Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014275.1 Corchorus olitorius cultivar O-4 contig14308, 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: 77586
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1411 original size:334 final size:332
Alignment explanation
Indices: 1--2559 Score: 3642
Period size: 334 Copynumber: 7.7 Consensus size: 332
* *
1 TTTTGCAAAAAACTGTCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCTTCAAAAATAT
1 TTTTGC-AAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATAT
* * * * **
66 ATATTTAAATGCCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTCTAACTATTATTT
65 ATAATTCAGTG-CCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATTT
* *
131 TCTGAATTAAATTT-TAATAAAATCGAAAAAAGATTCTGATGCTCGTAAAAACAAATCCTTAAAT
129 TCCGAATT-AATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAAT
* * *
195 CCAACGTGGCTGA-ACTTTGTTTAGATGAATATAGATATTTTAACGATTTTGGGCTCCAAAAATC
193 CCAATGTGGCTGAGA-TTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATC
* * * *
259 TTGCAAAACTAAGCCGGGACCCGGAACGCGTTTTTTGCCTAAACCTGTGATGGATAGTACATGAT
257 ATGCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGATAGTACACGAT
*
324 TTCTGCTAAAA
322 TTCGGCTAAAA
* * * *
335 TTTTGCACAAACTACCCCGAAAGGATTTTTCCCAAATTTTTGCCACAATTTTCATCAAAAATATA
1 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATATA
* * * * *
400 TAATTAAGTTCCAAAAGGATTGAAGGGCTTTGAACGCTTCTAAAATAGTTCTTCCTATTATTTTT
66 TAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTA-TTTT
* * * *
465 CCGAATTAGTTTCTAATAAAATCGAGACAAGATTCTGATGCACGTAAAAACAAATCCTTAAATGC
130 CCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCC
* * *
530 AATGCGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTAGGCTCCAAAATTCATG
195 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATCATG
** *
595 CAAAACTGAGCCGGGACCTAGAACGCGTTTTTTGCCAAAACATGTGATGGATAGTACACGATTTC
260 CAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGATAGTACACGATTTC
*
660 GGCTTAAA
325 GGCTAAAA
* *
668 -TTTGCAAAAACTGCCCCGAAAGGTTTTTTCCCAAATTTTTGCCACAATTTTCATCAAAACTATA
1 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATATA
*
732 TAATTCAGTGCCAAAAAGATTGAAGGGATTTTAACGCTTCTAATATAGTTCTTCCTATTATTTTC
66 TAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATTTTC
* * * * * *
797 CAAATTAAATTCTAA-AAAGATCGAAATATGATTATGATGCTCGTAAAAACAAATCCTTAAATGC
131 CGAATTAATTTCTAATAAA-ATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCC
* * * *
861 AATGTGGCTGAGATTTGGTTACATGAATATAGGTATTTTAACGAGTTTGGACGCCAAAAATCATG
195 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATCATG
* * *
926 CAAAACTGAGCTGGGACCCGGAACGCGTTTTTTGCCCAAACCTGTGATGGATAGTACACCATTTC
260 CAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGATAGTACACGATTTC
991 GGCTAAAA
325 GGCTAAAA
* * * * *
999 TTTTGCAAAAAATGCCCTGAAACGTTTTTTCCAAAATTTTTGACACAATTTTCATCAAAACTATA
1 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATATA
1064 TAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATTTTC
66 TAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATTTTC
* * *
1129 CGAATTAATTTCTAATAAAAACGAAACAAGATTCAGATGCTCGAAAAAAACAAATCCTTAAATCC
131 CGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCG-TAAAAACAAATCCTTAAATCC
* * *
1194 AACGTGGCTGATATTTGGTTAGATGAATATAGAAATTTTAACGAGTTTGGGCTCCAAAAATCATG
195 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATCATG
* *
1259 CAAAACTGAGCCGGGACCCGGAACGCGTTTTTGTGCCAAAACCTGTGATGGATAATACAAGATTT
260 CAAAACTGAGCCGGGACCCGGAACGCGTTTTT-TGCCAAAACCTGTGATGGATAGTACACGATTT
1324 CGGCTAAAA
324 CGGCTAAAA
*
1333 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAACTATA
1 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATATA
*
1398 TAATTCAGTGCCAAAAAGATTGAAGGGATTTTAACGCTTCTAATATAGTTCTTCCTATTATTTTC
66 TAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATTTTC
* * * *
1463 CGAATTACA-TTCTAA-AAAGATCGAGACAAGATTGTGATACTCGTAAAAACAAATCCTTAAATG
131 CGAATTA-ATTTCTAATAAA-ATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATC
* * *
1526 CAATGTGGCTGAGATTTGGTTAAATGAATATAGATGTTTTAACGAGTTTGGGCGCCAAAAATCAT
194 CAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATCAT
* *
1591 GCAAAACTGAGCCGGTACCCGGAACGCGTTTTTTGCCAAAACCTCT-AGTGGATAGTACACGATT
259 GCAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGA-TGGATAGTACACGA-T
1655 TTCGGCTAAAA
322 TTCGGCTAAAA
*
1666 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAGAAATATA
1 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATATA
* * * * **
1731 TATTTAAATGCGCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTCTAACTATTATTTT
66 TAATTCAGTGC-CAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATTTT
* *
1796 CGGAATTAAATTT-TAATAAAATCGAAAAAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATC
130 CCGAATT-AATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATC
* * * * *
1860 CAACGTGGCTGAGTTTTGTTTAGATGAATATAGATATTTTAACGATTTTGGGCTCCAAAAATAAT
194 CAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATCAT
* * * *
1925 GCAAAATTGATCAGGGACCCGGAACGCGTTTTTTTGCCAAAACCTGTGATGGATAGTACATGATT
259 GCAAAACTGAGCCGGGACCCGGAACGCG-TTTTTTGCCAAAACCTGTGATGGATAGTACACGATT
*
1990 TCGACTAAAA
323 TCGGCTAAAA
* * * * *
2000 TTTTGCAAAAACTGCCCTGAAAGGATTTTTCCCAAATTTTGGCCACAATTTTCATCAAAATTATA
1 TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATATA
* * * * * *
2065 TAATTCAGTTCCGAAAAGATTGGAGGGCTTTGAACGCTTCTAAAATAGTTCTTCCTATAATTTTT
66 TAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTA-TTTT
* * * *
2130 CCGAATTAGTTTCTAATAAAATCGAGACAAGATTCTGATGCACCTAAAAACAAATCCTTAAATCC
130 CCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCC
* * * * * *
2195 AATATGGTTGAGATTTGTTTAGATGAATCTTGATATTTTAACGAGTTTGGGCGCCAAAAATCATG
195 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATCATG
* * * * * *
2260 CAAAACTTAGCTGGGACCCGGAACACGTTTTTTGCCAAAACCGGTGATGGATACTACATGATTTC
260 CAAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGATAGTACACGATTTC
*
2325 CGC-AAAA
325 GGCTAAAA
* * * *
2332 GTTTTGCAAAAATTGCCTCGAAAGGTTTTTTCCCAAATTTTTACCACAATTTTCATCAAAAAAAT
1 -TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATC--AAAAAT
* * *
2397 ATATAATTCAGTGCCTAAAAGATTGATGGGATTTTAACGCTTCTAATATAGTTCTTCCTATTATT
63 ATATAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATT
* * * *
2462 TTCTGAATAAATTTCTAATAAAATCGAAACAAAATTTTGATGCTCGTAAAAACAAATCCTTAAAT
128 TTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAAT
* *
2527 GCAATGTGGCTGAGATTTGATTAGATGAATATA
193 CCAATGTGGCTGAGATTTGGTTAGATGAATATA
2560 AATAATTAGA
Statistics
Matches: 1984, Mismatches: 218, Indels: 46
0.88 0.10 0.02
Matches are distributed among these distances:
330 3 0.00
331 182 0.09
332 345 0.17
333 677 0.34
334 679 0.34
335 97 0.05
336 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (332 bp):
TTTTGCAAAAACTGCCCCGAAAGGTTTTTTCCAAAATTTTTGCCACAATTTTCATCAAAAATATA
TAATTCAGTGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATAGTTCTTCCTATTATTTTC
CGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCA
ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGAGTTTGGGCTCCAAAAATCATGC
AAAACTGAGCCGGGACCCGGAACGCGTTTTTTGCCAAAACCTGTGATGGATAGTACACGATTTCG
GCTAAAA
Found at i:2986 original size:14 final size:15
Alignment explanation
Indices: 2967--2995 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2957 AATACATCAC
2967 AATGCAA-AAAATGG
1 AATGCAACAAAATGG
2981 AATGCAACAAAATGG
1 AATGCAACAAAATGG
2996 GCACAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (15 bp):
AATGCAACAAAATGG
Found at i:4228 original size:52 final size:52
Alignment explanation
Indices: 4147--4323 Score: 304
Period size: 52 Copynumber: 3.4 Consensus size: 52
4137 AGTCACAATG
* *
4147 CTAATTGCTAAA-CTTTTTAAAATGCTTGGAGGGACAGCCCTCATCGGTCTCC
1 CTAATTACTAAATC-TTTTAAAATGTTTGGAGGGACAGCCCTCATCGGTCTCC
4199 CTAATTACTAAATCTTTTAAAATGTTTGGAGGGACAGCCCTCATCGGTCTCC
1 CTAATTACTAAATCTTTTAAAATGTTTGGAGGGACAGCCCTCATCGGTCTCC
4251 CTAATTACTAAATCTTTTAAAATGTTTGGAGGGACAGCCCTCATCGGTCTCC
1 CTAATTACTAAATCTTTTAAAATGTTTGGAGGGACAGCCCTCATCGGTCTCC
4303 CTAATTACTAAAAT-TTTTAAA
1 CTAATTACT-AAATCTTTTAAA
4324 CTCTTAAATT
Statistics
Matches: 121, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
52 116 0.96
53 5 0.04
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (52 bp):
CTAATTACTAAATCTTTTAAAATGTTTGGAGGGACAGCCCTCATCGGTCTCC
Found at i:6663 original size:27 final size:27
Alignment explanation
Indices: 6625--6694 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 27
6615 CATTTCAGAT
6625 TGGAGTAACATAATAAACACCTTGCTG
1 TGGAGTAACATAATAAACACCTTGCTG
*
6652 TGGAGTAACATATCATAATAAACACCTTGGTG
1 TGGAGT---A-A-CATAATAAACACCTTGCTG
6684 TGGAGTAACAT
1 TGGAGTAACAT
6695 CATTTCAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
27 9 0.24
28 1 0.03
29 1 0.03
30 1 0.03
31 1 0.03
32 24 0.65
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (27 bp):
TGGAGTAACATAATAAACACCTTGCTG
Found at i:6674 original size:32 final size:32
Alignment explanation
Indices: 6633--6694 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
6623 ATTGGAGTAA
6633 CATAATAAACACCTTGCTGTGGAGTAACATAT
1 CATAATAAACACCTTGCTGTGGAGTAACATAT
*
6665 CATAATAAACACCTTGGTGTGGAGTAACAT
1 CATAATAAACACCTTGCTGTGGAGTAACAT
6695 CATTTCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (32 bp):
CATAATAAACACCTTGCTGTGGAGTAACATAT
Found at i:11054 original size:19 final size:20
Alignment explanation
Indices: 11024--11087 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
11014 TTGACACTGT
11024 TTAGCAACTGTATAGATGAGA
1 TTAGC-ACTGTATAGATGAGA
*
11045 TTA-CACTGTATAGATTAGA
1 TTAGCACTGTATAGATGAGA
* *
11064 TTAGGTACTGTACAGATGAGA
1 TTA-GCACTGTATAGATGAGA
11085 TTA
1 TTA
11088 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (20 bp):
TTAGCACTGTATAGATGAGA
Found at i:11075 original size:21 final size:19
Alignment explanation
Indices: 11030--11087 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
11020 CTGTTTAGCA
11030 ACTGTATAGATGAGATTAC
1 ACTGTATAGATGAGATTAC
* *
11049 ACTGTATAGATTAGATTAGGT
1 ACTGTATAGATGAGATTA--C
*
11070 ACTGTACAGATGAGATTA
1 ACTGTATAGATGAGATTA
11088 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (19 bp):
ACTGTATAGATGAGATTAC
Found at i:14233 original size:3 final size:3
Alignment explanation
Indices: 14225--14252 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14215 TAATTAGCAT
14225 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
14253 GTTGTGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:22952 original size:133 final size:123
Alignment explanation
Indices: 22707--22961 Score: 384
Period size: 133 Copynumber: 2.0 Consensus size: 123
22697 ATTGTTTAAA
* *
22707 CTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAATT
1 CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATACCTTTATAATT
22772 TTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
66 TTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
*
22830 CTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATAACCTTATACC
1 CTTTTACAGTTTTACTCAACTAAAAACTCTA-ATTTTATTTAATTAAATCTAAT-ACCTT-TA--
*
22895 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAAACTTATATATATTAGAATTTTTTAAAT
61 TA----ATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAAT
22960 AT
121 AT
22962 ATTTCTTAAA
Statistics
Matches: 118, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
123 30 0.25
124 21 0.18
125 4 0.03
126 2 0.02
128 2 0.02
132 25 0.21
133 34 0.29
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATACCTTTATAATT
TTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
Found at i:22984 original size:14 final size:13
Alignment explanation
Indices: 22948--22986 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
22938 TATATATTAG
22948 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
22961 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
22975 AATTTTTTAAAT
1 AATTTTTTAAAT
22987 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:40602 original size:23 final size:23
Alignment explanation
Indices: 40572--40632 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 23
40562 AATGAAATCT
*
40572 CATCGACTTAGACTTTATGCAGC
1 CATCGACTTGGACTTTATGCAGC
* *
40595 CATCGACTTGGAATTTTCTGCAGC
1 CATCGACTTGG-ACTTTATGCAGC
40619 CATCGACTTGGACT
1 CATCGACTTGGACT
40633 GAAACCAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 12 0.36
24 21 0.64
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (23 bp):
CATCGACTTGGACTTTATGCAGC
Found at i:42799 original size:24 final size:24
Alignment explanation
Indices: 42772--42819 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
42762 GCATGAATGG
*
42772 GGTGCCACTCTTGGCCATTCAGAT
1 GGTGCCACTCTTGCCCATTCAGAT
*
42796 GGTGCCACTCTTTCCCATTCAGAT
1 GGTGCCACTCTTGCCCATTCAGAT
42820 CGTATGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (24 bp):
GGTGCCACTCTTGCCCATTCAGAT
Found at i:43933 original size:12 final size:12
Alignment explanation
Indices: 43916--43959 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
43906 AATCGAAGTA
43916 AATCTACCTTAT
1 AATCTACCTTAT
43928 AATCTACC--AT
1 AATCTACCTTAT
43938 AATCCT-CCTTAT
1 AAT-CTACCTTAT
43950 AATCTACCTT
1 AATCTACCTT
43960 GATTTGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 7 0.25
11 4 0.14
12 17 0.61
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.39
Consensus pattern (12 bp):
AATCTACCTTAT
Found at i:51659 original size:15 final size:16
Alignment explanation
Indices: 51639--51675 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
51629 TATAAAATAA
*
51639 TAATAATATATA-TAG
1 TAATAATAAATACTAG
51654 TAATAATAAATACTAG
1 TAATAATAAATACTAG
51670 TAATAA
1 TAATAA
51676 GGGTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (16 bp):
TAATAATAAATACTAG
Found at i:54706 original size:77 final size:77
Alignment explanation
Indices: 54575--54728 Score: 272
Period size: 77 Copynumber: 2.0 Consensus size: 77
54565 TGAAGTTTTG
* * *
54575 AGTCCCACTGGCTCTAGCTGTTGAGACTATTATTGTGATATTTTGGGATGTATTAGACCAATTGG
1 AGTCCCACTGACTCTAGCTGTTGAGACTATTATTGTGATATTTTCGGATATATTAGACCAATTGG
54640 ATTTTGTGTTCT
66 ATTTTGTGTTCT
54652 AGTCCCACTGACTCTAGCTGTTGAGACTATTATTGTGATATTTTCGGATATATTAGACCAATTGG
1 AGTCCCACTGACTCTAGCTGTTGAGACTATTATTGTGATATTTTCGGATATATTAGACCAATTGG
*
54717 ATTTTGTTTTCT
66 ATTTTGTGTTCT
54729 TCCGACTGTC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (77 bp):
AGTCCCACTGACTCTAGCTGTTGAGACTATTATTGTGATATTTTCGGATATATTAGACCAATTGG
ATTTTGTGTTCT
Found at i:62325 original size:45 final size:45
Alignment explanation
Indices: 62261--62395 Score: 270
Period size: 45 Copynumber: 3.0 Consensus size: 45
62251 CCCTGCCCCC
62261 GAAACAATCCATGGAGGAGCTGCTAGCTGATATGGAAAAGAAGTT
1 GAAACAATCCATGGAGGAGCTGCTAGCTGATATGGAAAAGAAGTT
62306 GAAACAATCCATGGAGGAGCTGCTAGCTGATATGGAAAAGAAGTT
1 GAAACAATCCATGGAGGAGCTGCTAGCTGATATGGAAAAGAAGTT
62351 GAAACAATCCATGGAGGAGCTGCTAGCTGATATGGAAAAGAAGTT
1 GAAACAATCCATGGAGGAGCTGCTAGCTGATATGGAAAAGAAGTT
62396 TATGCAGCAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 90 1.00
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (45 bp):
GAAACAATCCATGGAGGAGCTGCTAGCTGATATGGAAAAGAAGTT
Found at i:63101 original size:33 final size:33
Alignment explanation
Indices: 63058--63171 Score: 219
Period size: 33 Copynumber: 3.5 Consensus size: 33
63048 GAGGATGGAA
*
63058 AGAAAGAGATTGCTGAAAAGGTGCCAGTGCCAG
1 AGAAAAAGATTGCTGAAAAGGTGCCAGTGCCAG
63091 AGAAAAAGATTGCTGAAAAGGTGCCAGTGCCAG
1 AGAAAAAGATTGCTGAAAAGGTGCCAGTGCCAG
63124 AGAAAAAGATTGCTGAAAAGGTGCCAGTGCCAG
1 AGAAAAAGATTGCTGAAAAGGTGCCAGTGCCAG
63157 AGAAAAAGATTGCTG
1 AGAAAAAGATTGCTG
63172 GAGAGGAGGC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.39, C:0.14, G:0.31, T:0.16
Consensus pattern (33 bp):
AGAAAAAGATTGCTGAAAAGGTGCCAGTGCCAG
Found at i:63198 original size:24 final size:24
Alignment explanation
Indices: 63170--63219 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
63160 AAAAGATTGC
*
63170 TGGAGAGGAGGCAAAGACTAAAGT
1 TGGAGAGGAGGCAAAGACGAAAGT
*
63194 TGGAGAGGTGGCAAAGACGAAAGT
1 TGGAGAGGAGGCAAAGACGAAAGT
63218 TG
1 TG
63220 ATCCAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.40, T:0.14
Consensus pattern (24 bp):
TGGAGAGGAGGCAAAGACGAAAGT
Found at i:64802 original size:17 final size:16
Alignment explanation
Indices: 64780--64823 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
64770 TGCATAAGTT
64780 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAA-AAA
*
64797 AAAAAAGAGAAACAAAA
1 AAAAAAGA-AAAAAAAA
*
64814 AAAAGAGAAA
1 AAAAAAGAAA
64824 GAAGGAGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 18 0.75
18 4 0.17
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAA
Found at i:64813 original size:15 final size:15
Alignment explanation
Indices: 64795--64823 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
64785 AGAAAAAAGA
64795 AAAAAAAAGAGAAAC
1 AAAAAAAAGAGAAAC
64810 AAAAAAAAGAGAAA
1 AAAAAAAAGAGAAA
64824 GAAGGAGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGAAAC
Found at i:67029 original size:16 final size:16
Alignment explanation
Indices: 67008--67038 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66998 GCTCATCCTC
*
67008 TCTCTTTCTTTCTCTT
1 TCTCTTTCTCTCTCTT
67024 TCTCTTTCTCTCTCT
1 TCTCTTTCTCTCTCT
67039 AAATCAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TCTCTTTCTCTCTCTT
Done.