Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019008.1 Corchorus olitorius cultivar O-4 contig19041, 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: 46570
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:7244 original size:18 final size:18
Alignment explanation
Indices: 7217--7251 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7207 ATATACGGTG
7217 TTAATTAATTTT-AATTA
1 TTAATTAATTTTCAATTA
7234 TTAATTTAATTTTCAATT
1 TTAA-TTAATTTTCAATT
7252 TATTTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTAATTTTCAATTA
Found at i:8884 original size:23 final size:23
Alignment explanation
Indices: 8841--8885 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
8831 AAGGAAAAAA
**
8841 AAAACTTGCACTAAGGCAAGACG
1 AAAACTTGCACTAAGAAAAGACG
*
8864 AAAACTTGCACTATGAAAAGAC
1 AAAACTTGCACTAAGAAAAGAC
8886 TAAAGCTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.16
Consensus pattern (23 bp):
AAAACTTGCACTAAGAAAAGACG
Found at i:12448 original size:16 final size:16
Alignment explanation
Indices: 12427--12461 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12417 ACAATTCAGA
12427 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
12443 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
12459 AAG
1 AAG
12462 TATTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:12614 original size:41 final size:41
Alignment explanation
Indices: 12557--12757 Score: 235
Period size: 41 Copynumber: 4.9 Consensus size: 41
12547 TTTTTGTTTG
12557 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
12598 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
12639 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * * * *
12683 TTCAAGACCAAGTCGTCAAGACCTTTAAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
12724 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
12758 CAAATGAAAC
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
40 12 0.09
41 87 0.64
42 4 0.03
43 1 0.01
44 33 0.24
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:12727 original size:85 final size:83
Alignment explanation
Indices: 12557--12757 Score: 239
Period size: 85 Copynumber: 2.4 Consensus size: 83
12547 TTTTTGTTTG
* * *** *
12557 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAAATTATCAATTCAAGATTGAGTCATCGAGACC
1 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAAATTATCAATTCAAGACCAAGTCATCAAGACC
*
12621 CTTGAATTAAATTATCAA
66 CTTAAATTAAATTATCAA
*
12639 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAATTCAAGACCAAGTCGTCAAGA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAA--ATTATCAATTCAAGACCAAGTCATCAAGA
* * *
12704 CCTTTAAATTAGATTGTCAA
64 CCCTTAAATTAAATTATCAA
*
12724 TTCAAGACCAAGTCATTC--GACCCTTGAATC-AAAT
1 TTCAAGAACAAGTCA-TCGAGACCCTTGAATCGAAAT
12758 CAAATGAAAC
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
81 2 0.02
82 29 0.28
83 4 0.04
84 12 0.12
85 54 0.52
86 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (83 bp):
TTCAAGAACAAGTCATCGAGACCCTTGAATCGAAATTATCAATTCAAGACCAAGTCATCAAGACC
CTTAAATTAAATTATCAA
Found at i:15096 original size:420 final size:420
Alignment explanation
Indices: 14314--15109 Score: 1109
Period size: 420 Copynumber: 1.9 Consensus size: 420
14304 TCTGTCTATT
* * * * * *
14314 ATTAAAATGTAATTTCATGATCTACAATTTTTATTAAGGACCCAAAAGCCAATTTTTATGTTTCT
1 ATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACCCAAAAACCAATTTTTATGTTTCA
* * *
14379 ATTAAAAAAATGCTTCCAAAATTTTGTGATTCGGATTGCCGGTCTATTTAATATCGTATAATTTT
66 ATTAAAAAAATGCTTCCAAAATCTGGTGATTCGGATTGCCGGTCTATTTAATATCATATAATTTT
* * * *
14444 CAATCCATATATCTGATTAAAGTTATTCAAGTATCGGTTAGAAGGTTATTGCATGATCTACGAAT
131 CAATCCACATATCTGATCAAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACGAAT
* * *
14509 TTCATGAAGAACTCGAAAGCTAAATTTGATTTACGAGTTTCATGAAGGGCTCAAAAGGGAATTTT
196 TTCAAGAAGAACTCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGCTCAAAAGGAAATTTT
* * * * *
14574 TATGTTTAAAGATCTCCATCAATAAGCATTTTCTTGTTTGGATTATTTTTCAAATGATCATCATA
261 TATGTTTAAAGATCTCCATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCATCATA
* *
14639 TTTTTTACTTTATACTACTTAGTACTTTACTAATTCTATCTTGA-TTGATTTAACACTTAAGATT
326 TTTTCTACTTTATACTACTTAGTACTTTACAAATTCTATCTT-ACTTGATTTAACACTTAAGATT
14703 TATTTGTTTTATTTGTCTGATTAAGGTATCC
390 TATTTGTTTTATTTGTCTGATTAAGGTATCC
** * *
14734 ATTAAAAGGTAATTTCATGATCTATGACTTTCATGAATGACTCAAAAACCAATTTTTATGTTTCA
1 ATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACCCAAAAACCAATTTTTATGTTTCA
* * * *
14799 ATTATGAAGAATGCTTCCGAAATCTGGTGGCTTC-GATTG-CGGTCTATTTAATAAT-ATATAAT
66 ATTA-AAAAAATGCTTCCAAAATCTGGT-GATTCGGATTGCCGGTCTATTTAAT-ATCATATAAT
* * *
14861 TTTCGATCCACATGTCTGATCAAAATTATTCAAGTGTCGGTTAAAAGGTTATTGCATGATCTACG
128 TTTCAATCCACATATCTGATCAAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACG
* *
14926 ACTTTCAAGAAGGAAC-CGAAAGCTAAATTTGATCTGCGAGTTTCATGAAGGGCTCAAAAGGAAA
193 AATTTCAAGAA-GAACTCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGCTCAAAAGGAAA
* * *
14990 TTTTTATGTTTCAAGCTCTCCATCAACAAACATTTTCTTATTTGGATT-TTTATCAAATGACCCT
257 TTTTTATGTTTAAAGATCTCCATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCAT
* * * *
15054 CATACTTTTCTATTTTATATTATTTAGTTCTTTACAAATTCTATCTTACTTGATTT
322 CATA-TTTTCTACTTTATACTACTTAGTACTTTACAAATTCTATCTTACTTGATTT
15110 GACGCTTTAG
Statistics
Matches: 327, Mismatches: 43, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
419 18 0.06
420 276 0.84
421 29 0.09
422 4 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (420 bp):
ATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACCCAAAAACCAATTTTTATGTTTCA
ATTAAAAAAATGCTTCCAAAATCTGGTGATTCGGATTGCCGGTCTATTTAATATCATATAATTTT
CAATCCACATATCTGATCAAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACGAAT
TTCAAGAAGAACTCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGCTCAAAAGGAAATTTT
TATGTTTAAAGATCTCCATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCATCATA
TTTTCTACTTTATACTACTTAGTACTTTACAAATTCTATCTTACTTGATTTAACACTTAAGATTT
ATTTGTTTTATTTGTCTGATTAAGGTATCC
Found at i:16775 original size:31 final size:31
Alignment explanation
Indices: 16726--16888 Score: 159
Period size: 31 Copynumber: 5.3 Consensus size: 31
16716 ACGGTATCCG
* * *
16726 ACGTGGCATGCCATGTGTACCAAAAAGCAAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
*
16757 ATGTGGCACGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
* * * *
16788 ACATGGCATGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
** * *
16819 ACGTGTTACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
* * *
16850 ACGTGGCATGCCTCGTGCA-CAAAAAG-GAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
* *
16879 ATGTGCCACG
1 ACGTGGCACG
16889 TGTCATTTTT
Statistics
Matches: 108, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
29 10 0.09
30 7 0.06
31 91 0.84
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGCGAC
Found at i:16830 original size:62 final size:62
Alignment explanation
Indices: 16729--16861 Score: 176
Period size: 62 Copynumber: 2.1 Consensus size: 62
16719 GTATCCGACG
** *
16729 TGGCATGCCATGTGTACCAAAAAGCAACATGTGGCACGCCACGTGTACCAAAAAGCGACACA
1 TGGCATGCCACATGTACCAAAAAGCAACACGTGGCACGCCACGTGTACCAAAAAGCGACACA
** ** * * *
16791 TGGCATGCCACATGTACCAAAAAGTGACACGTGTTACGCCATGTGTACCAAAAAGTGACACG
1 TGGCATGCCACATGTACCAAAAAGCAACACGTGGCACGCCACGTGTACCAAAAAGCGACACA
16853 TGGCATGCC
1 TGGCATGCC
16862 TCGTGCACAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (62 bp):
TGGCATGCCACATGTACCAAAAAGCAACACGTGGCACGCCACGTGTACCAAAAAGCGACACA
Found at i:17787 original size:13 final size:13
Alignment explanation
Indices: 17769--17793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17759 ATAATAAAGC
17769 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
17782 AAAAAAGAAAAA
1 AAAAAAGAAAAA
17794 TGTTAAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:22284 original size:3 final size:3
Alignment explanation
Indices: 22278--22362 Score: 57
Period size: 3 Copynumber: 28.3 Consensus size: 3
22268 TACATACCAC
* * *
22278 TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA GT-T TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* * * * * *
22323 TAC CAT TAA TAA TAA GT-T TAA TAA TTA TTA TAA TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA T
22363 GTCTAAATTA
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
2 2 0.03
3 59 0.94
4 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:22317 original size:30 final size:30
Alignment explanation
Indices: 22281--22362 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
22271 ATACCACTAA
*
22281 TAATAATAATAATAATTATAATAATAAGTT
1 TAATAATTATAATAATTATAATAATAAGTT
22311 TAATAATTATAATACCA-T-TAATAATAAGTT
1 TAATAATTATAATA--ATTATAATAATAAGTT
* *
22341 TAATAATTATTATAATAATAAT
1 TAATAATTATAATAATTATAAT
22363 GTCTAAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 1 0.02
30 42 0.93
31 1 0.02
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
TAATAATTATAATAATTATAATAATAAGTT
Found at i:22840 original size:21 final size:21
Alignment explanation
Indices: 22816--22863 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
22806 ACCACTAATA
* *
22816 ATAATAATAA-TTATTATTATT
1 ATAATAATAAGTT-TAATAATT
22837 ATAATAATAAGTTTAATAATT
1 ATAATAATAAGTTTAATAATT
22858 ATAATA
1 ATAATA
22864 CCACTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAATAATAAGTTTAATAATT
Found at i:22854 original size:30 final size:30
Alignment explanation
Indices: 22820--22901 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
22810 CTAATAATAA
*
22820 TAATAATTATTATTATTATAATAATAAGTT
1 TAATAATTATTATTATAATAATAATAAGTT
* * *
22850 TAATAATTA-TAATACCACTAATAATAAGTT
1 TAATAATTATTATTA-TAATAATAATAAGTT
*
22880 TAATAATTATTATAATAATAAT
1 TAATAATTATTATTATAATAAT
22902 GTCTAAATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 4 0.10
30 35 0.83
31 3 0.07
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (30 bp):
TAATAATTATTATTATAATAATAATAAGTT
Found at i:23816 original size:11 final size:11
Alignment explanation
Indices: 23773--23810 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23763 TTCCTATATA
*
23773 AAATAAATTAT
1 AAATTAATTAT
23784 CAAA-TAATTAT
1 -AAATTAATTAT
23795 AAATTAATTAT
1 AAATTAATTAT
23806 AAATT
1 AAATT
23811 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:24031 original size:17 final size:17
Alignment explanation
Indices: 24009--24052 Score: 81
Period size: 16 Copynumber: 2.6 Consensus size: 17
23999 CTTTCTCCCC
24009 TTCTTCATATTTTTTTT
1 TTCTTCATATTTTTTTT
24026 TTCTTCATA-TTTTTTT
1 TTCTTCATATTTTTTTT
24042 TTCTTCATATT
1 TTCTTCATATT
24053 CTATTGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (17 bp):
TTCTTCATATTTTTTTT
Found at i:27804 original size:19 final size:19
Alignment explanation
Indices: 27765--27805 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27755 ACATACAAAT
*
27765 ATAAAATTATATATATGTG
1 ATAAAATTATATATAAGTG
27784 ATAAAA-TATATATAAGATG
1 ATAAAATTATATATAAG-TG
27803 ATA
1 ATA
27806 TTGATAGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAAAATTATATATAAGTG
Found at i:33370 original size:7 final size:7
Alignment explanation
Indices: 33358--33384 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
33348 TCATATATAA
33358 TGCAGAT
1 TGCAGAT
33365 TGCAGAT
1 TGCAGAT
33372 TGCAGAT
1 TGCAGAT
33379 TGCAGA
1 TGCAGA
33385 AAAGGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (7 bp):
TGCAGAT
Found at i:36046 original size:15 final size:15
Alignment explanation
Indices: 36028--36057 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36018 CTTTCTCTTT
36028 TTTTTTTCCTTTTAC
1 TTTTTTTCCTTTTAC
*
36043 TTTTTTTTCTTTTAC
1 TTTTTTTCCTTTTAC
36058 AAGTGAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTCCTTTTAC
Found at i:36046 original size:16 final size:15
Alignment explanation
Indices: 36027--36057 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
36017 TCTTTCTCTT
36027 TTTTTTTTCCTTTTAC
1 TTTTTTTT-CTTTTAC
36043 TTTTTTTTCTTTTAC
1 TTTTTTTTCTTTTAC
36058 AAGTGAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTCTTTTAC
Found at i:36992 original size:160 final size:162
Alignment explanation
Indices: 36808--37098 Score: 473
Period size: 161 Copynumber: 1.8 Consensus size: 162
36798 TTGTATAGAT
*
36808 ATTTATAGTTTTACTCAACTAAAAAATCCATTTT-TATTTAATTAAATCTAATATCCTTATAAC-
1 ATTTATAGTTTTACTCAACTAAAAAATCCATTTTCTATTTAATTAAATATAATATCCTTAT-ACG
* * *
36871 TATTTAATTTTTA-CAATTTTACTATTTTAATT-AAAAACTTATATATATTAGAATTTTTTAAAA
65 TATTTAATTTTTATC-ATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTTTAAAA
36934 TATTTTTTTTGAGATAAGAATTTTTTAAAATATA
129 TATTTTTTTTGAGATAAGAATTTTTTAAAATATA
* *
36968 ATTTATAGTTTTACTCAACTAAAAACTCTATTTTCTATTTAATTAAATATAATATCCTTATACGT
1 ATTTATAGTTTTACTCAACTAAAAAATCCATTTTCTATTTAATTAAATATAATATCCTTATACGT
*
37033 ATTTTATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTTTAAAATA
66 ATTTAATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTTTAAAATA
37098 T
131 T
37099 ATTTCTTAAA
Statistics
Matches: 120, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
160 34 0.28
161 53 0.44
162 33 0.28
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (162 bp):
ATTTATAGTTTTACTCAACTAAAAAATCCATTTTCTATTTAATTAAATATAATATCCTTATACGT
ATTTAATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTTTAAAATA
TTTTTTTTGAGATAAGAATTTTTTAAAATATA
Found at i:37469 original size:27 final size:27
Alignment explanation
Indices: 37431--37494 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
37421 TTTGACTTAT
37431 AAAGTTAGAGGAGTTGACGCCAAAAAA
1 AAAGTTAGAGGAGTTGACGCCAAAAAA
37458 AAAGTTAGAGGAGTTGACGCCAAAAAA
1 AAAGTTAGAGGAGTTGACGCCAAAAAA
37485 AAAGTTAGAG
1 AAAGTTAGAG
37495 AAGTCAATCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.48, C:0.09, G:0.27, T:0.16
Consensus pattern (27 bp):
AAAGTTAGAGGAGTTGACGCCAAAAAA
Found at i:43321 original size:16 final size:16
Alignment explanation
Indices: 43287--43407 Score: 91
Period size: 16 Copynumber: 7.6 Consensus size: 16
43277 GGCAATTGGG
**
43287 CGGGTTCGGG-TACTT
1 CGGGTTCGGGTTTTTT
43302 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTTTTT
* *
43318 CGGGTTCGAGTTTATT
1 CGGGTTCGGGTTTTTT
* * * *
43334 CGGGTTTGGATTCTGT
1 CGGGTTCGGGTTTTTT
* *
43350 CGAGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
* * * *
43366 CGAGCTCGGGTTATGT
1 CGGGTTCGGGTTTTTT
*
43382 CGGGTTCGAGTATTTTT
1 CGGGTTCGGGT-TTTTT
43399 CGGGTTCGG
1 CGGGTTCGG
43408 TCTCGGGTCG
Statistics
Matches: 78, Mismatches: 26, Indels: 2
0.74 0.25 0.02
Matches are distributed among these distances:
15 10 0.13
16 57 0.73
17 11 0.14
ACGTcount: A:0.08, C:0.15, G:0.36, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTTTTTT
Found at i:43339 original size:32 final size:32
Alignment explanation
Indices: 43287--43407 Score: 111
Period size: 32 Copynumber: 3.8 Consensus size: 32
43277 GGCAATTGGG
* * * *
43287 CGGGTTCGGGTA-CTTCGGGTTCGGGTTTTTT
1 CGGGTTCGAGTATTTTCGGGTTCGGGTTATGT
* * *
43318 CGGGTTCGAGT-TTATTCGGGTTTGGATTCTGT
1 CGGGTTCGAGTATT-TTCGGGTTCGGGTTATGT
* * * *
43350 CGAGTTCGGGTATTTTCGAGCTCGGGTTATGT
1 CGGGTTCGAGTATTTTCGGGTTCGGGTTATGT
43382 CGGGTTCGAGTATTTTTCGGGTTCGG
1 CGGGTTCGAGTA-TTTTCGGGTTCGG
43408 TCTCGGGTCG
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
31 10 0.14
32 46 0.67
33 13 0.19
ACGTcount: A:0.08, C:0.15, G:0.36, T:0.40
Consensus pattern (32 bp):
CGGGTTCGAGTATTTTCGGGTTCGGGTTATGT
Found at i:43593 original size:8 final size:8
Alignment explanation
Indices: 43573--43606 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
43563 AAGTTTATTG
43573 ATAATAT-
1 ATAATATA
43580 ATAATATA
1 ATAATATA
43588 ATAATATA
1 ATAATATA
43596 ATAATATA
1 ATAATATA
43604 ATA
1 ATA
43607 TAACATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:43596 original size:13 final size:13
Alignment explanation
Indices: 43573--43609 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
43563 AAGTTTATTG
43573 ATAAT-ATATAAT
1 ATAATAATATAAT
43585 ATAATAATATAAT
1 ATAATAATATAAT
43598 A-ATATAATATAA
1 ATA-ATAATATAA
43610 CATGATTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:43628 original size:2 final size:2
Alignment explanation
Indices: 43621--43645 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43611 ATGATTACCA
43621 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
43646 AAGGTTGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45748 original size:22 final size:22
Alignment explanation
Indices: 45723--45766 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
45713 TTTGGGTATT
45723 TTCGGACTCGGGT-GATTTCGGG
1 TTCGGACTCGGGTGGA-TTCGGG
*
45745 TTCGGATTCGGGTGGATTCGGG
1 TTCGGACTCGGGTGGATTCGGG
45767 ACGTTGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.09, C:0.16, G:0.43, T:0.32
Consensus pattern (22 bp):
TTCGGACTCGGGTGGATTCGGG
Found at i:46278 original size:49 final size:47
Alignment explanation
Indices: 46177--46318 Score: 180
Period size: 49 Copynumber: 3.0 Consensus size: 47
46167 GAGTGTGCCA
* * *
46177 ATCAATTTTGTCAAAAAATTGATAAAAAGTGC-GATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAG-TGAAAAGTAAAAG
46224 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAGTAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTGAAAAGTAAAAG
* *
46273 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
46319 GGATTGCTTG
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
47 15 0.18
48 27 0.32
49 40 0.48
50 1 0.01
51 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAAAG
Done.