406 TTCTCCCAGA
Statistics
Matches: 368, Mismatches: 75, Indels: 73
0.71 0.15 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 1 0.00
21 36 0.10
22 248 0.67
23 68 0.18
24 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
ACCTCTCTATGAAATTTTGATA
Found at i:11249 original size:23 final size:22
Alignment explanation
Indices: 11218--11302 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
11208 GATAACCTCA
*
11218 CTATGAAATTTTGATAAACATTC
1 CTATAAAATTTTGATAAAC-TTC
*
11241 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAA-CTTC
11264 CTATAAAATTTTGAT-AACTTC
1 CTATAAAATTTTGATAAACTTC
* *
11285 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
11303 CTACAAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 4 0.07
22 14 0.26
23 35 0.65
24 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACTTC
Found at i:11340 original size:60 final size:61
Alignment explanation
Indices: 11246--11363 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 61
11236 CATTCCTATA
* *
11246 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTCCTTATGAAATCTTGATAACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGATAACTAC
* ** *
11307 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGATAAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGATAAC
11364 CCTCTTATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 41 0.80
61 10 0.20
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.40
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGATAACTAC
Found at i:11688 original size:25 final size:23
Alignment explanation
Indices: 11635--11698 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 23
11625 TTGATAACAA
* *
11635 TATGAAATTTTGATAAT-CTTCC
1 TATGAAATTTTCATAATCCATCC
11657 TAT-AAATTTTCATAATCCGATCTC
1 TATGAAATTTTCATAATCC-ATC-C
11681 TATGAAA-TTTCGATAATC
1 TATGAAATTTTC-ATAATC
11699 ACTCTATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 12 0.34
22 4 0.11
23 2 0.06
24 8 0.23
25 9 0.26
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTCATAATCCATCC
Found at i:11850 original size:17 final size:17
Alignment explanation
Indices: 11828--11860 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11818 GAAATTTTGA
11828 TAACCTCCCTATGAAAG
1 TAACCTCCCTATGAAAG
*
11845 TAACCTCCTTATGAAA
1 TAACCTCCCTATGAAA
11861 TTTTGTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (17 bp):
TAACCTCCCTATGAAAG
Found at i:11883 original size:22 final size:22
Alignment explanation
Indices: 11503--11913 Score: 126
Period size: 22 Copynumber: 18.9 Consensus size: 22
11493 CCATAAATAC
* *
11503 CACTATGAAATTTTGGTAATCA
1 CACTATGAAATTTTGATAACCA
* * * *
11525 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * * *
11547 CTCTAT-ATAATTTTGTTGACCC
1 CACTATGA-AATTTTGATAACCA
* *
11569 CTCTATGAAATTTTGATAATCA
1 CACTATGAAATTTTGATAACCA
* * *
11591 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** *
11613 TGCTTTGAAATTTTGATAA-CA
1 CACTATGAAATTTTGATAACCA
**
11634 -A-TATGAAATTTTGATAATCTT
1 CACTATGAAATTTTGATAA-CCA
*
11655 C-CTAT-AAATTTTCATAATCCGA
1 CACTATGAAATTTTGATAA-CC-A
* * *
11677 TCTCTATGAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAACCA
* *
11700 CTCTATGAGA-TTTGATAA--A
1 CACTATGAAATTTTGATAACCA
* * *
11719 CTTCTATCAAATTTTGGT-ACTC-
1 C-ACTATGAAATTTTGATAAC-CA
* * * * *
11741 C-TTGTGAAATTGAGACTTTTAAAACCTT
1 CACTATGAAA-T-----TTTGATAACC-A
11769 CA-TATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
*
11790 CACTA-AAAAGTTTTGATAACCA
1 CACTATGAAA-TTTTGATAACCA
* *
11812 TACTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* *
11834 CCCTATGAAA----G-TAACCT
1 CACTATGAAATTTTGATAACCA
*
11851 C-CTTATGAAATTTTGTTAACCA
1 CAC-TATGAAATTTTGATAACCA
* *
11873 CACTATAAAATTCTT-ATAACCT
1 CACTATGAAATT-TTGATAACCA
* *
11895 CGCTATGACATTTTGATAA
1 CACTATGAAATTTTGATAA
11914 TCTCTTTGAT
Statistics
Matches: 286, Mismatches: 66, Indels: 74
0.67 0.15 0.17
Matches are distributed among these distances:
16 1 0.00
17 14 0.05
18 1 0.00
19 17 0.06
20 13 0.05
21 36 0.13
22 166 0.58
23 9 0.03
24 5 0.02
25 10 0.03
26 4 0.01
27 3 0.01
28 7 0.02
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:11969 original size:22 final size:22
Alignment explanation
Indices: 11931--12096 Score: 135
Period size: 22 Copynumber: 7.5 Consensus size: 22
11921 GATAACCTTT
* *
11931 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
** *
11953 CTATGAAATTTCAATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* *
11975 CTAAGAAATTTTAATAACCTGATC-
1 CTATGAAATTTTGATAACC--A-CA
*
11999 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
12021 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
12044 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
12065 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
12086 CTCATGAAATT
1 CT-ATGAAATT
12097 ATAATGACCA
Statistics
Matches: 117, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 90 0.77
23 3 0.03
24 18 0.15
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:12061 original size:44 final size:43
Alignment explanation
Indices: 11979--12096 Score: 164
Period size: 44 Copynumber: 2.6 Consensus size: 43
11969 ACCTTCCTAA
*
11979 GAAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACC---TCCTATGAAATTTTGGTAACCACACTAT
*
12025 GAAATTTTGATAACTTCCATATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCTCC-TATGAAATTTTGGTAACCACACTAT
*
12069 GGAATTTTGATAACCTCCTCATGAAATT
1 GAAATTTTGATAACCTCCT-ATGAAATT
12097 ATAATGACCA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
43 4 0.06
44 49 0.74
46 13 0.20
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (43 bp):
GAAATTTTGATAACCTCCTATGAAATTTTGGTAACCACACTAT
Found at i:12119 original size:44 final size:44
Alignment explanation
Indices: 11931--12120 Score: 122
Period size: 44 Copynumber: 4.3 Consensus size: 44
11921 GATAACCTTT
* * * *
11931 CTATAAAATTGTGATAACC-ACACTATGAAATT-TCAATAACCTTC-
1 CTATGAAATTTTGATAACCTCCA-TATGAAATTAT-AATAACC-ACA
* * * **
11975 CTAAGAAATTTTAATAACCTGATCC-TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACC---TCCATATGAAATTATAATAACCACA
* * **
12021 CTATGAAATTTTGATAACTTCCATATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCTCCATATGAAATTATAATAACCACA
* *
12065 CTATGGAATTTTGATAACCTCC-TCATGAAATTATAATGACCATC-
1 CTATGAAATTTTGATAACCTCCAT-ATGAAATTATAATAACCA-CA
*
12109 TTATGAAATTTT
1 CTATGAAATTTT
12121 TTTAACACAG
Statistics
Matches: 118, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
43 4 0.03
44 80 0.68
45 2 0.02
46 30 0.25
47 1 0.01
48 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCTCCATATGAAATTATAATAACCACA
Found at i:12335 original size:20 final size:20
Alignment explanation
Indices: 12302--12340 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12292 TATTGAAATT
* *
12302 TAAAAAATTGAATTTAAAAG
1 TAAAAAATTAAATTCAAAAG
*
12322 TAAAATATTAAATTCAAAA
1 TAAAAAATTAAATTCAAAA
12341 AATAATAGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (20 bp):
TAAAAAATTAAATTCAAAAG
Found at i:12772 original size:10 final size:11
Alignment explanation
Indices: 12742--12773 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
12732 GTTATTATGT
12742 TATATATAT-A
1 TATATATATAA
12752 TATATATATAA
1 TATATATATAA
12763 TATA-ATATAA
1 TATATATATAA
12773 T
1 T
12774 TTCAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATATATAA
Found at i:17404 original size:41 final size:42
Alignment explanation
Indices: 17302--17583 Score: 252
Period size: 41 Copynumber: 6.7 Consensus size: 42
17292 TTACCCAATA
* *
17302 ACCAAAGTCCCCAAATACATTTATAACACAGGGGCAACTATTCT-T
1 ACCAAAGTCCCCAAACACATTTATAACACAGAGG---C-ATTCTAT
*
17347 A-CAAAGTCCTCAAACACATTTATAACACAGAGGCATTC-AT
1 ACCAAAGTCCCCAAACACATTTATAACACAGAGGCATTCTAT
*
17387 ACCAAAGTCCCCAAACACATTTATAACACA-AGGGCAATTCTCTT
1 ACCAAAGTCCCCAAACACATTTATAACACAGA-GGC-ATTCT-AT
* * * * *
17431 TCTAAGGTCCTCAAACACATTTATAACACAGAGACA-TCTAT
1 ACCAAAGTCCCCAAACACATTTATAACACAGAGGCATTCTAT
* * *
17472 ATCAAAGTCCCCAAACACAATTATAACACAGGGGCATCTCTAT
1 ACCAAAGTCCCCAAACACATTTATAACACAGAGGCAT-TCTAT
* * * * * * *
17515 TCGAAAGTCCTCAAGCACATTTATAACACAAAGCCA-CCTAT
1 ACCAAAGTCCCCAAACACATTTATAACACAGAGGCATTCTAT
* * *
17556 ACTAAAGTCCCTAAACACAATTATAACA
1 ACCAAAGTCCCCAAACACATTTATAACA
17584 TAAGGGCAAC
Statistics
Matches: 193, Mismatches: 35, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
40 7 0.04
41 86 0.45
42 7 0.04
43 33 0.17
44 58 0.30
45 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (42 bp):
ACCAAAGTCCCCAAACACATTTATAACACAGAGGCATTCTAT
Found at i:17407 original size:85 final size:84
Alignment explanation
Indices: 17302--17595 Score: 351
Period size: 85 Copynumber: 3.5 Consensus size: 84
17292 TTACCCAATA
* * *
17302 ACCAAAGTCCCCAAATACATTTATAACACAGGGGCAACTATTCTTAC-AAAGTCCTCAAACACAT
1 ACCAAAGTCCCCAAACACAATTATAACACAAGGGCAACT-TTCTT-CGAAAGTCCTCAAACACAT
*
17366 TTATAACACAGAGGCAT-TCAT
64 TTATAACACAGAGACATCT-AT
* * *
17387 ACCAAAGTCCCCAAACACATTTATAACACAAGGGCAA-TTCTCTTTCTAAGGTCCTCAAACACAT
1 ACCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTT-TC-TTCGAAAGTCCTCAAACACAT
17451 TTATAACACAGAGACATCTAT
64 TTATAACACAGAGACATCTAT
* * * * * *
17472 ATCAAAGTCCCCAAACACAATTATAACACAGGGGCATCTCTATTCGAAAGTCCTCAAGCACATTT
1 ACCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTTTCTTCGAAAGTCCTCAAACACATTT
* * *
17537 ATAACACAAAGCCACCTAT
66 ATAACACAGAGACATCTAT
* * *
17556 ACTAAAGTCCCTAAACACAATTATAACATAAGGGCAACTT
1 ACCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTT
17596 CTATATGGCA
Statistics
Matches: 181, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
83 1 0.01
84 73 0.40
85 105 0.58
86 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (84 bp):
ACCAAAGTCCCCAAACACAATTATAACACAAGGGCAACTTTCTTCGAAAGTCCTCAAACACATTT
ATAACACAGAGACATCTAT
Found at i:17652 original size:2 final size:2
Alignment explanation
Indices: 17645--17676 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17635 AATTATTCAT
17645 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
17677 GCAAAGGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.