Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012752.1 Corchorus olitorius cultivar O-4 contig12785, 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: 48175
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:90 original size:2 final size:2
Alignment explanation
Indices: 83--112 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73 TATTCTAGTT
83 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
113 ATAAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1156 original size:19 final size:20
Alignment explanation
Indices: 1115--1156 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1105 TGATTAAATG
*
1115 AACTCTAGAAAGTGTATTCA
1 AACTCTAGAAACTGTATTCA
1135 AACTCT-GAAACTCGTATT-A
1 AACTCTAGAAACT-GTATTCA
1154 AAC
1 AAC
1157 CCTATAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
AACTCTAGAAACTGTATTCA
Found at i:1936 original size:12 final size:13
Alignment explanation
Indices: 1914--1939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1904 TTGATTGATT
1914 TTGATTTTTTTTA
1 TTGATTTTTTTTA
1927 TTGATTTTTTTTA
1 TTGATTTTTTTTA
1940 ATTTCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTGATTTTTTTTA
Found at i:2334 original size:14 final size:15
Alignment explanation
Indices: 2315--2348 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
2305 AAGTGCCTTT
2315 ATTTTCCTTTTTTC-
1 ATTTTCCTTTTTTCA
2329 ATTTTCCTTTTTTCA
1 ATTTTCCTTTTTTCA
2344 ATTTT
1 ATTTT
2349 TCATTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTCCTTTTTTCA
Found at i:2373 original size:6 final size:6
Alignment explanation
Indices: 2357--2406 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
2347 TTTCATTCAT
* *
2357 TTTTTA TTTTTTA TTTTTA -TTTT- TGTTTA TTTTTA TTTTTT TTGTTTA
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA
2405 TT
1 TT
2407 GGGAAATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 7 0.19
6 18 0.50
7 11 0.31
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:2379 original size:19 final size:18
Alignment explanation
Indices: 2357--2406 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
2347 TTTCATTCAT
2357 TTTTTATTTTTTATTTTTA
1 TTTTT-TTTTTTATTTTTA
*
2376 --TTTTTGTTTATTTTTA
1 TTTTTTTTTTTATTTTTA
2392 TTTTTTTTGTTTATT
1 TTTTTTTT-TTTATT
2407 GGGAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
18 5 0.19
19 6 0.23
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTTATTTTTA
Found at i:2387 original size:10 final size:10
Alignment explanation
Indices: 2372--2406 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2362 ATTTTTTATT
2372 TTTATTTTTG
1 TTTATTTTTG
*
2382 TTTATTTTTA
1 TTTATTTTTG
2392 TTT-TTTTTG
1 TTTATTTTTG
2401 TTTATT
1 TTTATT
2407 GGGAAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (10 bp):
TTTATTTTTG
Found at i:2387 original size:16 final size:16
Alignment explanation
Indices: 2366--2396 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2356 TTTTTTATTT
2366 TTTATTTTTATTTTTG
1 TTTATTTTTATTTTTG
2382 TTTATTTTTATTTTT
1 TTTATTTTTATTTTT
2397 TTTGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTATTTTTATTTTTG
Found at i:2927 original size:74 final size:75
Alignment explanation
Indices: 2784--2934 Score: 193
Period size: 76 Copynumber: 2.0 Consensus size: 75
2774 ATTTAGTCAT
*
2784 CTCGAAATTCATTGCTTTGACCAAAACTGATTTTGAAACACCTTTTGATTAAATCACCGTCATTC
1 CTCGAAATTCATAGCTTTGACCAAAACTGATTTTGAAACACCTTTTGATTAAATCA-C-TCATTC
2849 CTTTGCTCACAG
64 CTTTGCTCACAG
* * *
2861 CTCGAAA-TCATAG-TTTCGACTAAAACTGATTTTGAAA-ACTTTTTTATTGAAACTCA-TCATT
1 CTCGAAATTCATAGCTTT-GACCAAAACTGATTTTGAAACACCTTTTGATT-AAA-TCACTCATT
2922 CCTTTGCTCACAG
63 CCTTTGCTCACAG
2935 TCAAAATAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
74 18 0.27
75 12 0.18
76 27 0.40
77 10 0.15
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (75 bp):
CTCGAAATTCATAGCTTTGACCAAAACTGATTTTGAAACACCTTTTGATTAAATCACTCATTCCT
TTGCTCACAG
Found at i:7207 original size:13 final size:13
Alignment explanation
Indices: 7189--7213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7179 AACATACTTA
7189 AAAACACTTTTGG
1 AAAACACTTTTGG
7202 AAAACACTTTTG
1 AAAACACTTTTG
7214 ATTTTTTTTC
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:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
AAAACACTTTTGG
Found at i:8400 original size:2 final size:2
Alignment explanation
Indices: 8388--8423 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
8378 AACCCACTTG
*
8388 TA TA TA AA 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
8424 AACATCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11533 original size:26 final size:26
Alignment explanation
Indices: 11496--11568 Score: 94
Period size: 26 Copynumber: 2.7 Consensus size: 26
11486 AAGTGAACCT
11496 AAAATGACCAAAATGCCCCTAACGTG-
1 AAAATGACCAAAATGCCCCT-ACGTGA
* *
11522 CAAATGACCAAAATGCCCCCTAGGTGTA
1 AAAATGACCAAAATG-CCCCTACGTG-A
11550 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
11569 CTAGATGACC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 18 0.44
27 9 0.22
28 14 0.34
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTACGTGA
Found at i:11588 original size:28 final size:28
Alignment explanation
Indices: 11496--11575 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
11486 AAGTGAACCT
* *
11496 AAAATGACCAAAATG-CCCCTA-ACGTG
1 AAAATGACCAAAATGCCCCCTAGATGTA
* *
11522 CAAATGACCAAAATGCCCCCTAGGTGTA
1 AAAATGACCAAAATGCCCCCTAGATGTA
11550 AAAATGACCAAAATGCCCCCTAGATG
1 AAAATGACCAAAATGCCCCCTAGATG
11576 ACCATAATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 14 0.30
27 6 0.13
28 26 0.57
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCCTAGATGTA
Found at i:12192 original size:36 final size:35
Alignment explanation
Indices: 12061--12828 Score: 794
Period size: 36 Copynumber: 21.4 Consensus size: 35
12051 TTAATCTCTT
* ** *
12061 TGAATTAAGTTATTTACTGACCTT-CTTAATTTCCC
1 TGAATTAAG-TCTTTACTGATTTTACTTAATTACCC
* *
12096 TGAATTAAGTTATTTACTGA-CTTACTTAATTACCC
1 TGAATTAAG-TCTTTACTGATTTTACTTAATTACCC
* * * * ** *
12131 AGAATCAACTTCTTTATTGGCTTTACTTAATTACCT
1 TGAATTAA-GTCTTTACTGATTTTACTTAATTACCC
** * *
12167 TGAATTAAGTCCTTTTTTGATTTTACTTAATCACCT
1 TGAATTAAGT-CTTTACTGATTTTACTTAATTACCC
* * * *
12203 TCAATTAAGTCTTTTACTGATTTCATTTAATTACCT
1 TGAATTAAGTC-TTTACTGATTTTACTTAATTACCC
* *
12239 TGAATTTAGTCTTTTACTGATTTTA-TACAATTACCC
1 TGAATTAAGTC-TTTACTGATTTTACT-TAATTACCC
*
12275 TGAATTAAATCTTTTACTGATTTTACTTAATTACCC
1 TGAATTAAGTC-TTTACTGATTTTACTTAATTACCC
* *
12311 TGAATTAAGT-TGACTACTGACTTTACTTAATTACCC
1 TGAATTAAGTCT--TTACTGATTTTACTTAATTACCC
*
12347 TGAATTAAGT-TGATTACTGACTTTACTTAATTACCC
1 TGAATTAAGTCT--TTACTGATTTTACTTAATTACCC
*
12383 TGAATTAAGT-TACTAACTGATTTTACTTAATTACCC
1 TGAATTAAGTCT--TTACTGATTTTACTTAATTACCC
*
12419 TGAATTAAGT-TACTAACTGATTTTACTTAATTACCC
1 TGAATTAAGTCT--TTACTGATTTTACTTAATTACCC
* * *
12455 TGAATTAAGTCTTTGAATGAATTTACTTAGTTACCC
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
12491 TGAATTAAGTCTTTGACTGATTTTACTTAATTACCC
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
*
12527 TGAATTAAGTCTTTGACTGATCTTACTTAATTACCC
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
* * * *
12563 TGAATTAAGTGTTTTACTGATCTTACTTAGTTACCT
1 TGAATTAAGT-CTTTACTGATTTTACTTAATTACCC
* *
12599 TGAATTAAGTGTTTGATTGATTTTACTTAATTACCC
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
*
12635 TGAATTAAGTATTTGACTGATTTTACTTAATTACCC
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
* * *
12671 TAAATTAAGTCCTTGACTGATTTTACTTGATTACCC
1 TGAATTAAGT-CTTTACTGATTTTACTTAATTACCC
*
12707 TGAATTAAGTCTTTGATTGATTTTACTTAATTACCC
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
* * *
12743 TGAATTGAGTTTTTGACTGATTTTACTTAATTTCCC
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
* * *
12779 TGAATTAAGTCTTTGATTGATTTTACTTAAATACCA
1 TGAATTAAGTCTTT-ACTGATTTTACTTAATTACCC
*
12815 TGATTTAAGTCTTT
1 TGAATTAAGTCTTT
12829 TACATACCTA
Statistics
Matches: 643, Mismatches: 75, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
34 4 0.01
35 53 0.08
36 579 0.90
37 7 0.01
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (35 bp):
TGAATTAAGTCTTTACTGATTTTACTTAATTACCC
Found at i:17679 original size:34 final size:33
Alignment explanation
Indices: 17612--17707 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 33
17602 ATTGCAAGAA
* *
17612 TTGTGAATTAATCTCGTAGGAAGA-AC-A---A
1 TTGTGAATTAATCTCTTAGGAAGAGACTACTTT
17640 TTGTGAATTAATCTCTTA-GAAGAGAAACTACTTT
1 TTGTGAATTAATCTCTTAGGAAGAG--ACTACTTT
*
17674 TTGTGAATTAATTTCTTAGGAAGAGACTACTTT
1 TTGTGAATTAATCTCTTAGGAAGAGACTACTTT
17707 T
1 T
17708 GTTTTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
27 5 0.09
28 17 0.30
30 2 0.04
31 1 0.02
33 9 0.16
34 17 0.30
35 6 0.11
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (33 bp):
TTGTGAATTAATCTCTTAGGAAGAGACTACTTT
Found at i:18150 original size:20 final size:20
Alignment explanation
Indices: 18125--18181 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
18115 TCTCAACCTT
18125 AAAATAAAAAAAGAAGATTA
1 AAAATAAAAAAAGAAGATTA
*
18145 AAAATAAAAATGAA-AGGATTA
1 AAAATAAAAA--AAGAAGATTA
18166 AAAATAAAGAAAAGAA
1 AAAATAAA-AAAAGAA
18182 CACAATAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 12 0.39
21 15 0.48
22 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (20 bp):
AAAATAAAAAAAGAAGATTA
Found at i:20181 original size:106 final size:106
Alignment explanation
Indices: 20054--20287 Score: 459
Period size: 106 Copynumber: 2.2 Consensus size: 106
20044 TTTTAATTTT
*
20054 AATTTGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTTTAAAACCCTATAACAATAAGTTA
1 AATTGGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTTTAAAACCCTATAACAATAAGTTA
20119 TTAATTATGGAATTTACCCTTAAAATAACAGTAAAATATTA
66 TTAATTATGGAATTTACCCTTAAAATAACAGTAAAATATTA
20160 AATTGGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTTTAAAACCCTATAACAATAAGTTA
1 AATTGGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTTTAAAACCCTATAACAATAAGTTA
20225 TTAATTATGGAATTTACCCTTAAAATAACAGTAAAATATTA
66 TTAATTATGGAATTTACCCTTAAAATAACAGTAAAATATTA
20266 AATTGGGGCTAAACTTAGTGAA
1 AATTGGGGCTAAACTTAGTGAA
20288 AATAGGGCTA
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 127 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (106 bp):
AATTGGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTTTAAAACCCTATAACAATAAGTTA
TTAATTATGGAATTTACCCTTAAAATAACAGTAAAATATTA
Found at i:20310 original size:21 final size:21
Alignment explanation
Indices: 20271--20310 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20261 TATTAAATTG
* *
20271 GGGCTAAACTTAGTGAAAATA
1 GGGCTAAACTTAATAAAAATA
20292 GGGCTAAACTTAATAAAAA
1 GGGCTAAACTTAATAAAAA
20311 GAATGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (21 bp):
GGGCTAAACTTAATAAAAATA
Found at i:24815 original size:22 final size:22
Alignment explanation
Indices: 24787--24846 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
24777 ACATTAAAAA
*
24787 TGGGTCGTGTTGTGCCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
24809 TGGGTCGTGCTGTGCCGGCACG
1 TGGGTCGTGCTGTGCCGGCACG
*
24831 TGGGTCGTGCCGTGCC
1 TGGGTCGTGCTGTGCC
24847 ATGCCATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.03, C:0.27, G:0.45, T:0.25
Consensus pattern (22 bp):
TGGGTCGTGCTGTGCCGGCACG
Found at i:25849 original size:7 final size:8
Alignment explanation
Indices: 25822--25857 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
25812 AATTAGTATA
25822 ATAAAATC
1 ATAAAATC
25830 ATAAAA--
1 ATAAAATC
25836 ATAAAATC
1 ATAAAATC
25844 -TAAAATC
1 ATAAAATC
25851 ATAAAAT
1 ATAAAAT
25858 ACAAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.24
7 7 0.28
8 12 0.48
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (8 bp):
ATAAAATC
Found at i:25868 original size:21 final size:21
Alignment explanation
Indices: 25822--25868 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
25812 AATTAGTATA
*
25822 ATAAAATCATAAAAATAAAAT
1 ATAAAATCATAAAAATAAAAG
*
25843 CTAAAATCAT-AAAATACAAAG
1 ATAAAATCATAAAAATA-AAAG
25864 ATAAA
1 ATAAA
25869 TAATCAGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (21 bp):
ATAAAATCATAAAAATAAAAG
Found at i:26897 original size:21 final size:21
Alignment explanation
Indices: 26873--26914 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
26863 CAAATCACAA
26873 CTTGTCACTGGGAAGATCTTT
1 CTTGTCACTGGGAAGATCTTT
26894 CTTGTCACTGGGAAGATCTTT
1 CTTGTCACTGGGAAGATCTTT
26915 GCGGTAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
CTTGTCACTGGGAAGATCTTT
Found at i:35692 original size:27 final size:28
Alignment explanation
Indices: 35638--35704 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
35628 TGTACCCCTT
*
35638 TTCTTCAAAT-ATATTTCTAAATTGCCA
1 TTCTTAAAATAATATTTCTAAATTGCCA
35665 TTCTT-AAATAATATTT-TAATTATT-CCA
1 TTCTTAAAATAATATTTCTAA--ATTGCCA
*
35692 TTATTAAAATAAT
1 TTCTTAAAATAAT
35705 GGAAATTTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 7 0.20
27 18 0.51
28 10 0.29
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (28 bp):
TTCTTAAAATAATATTTCTAAATTGCCA
Found at i:37611 original size:19 final size:18
Alignment explanation
Indices: 37587--37622 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
37577 TGAAGACCAT
37587 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
37606 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
37623 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:39362 original size:22 final size:22
Alignment explanation
Indices: 39337--39380 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39327 TTCTAAAAAA
39337 AATTTTTGAT-TTTTGCGTTTTT
1 AATTTTTG-TGTTTTGCGTTTTT
*
39359 AATTTTTGTGTTTTGTGTTTTT
1 AATTTTTGTGTTTTGCGTTTTT
39381 TCTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.11, C:0.02, G:0.16, T:0.70
Consensus pattern (22 bp):
AATTTTTGTGTTTTGCGTTTTT
Found at i:39363 original size:15 final size:15
Alignment explanation
Indices: 39339--39372 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39329 CTAAAAAAAA
*
39339 TTTTTGATTTTTGCG
1 TTTTTAATTTTTGCG
*
39354 TTTTTAATTTTTGTG
1 TTTTTAATTTTTGCG
39369 TTTT
1 TTTT
39373 GTGTTTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.74
Consensus pattern (15 bp):
TTTTTAATTTTTGCG
Found at i:46470 original size:2 final size:2
Alignment explanation
Indices: 46463--46499 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
46453 TAGTATAAAT
*
46463 TA TA TA TA TA TA TA TA TA TA TC TA TA -A 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
46500 AAAGTACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.