Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017386.1 Corchorus olitorius cultivar O-4 contig17419, 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: 55711
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:294 original size:2 final size:2
Alignment explanation
Indices: 263--306 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
253 AGTTTAGACT
* * *
263 TA TA TA -A TA TA GA TA TA GA TA TA GA 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 TA
304 TA T
1 TA T
307 TATTTTTGCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:304 original size:12 final size:12
Alignment explanation
Indices: 263--306 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
253 AGTTTAGACT
263 TATATAATATAGA
1 TATAT-ATATAGA
*
276 TATAGATATAGA
1 TATATATATAGA
*
288 TATATATATATA
1 TATATATATAGA
300 TATATAT
1 TATATAT
307 TATTTTTGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
TATATATATAGA
Found at i:8641 original size:30 final size:30
Alignment explanation
Indices: 8605--8764 Score: 225
Period size: 30 Copynumber: 5.3 Consensus size: 30
8595 AATCAAGCAA
*
8605 CCAAAGGTCCTGCACAAGCCACTGCACGAG
1 CCAAAGGTCCTGCACAAGCCACTGCACCAG
8635 CCAAAGGTCCTGCACAAGCCACTGCACCAAG
1 CCAAAGGTCCTGCACAAGCCACTGCACC-AG
* *
8666 -CAAAGGTCCTGGA-AACTCCACTGCACCAG
1 CCAAAGGTCCTGCACAA-GCCACTGCACCAG
* *
8695 CCAAAGGTCCTGCACAAGCCACTACACCAA
1 CCAAAGGTCCTGCACAAGCCACTGCACCAG
* *
8725 CCAAAGATCCTGCACAAGCCACTGCACCAA
1 CCAAAGGTCCTGCACAAGCCACTGCACCAG
8755 CCAAAGGTCC
1 CCAAAGGTCC
8765 ACCAAGGAGG
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
29 4 0.03
30 108 0.93
31 4 0.03
ACGTcount: A:0.33, C:0.38, G:0.18, T:0.11
Consensus pattern (30 bp):
CCAAAGGTCCTGCACAAGCCACTGCACCAG
Found at i:9292 original size:33 final size:33
Alignment explanation
Indices: 9218--9307 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
9208 TTGGAAATGC
* * * *
9218 AGATTTCTACAAATGTAAAAATTAGGTGATAGT
1 AGATTTCTGCAAATGTTAACATTAGGTGATAGA
* *
9251 AGATTTCTGGAAATGTTAACATTAGGTGATGGA
1 AGATTTCTGCAAATGTTAACATTAGGTGATAGA
*
9284 AGATTTCTGTAAATGTTAACATTA
1 AGATTTCTGCAAATGTTAACATTA
9308 ACATTAGATG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (33 bp):
AGATTTCTGCAAATGTTAACATTAGGTGATAGA
Found at i:9633 original size:153 final size:153
Alignment explanation
Indices: 9355--9660 Score: 603
Period size: 153 Copynumber: 2.0 Consensus size: 153
9345 ATTTTGGGAC
9355 AAATCTGAATATTGTAGCAGGTATTGGATTACCAAACAGTTTTTTTGTTTCACAGGTTATTCATA
1 AAATCTGAATATTGTAGCAGGTATTGGATTACCAAACAGTTTTTTTGTTTCACAGGTTATTCATA
9420 TGAATGAAAGCAATTATTTGGTCCAACATATTATATTTTCACTTTCTTGGTCATATTATCACTTT
66 TGAATGAAAGCAATTATTTGGTCCAACATATTATATTTTCACTTTCTTGGTCATATTATCACTTT
9485 CTTGAAGCTACCAAACTTATAGT
131 CTTGAAGCTACCAAACTTATAGT
9508 AAATCTGAATATTGTAGCAGGTATTGGATTACCAAACAGTTTTTTTGTTTCACAGGTTATTCATA
1 AAATCTGAATATTGTAGCAGGTATTGGATTACCAAACAGTTTTTTTGTTTCACAGGTTATTCATA
*
9573 TGAATGAAAGCAATTATTTGGTCCAACATATTATATTTTCACTTTCTTGGTGATATTATCACTTT
66 TGAATGAAAGCAATTATTTGGTCCAACATATTATATTTTCACTTTCTTGGTCATATTATCACTTT
9638 CTTGAAGCTACCAAACTTATAGT
131 CTTGAAGCTACCAAACTTATAGT
9661 TTCATTGATA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 152 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (153 bp):
AAATCTGAATATTGTAGCAGGTATTGGATTACCAAACAGTTTTTTTGTTTCACAGGTTATTCATA
TGAATGAAAGCAATTATTTGGTCCAACATATTATATTTTCACTTTCTTGGTCATATTATCACTTT
CTTGAAGCTACCAAACTTATAGT
Found at i:10530 original size:24 final size:25
Alignment explanation
Indices: 10502--10564 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
10492 ATCTTCTTTT
10502 ATTTTCTTTTCTTTTT-C-CTTTTCC
1 ATTTT-TTTTCTTTTTGCACTTTTCC
*
10526 ATTTTTTTT-TTTTTGCATTTTTCC
1 ATTTTTTTTCTTTTTGCACTTTTCC
*
10550 TTTTTTTTTCTTTTT
1 ATTTTTTTTCTTTTT
10565 ATGTTGGGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 5 0.15
23 5 0.15
24 19 0.56
25 5 0.15
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.78
Consensus pattern (25 bp):
ATTTTTTTTCTTTTTGCACTTTTCC
Found at i:12622 original size:76 final size:76
Alignment explanation
Indices: 12485--12636 Score: 173
Period size: 76 Copynumber: 2.0 Consensus size: 76
12475 ACAAGGGCCC
** * *
12485 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCAAGTGGTTTGTTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAAAACCCAAGTGGTTTGCTTGAGAACCCAGAT
12550 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * **
12561 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAAACCCATGT-GTTTCGCTTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAAAACCCAAGTGGTTT-GCTTGAGAACCCAG
*
12624 ATGGGCTGTGTCA
64 ATGGGCAGTGTCA
12637 TAGCTTATCA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
75 4 0.06
76 55 0.87
77 4 0.06
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAAAACCCAAGTGGTTTGCTTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:13680 original size:3 final size:3
Alignment explanation
Indices: 13672--13697 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13662 CTAATCTTAT
13672 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
13698 TAATTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17356 original size:27 final size:27
Alignment explanation
Indices: 17326--17378 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
17316 TTAGCACTCA
* *
17326 AACGAAAAATAAAAATAAAAAGAAAAT
1 AACGAAAAAGAAAAAGAAAAAGAAAAT
17353 AACGAAAAAGAAAAAGAAAAAGAAAA
1 AACGAAAAAGAAAAAGAAAAAGAAAA
17379 AGATAAGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.06
Consensus pattern (27 bp):
AACGAAAAAGAAAAAGAAAAAGAAAAT
Found at i:17366 original size:5 final size:6
Alignment explanation
Indices: 17329--17381 Score: 61
Period size: 6 Copynumber: 8.3 Consensus size: 6
17319 GCACTCAAAC
* *
17329 GAAAAA TAAAAA TAAAAA GAAAATAA CGAAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA G-AAA-AA -GAAAAA GAAAAA GAAAAA GAAAAA
17380 GA
1 GA
17382 TAAGGATAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 31 0.74
7 5 0.12
8 5 0.12
9 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:20590 original size:23 final size:23
Alignment explanation
Indices: 20540--20593 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
20530 GACGAAATCG
*
20540 CGGAGATTTCAGAGAAAAAAGCA
1 CGGAGCTTTCAGAGAAAAAAGCA
* * *
20563 CGGAGCTTTGAGAGAAATAAGTA
1 CGGAGCTTTCAGAGAAAAAAGCA
*
20586 TGGAGCTT
1 CGGAGCTT
20594 GGTTTTTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (23 bp):
CGGAGCTTTCAGAGAAAAAAGCA
Found at i:22492 original size:13 final size:13
Alignment explanation
Indices: 22474--22508 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
22464 AAGATCATTC
*
22474 AATCTCGGGGCGA
1 AATCTCGAGGCGA
22487 AATCTCGAGGCGA
1 AATCTCGAGGCGA
22500 AATCTCGAG
1 AATCTCGAG
22509 AGGTCGTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (13 bp):
AATCTCGAGGCGA
Found at i:23101 original size:20 final size:20
Alignment explanation
Indices: 23076--23144 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
23066 AACTACCCAT
23076 AAAGCCCAAATGCATAAATA
1 AAAGCCCAAATGCATAAATA
* * *
23096 AAAGCCTAAGT-CCTAAATTA
1 AAAGCCCAAATGCATAAA-TA
23116 AAA-CCC-AA-GACATAAATA
1 AAAGCCCAAATG-CATAAATA
23134 AAAGGCCCAAA
1 AAA-GCCCAAA
23145 CACATAAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
18 6 0.16
19 12 0.32
20 17 0.46
21 2 0.05
ACGTcount: A:0.54, C:0.22, G:0.10, T:0.14
Consensus pattern (20 bp):
AAAGCCCAAATGCATAAATA
Found at i:23112 original size:19 final size:19
Alignment explanation
Indices: 23088--23143 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
23078 AGCCCAAATG
* *
23088 CATAAATAAAAGCCTAAGT
1 CATAAATAAAAGCCCAAGA
*
23107 CCTAAATTAAAA-CCCAAGA
1 CATAAA-TAAAAGCCCAAGA
23126 CATAAATAAAAGGCCCAA
1 CATAAATAAAA-GCCCAA
23144 ACACATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.17
19 15 0.50
20 10 0.33
ACGTcount: A:0.54, C:0.21, G:0.09, T:0.16
Consensus pattern (19 bp):
CATAAATAAAAGCCCAAGA
Found at i:26231 original size:27 final size:28
Alignment explanation
Indices: 26201--26276 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
26191 TGTGAACTTA
26201 AAATGACCAAAATGCCCCT-GAAT-GTG
1 AAATGACCAAAATGCCCCTAGAATCGTG
* * * *
26227 CAAATGACTAAAATACCCCTAGATTCTTG
1 -AAATGACCAAAATGCCCCTAGAATCGTG
26256 AGAATGACCAAAATGCCCCTA
1 A-AATGACCAAAATGCCCCTA
26277 ATTGATCCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 17 0.43
28 4 0.10
29 19 0.47
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGAATCGTG
Found at i:28058 original size:26 final size:26
Alignment explanation
Indices: 28025--28079 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
28015 GCCAAAATAA
28025 AAATTATGAAATAAATTTAAGGTGGT
1 AAATTATGAAATAAATTTAAGGTGGT
*
28051 AAATTATGAAATAATTTTAAGGTGGT
1 AAATTATGAAATAAATTTAAGGTGGT
28077 AAA
1 AAA
28080 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (26 bp):
AAATTATGAAATAAATTTAAGGTGGT
Found at i:42119 original size:29 final size:29
Alignment explanation
Indices: 42077--42139 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
42067 ATTCTTTCTC
42077 CTTTTCCTTTTATCTTTTTGGTCCATTTA
1 CTTTTCCTTTTATCTTTTTGGTCCATTTA
42106 CTTTTCCTTTTATCTTTTTGGTCCATTTA
1 CTTTTCCTTTTATCTTTTTGGTCCATTTA
42135 CTTTT
1 CTTTT
42140 TGAGTCTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.10, C:0.21, G:0.06, T:0.63
Consensus pattern (29 bp):
CTTTTCCTTTTATCTTTTTGGTCCATTTA
Found at i:42140 original size:16 final size:17
Alignment explanation
Indices: 42085--42141 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
42075 TCCTTTTCCT
42085 TTTATCTTTTTGGTCCA
1 TTTATCTTTTTGGTCCA
*
42102 TTTA-C--TTT--TCCT
1 TTTATCTTTTTGGTCCA
42114 TTTATCTTTTTGGTCCA
1 TTTATCTTTTTGGTCCA
42131 TTTA-CTTTTTG
1 TTTATCTTTTTG
42142 AGTCTTCGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
12 7 0.21
13 1 0.03
14 3 0.09
15 3 0.09
16 8 0.24
17 11 0.33
ACGTcount: A:0.11, C:0.18, G:0.09, T:0.63
Consensus pattern (17 bp):
TTTATCTTTTTGGTCCA
Found at i:44804 original size:26 final size:25
Alignment explanation
Indices: 44761--44821 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
44751 TAACTTCAAG
* *
44761 TTGGGC-TCCTATTCCATTTATGCT
1 TTGGGCTTCTTATTCCATTGATGCT
* * *
44785 TTGGGCCTTCTTATTTCATTGCTGTT
1 TTGGG-CTTCTTATTCCATTGATGCT
44811 TTGGGCTTCTT
1 TTGGGCTTCTT
44822 TCACTTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 5 0.17
25 7 0.23
26 18 0.60
ACGTcount: A:0.08, C:0.21, G:0.20, T:0.51
Consensus pattern (25 bp):
TTGGGCTTCTTATTCCATTGATGCT
Found at i:45689 original size:67 final size:67
Alignment explanation
Indices: 45527--45900 Score: 372
Period size: 67 Copynumber: 5.6 Consensus size: 67
45517 CAGTTCTTTT
* * * * ** *
45527 TTTCC-AAAATAACATTTCGGTCGAAGGGTCAATTTTCATC-TTTTGCATTTAAGAGTAGTATTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTC-AGTTTCATCTTTTTGCATTTAAGTTTAGCATTT
*
45590 TCA
65 TCG
* *
45593 TTTCC-AAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCACTCAAGTTTAGCATTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTTAAGTTTAGCATTTT
45657 CG
66 CG
* * * * *
45659 TTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGTTTCTTCTTTTTGCATTCAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTTAAGTTTAGCATTTT
45724 CG
66 CG
* * * *
45726 TTTCCAAAAATACCCTTTCGGTGAAATGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAG--T
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATC---TTTTTGCATTTAAGTTTAGCAT
45789 CTTTC-
63 -TTTCG
* ** * *
45794 TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTTTTTCATTCTTGCATTTGA-TATTA-C-T
1 TTTCCAAA-AATACCCTTTCGGTCAAAGGGTCAGTTTCATC-TTTTTGCATTTAAGT-TTAGCAT
45856 TTT-G
63 TTTCG
*
45860 ATTTCCAAAAATACCCTTTCGGTCAAAAGGTCAGTTTCATC
1 -TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATC
45901 AGTTCCACAT
Statistics
Matches: 261, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
65 8 0.03
66 84 0.32
67 113 0.43
68 9 0.03
69 31 0.12
70 16 0.06
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (67 bp):
TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTTAAGTTTAGCATTTT
CG
Found at i:45912 original size:66 final size:63
Alignment explanation
Indices: 45585--45951 Score: 199
Period size: 67 Copynumber: 5.5 Consensus size: 63
45575 TTAAGAGTAG
* * *
45585 TATTTTCATTTCC-AAAATACCCTTTCGGTCAAAGGGTCAGTTTCATC-TTTTTGCACTCAAGTT
1 TATTTT-ATTTCCAAAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCAGTTCTGCA-T----TT
*
45648 -TAG
60 ATAT
* * * * * * * * *
45651 CATTTTCGTTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGTTTCTTC-TTTTTGCATTCAAGTT
1 TATTTT-ATTTCCAAAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCAGTTCTGCATT----TA
*
45715 TAG
61 TAT
* * * *
45718 TATTTTCGTTTCCAAAAATACCCTTTCGGTGAAATGGTCAGTTTCATCAGGTTGTTGCATTTA-A
1 TATTTT-ATTTCCAAAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCA-GTT-CTGCATTTATA
45782 GT
63 -T
* * * **
45784 CTAGTCTTTCTTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTTTTTCA-TTCTTGCATTTG
1 -TA-T-TTTATTTCCAAA-AATACCCTTTCGGTCAAAAGGTCAGTTTCATCAGTTC-TGCATTT-
45848 ATAT
60 ATAT
**
45852 TACTTTTGATTTCCAAAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCAGTTCCACATTTCAGT
1 TA-TTTT-ATTTCCAAAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCAGTTCTGCATTT-A-T
45917 -T
62 AT
* * *
45918 TATTCTATTTTCTAAAAATGCCCTTTCGGTCAAA
1 TATTTTA-TTTCCAAAAATACCCTTTCGGTCAAA
45952 GGGCGAACTT
Statistics
Matches: 247, Mismatches: 33, Indels: 43
0.76 0.10 0.13
Matches are distributed among these distances:
62 1 0.00
64 1 0.00
65 28 0.11
66 55 0.22
67 110 0.45
68 11 0.04
69 34 0.14
70 7 0.03
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (63 bp):
TATTTTATTTCCAAAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCAGTTCTGCATTTATAT
Found at i:51022 original size:19 final size:18
Alignment explanation
Indices: 50998--51033 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
50988 TGAAGACTTA
50998 TTGAAGATAATTTGAAGAT
1 TTGAAGATAATTT-AAGAT
*
51017 TTGAAGATCATTTAAGA
1 TTGAAGATAATTTAAGA
51034 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTTAAGAT
Found at i:54357 original size:22 final size:22
Alignment explanation
Indices: 54332--54373 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54322 TATTCTCTGC
54332 ATTTAATTAATTGTTTTCTTTA
1 ATTTAATTAATTGTTTTCTTTA
** *
54354 ATTTTCTTGATTGTTTTCTT
1 ATTTAATTAATTGTTTTCTT
54374 ATATAGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (22 bp):
ATTTAATTAATTGTTTTCTTTA
Done.