Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018689.1 Corchorus olitorius cultivar O-4 contig18722, 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: 112224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2364 original size:30 final size:30
Alignment explanation
Indices: 2328--2836 Score: 595
Period size: 30 Copynumber: 16.7 Consensus size: 30
2318 ACTCTCTAAA
* *
2328 TGACACCAGAAGTTGTCATGGTCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
2358 TGACACCAAAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
2388 TGACACCAGAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
2418 TGACACCAGAAGCTGTCATGATCTTGTAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
2448 TGACACCAGAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
2478 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
2508 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
2538 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
2568 TGACACCAGAAGCTGTCATGATGTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
2598 TGACACCAGACGCTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * * *
2628 TAACATCATAAGCTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
2658 TGACACCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
2688 TGACATCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*** * * * *
2718 TGACATTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
* *
2750 TGACACCAGAAGTTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAAT
* ** * * * *
2783 AGACACTTGAAGATGTCATAATTTTAATCAAT
1 TGACACCAGAAGTTGTCATGATCTT--GCAAT
2815 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
2837 TTTACCTTTC
Statistics
Matches: 420, Mismatches: 52, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
30 351 0.84
31 3 0.01
32 42 0.10
33 22 0.05
34 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:2753 original size:32 final size:32
Alignment explanation
Indices: 2714--2840 Score: 112
Period size: 32 Copynumber: 3.9 Consensus size: 32
2704 CATGATCTTG
*
2714 CAATTGACATTTGAAGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
** * ** *
2746 CAATTGACACCAGAAGTTGTCATGATAAATT-TC
1 CAATTGACACTTGAAGATGTCAT-A-ATTTTATT
* *
2779 CAATAGACACTTGAAGATGTCATAATTTTAAT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
** * *
2811 CAATTGACACCAGAAGTTGTCATGATTTTA
1 CAATTGACACTTGAAGATGTCATAATTTTA
2841 CCTTTCAAAA
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
31 3 0.04
32 45 0.62
33 21 0.29
34 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (32 bp):
CAATTGACACTTGAAGATGTCATAATTTTATT
Found at i:4953 original size:33 final size:33
Alignment explanation
Indices: 4890--4953 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
4880 ACACTGAATA
* **
4890 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGACATAAACCCATGAGC
* *
4923 ATATTGCCCCTGTAGTGACATAAACCCATGA
1 ATATTGCCCCTGAAGAGACATAAACCCATGA
4954 AAAGATCACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGACATAAACCCATGAGC
Found at i:7849 original size:119 final size:121
Alignment explanation
Indices: 7547--7862 Score: 331
Period size: 126 Copynumber: 2.6 Consensus size: 121
7537 TTTAAAGTGC
*
7547 GTTGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACAGGGTTTTCCGACTTAAGGTTTTTAAT
1 GTTGCACTCTTTTTCCCTTATGATCGGTTTT-TCCCACTGGGTTTTCCGACTTAAGGTTTTTAAT
* * * *
7612 GAGGTAATAATAGCACATTTAGATGTAATTGTCTCGAAGACATATACATGGACTTAATT
65 GAGGCAAAAAGAGCACATGTAGA-GTAATTGTCTCGAAGACA-ATACATGGACTTAATT
* * * **
7671 GCTCTAGCACTCTTTTTCCCTTTTGTTTGGTTTTTCCCACTGGGTTTTCCGACACAAGGTTTTTA
1 G-T-T-GCACTCTTTTTCCCTTATGATCGGTTTTTCCCACTGGGTTTTCCGACTTAAGGTTTTTA
* *
7736 ATGAGGCAACAAAGAGCACATGTA-A-TATTTGTC-CAGAAGAC-A-A-ATGGACTTGATAT
63 ATGAGGCAA-AAAGAGCACATGTAGAGTAATTGTCTC-GAAGACAATACATGGACTTAAT-T
* * * *
7792 GTTGCACTCTTTTTTCCTTATGACCGATTTTATCCCATTGGGTTTTCC-AGCTTAAGGTTTTTAA
1 GTTGCACTCTTTTTCCCTTATGATCGGTTTT-TCCCACTGGGTTTTCCGA-CTTAAGGTTTTTAA
*
7856 CGAGGCA
64 TGAGGCA
7863 CTAGCTACAT
Statistics
Matches: 162, Mismatches: 22, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
118 23 0.14
119 34 0.21
120 11 0.07
121 3 0.02
122 1 0.01
123 1 0.01
124 14 0.09
125 1 0.01
126 38 0.23
127 36 0.22
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (121 bp):
GTTGCACTCTTTTTCCCTTATGATCGGTTTTTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATG
AGGCAAAAAGAGCACATGTAGAGTAATTGTCTCGAAGACAATACATGGACTTAATT
Found at i:10417 original size:11 final size:11
Alignment explanation
Indices: 10401--10431 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
10391 GAAGTTCATG
*
10401 TTTGAAGACCA
1 TTTGAAGACAA
10412 TTTGAAGACAA
1 TTTGAAGACAA
10423 TTTGAAGAC
1 TTTGAAGAC
10432 TTGAAGACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (11 bp):
TTTGAAGACAA
Found at i:21381 original size:30 final size:30
Alignment explanation
Indices: 21342--21405 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
21332 TCGGCTGGCG
*
21342 CCTCAGCTGGTGGTGCTGGAGTCTTCTCCT
1 CCTCAGCTGGTGGTGCCGGAGTCTTCTCCT
* * *
21372 CCTCGGCTGGTGGTGCCGGAGTCTTTTCTT
1 CCTCAGCTGGTGGTGCCGGAGTCTTCTCCT
21402 CCTC
1 CCTC
21406 CTTGACTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.05, C:0.31, G:0.30, T:0.34
Consensus pattern (30 bp):
CCTCAGCTGGTGGTGCCGGAGTCTTCTCCT
Found at i:27695 original size:42 final size:43
Alignment explanation
Indices: 27644--27737 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
27634 AGTGCATTAC
*
27644 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
27685 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
27730 CAAATATT
1 CTAATATT
27738 AGTTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:29427 original size:21 final size:21
Alignment explanation
Indices: 29402--29484 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
29392 TATCTTAGAT
29402 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
29423 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
29444 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
29466 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
29485 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:29435 original size:25 final size:25
Alignment explanation
Indices: 29404--29452 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
29394 TCTTAGATAT
*
29404 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
29429 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
29453 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:29977 original size:56 final size:56
Alignment explanation
Indices: 29910--30022 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
29900 TATCTGTTTC
*
29910 CTTTCACACAATAAATATTATAATAAATCTTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
* *
29966 CTTTCATACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
30022 C
1 C
30023 CAAAAAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.24, G:0.01, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:30271 original size:55 final size:56
Alignment explanation
Indices: 30187--30299 Score: 192
Period size: 55 Copynumber: 2.0 Consensus size: 56
30177 TATCTGTTTC
30187 CTTTCACACAATAAATATTATAATAAATCCTAT-CCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
* * *
30242 CTTTCATACAATAAATGTTATGATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
30298 CT
1 CT
30300 ACAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 30 0.56
56 24 0.44
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:30410 original size:42 final size:42
Alignment explanation
Indices: 30363--30445 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
30353 GCTAAGGATC
* *
30363 ATGATTTGAGTTGAGTATTTCTTAATTTATAAAGAATTTTCT
1 ATGATTTGAGTTCAGTATTTCTTAATTTACAAAGAATTTTCT
*
30405 ATGATTTGAGTTCAGTATTTCTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTCAGTATTTCTTAATTTACAAAGAATTTTC
30446 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.48
Consensus pattern (42 bp):
ATGATTTGAGTTCAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:31844 original size:7 final size:7
Alignment explanation
Indices: 31832--31857 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31822 TTCTTCTTCG
31832 CCTCAGC
1 CCTCAGC
31839 CCTCAGC
1 CCTCAGC
31846 CCTCAGC
1 CCTCAGC
31853 CCTCA
1 CCTCA
31858 ACAAAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.58, G:0.12, T:0.15
Consensus pattern (7 bp):
CCTCAGC
Found at i:60994 original size:42 final size:44
Alignment explanation
Indices: 60943--61036 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
60933 AGTGCATTAC
*
60943 CTAA-ATTCTACT-TC-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCTATCTCTAGATAATTCATCAAAATAAAG
60984 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCTATCTCTAGATAATTCATCAAAATAAAG
*
61029 TTAATATT
1 CTAATATT
61037 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 2 0.04
45 33 0.70
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (44 bp):
CTAATATTCTACTCTCTATCTCTAGATAATTCATCAAAATAAAG
Found at i:62272 original size:11 final size:9
Alignment explanation
Indices: 62246--62270 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
62236 AAAATATATA
62246 TTATATAAG
1 TTATATAAG
62255 TTATATAAG
1 TTATATAAG
62264 TTATATA
1 TTATATA
62271 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (9 bp):
TTATATAAG
Found at i:62521 original size:78 final size:80
Alignment explanation
Indices: 62369--62542 Score: 244
Period size: 78 Copynumber: 2.2 Consensus size: 80
62359 CATTGTTTAA
* * *
62369 ATTTTTCTAGTTTCACTCAACTAAAAACTCTATACTTATTTAATTATTAAATCTAATATCTTTAT
1 ATTTTACTA-TTTTACTCAACTAAAAACTCTATACTTATTTAA-TATTAAATCTAATATCCTTAT
*
62434 AACTATTTTATTTTACC
64 AACTATTTTAGTTTACC
* **
62451 ATTTTACTATTTTACTCAACTAAATACTCTATTTTTATTT-A-ATTAAATCTAATATCCTTATAA
1 ATTTTACTATTTTACTCAACTAAAAACTCTATACTTATTTAATATTAAATCTAATATCCTTATAA
62514 CTATTTTAGTTTACC
66 CTATTTTAGTTTACC
*
62529 ATTTTACTGTTTTA
1 ATTTTACTATTTTA
62543 ATTTTTTTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 48 0.57
80 1 0.01
81 27 0.32
82 8 0.10
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.51
Consensus pattern (80 bp):
ATTTTACTATTTTACTCAACTAAAAACTCTATACTTATTTAATATTAAATCTAATATCCTTATAA
CTATTTTAGTTTACC
Found at i:63450 original size:17 final size:17
Alignment explanation
Indices: 63428--63460 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
63418 TCATTACATC
63428 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
63445 AATTAATAATATAAAT
1 AATTAATAATATAAAT
63461 ATCCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:63543 original size:3 final size:3
Alignment explanation
Indices: 63537--63691 Score: 292
Period size: 3 Copynumber: 51.3 Consensus size: 3
63527 AAATTATACA
63537 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
63583 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
63631 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
63679 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
63692 GACTACGGAA
Statistics
Matches: 149, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
3 146 0.98
4 3 0.02
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:69265 original size:10 final size:10
Alignment explanation
Indices: 69250--69276 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
69240 CCCGTTTCAG
69250 ACACACACAA
1 ACACACACAA
69260 ACACACACAA
1 ACACACACAA
69270 ACACACA
1 ACACACA
69277 TTTATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (10 bp):
ACACACACAA
Found at i:70264 original size:97 final size:97
Alignment explanation
Indices: 70087--70364 Score: 418
Period size: 97 Copynumber: 2.9 Consensus size: 97
70077 CTATATATGA
* *
70087 TCTTTATTGGTACAAGCCGCTAATATCTTATAGTCACATTGGATTTTAACTAATCCGGATCCAA-
1 TCTTTATTGGTACAAGCCCCCAATATCTTATAGTCACATTGGATTTTAACTAATCCGGAT-CAAG
* **
70151 TTGTGTTAAATTGGGAAACTTATG-ATTTGTATT
65 TTGTGTTGAACCGGGAAACTT-TGAATTTGTATT
* * *
70184 TCTTTATTGGTACAAGCCCCCAATATCTTATACTCACATTGAATTTTAACTAATCCGGATCTAGT
1 TCTTTATTGGTACAAGCCCCCAATATCTTATAGTCACATTGGATTTTAACTAATCCGGATCAAGT
*
70249 TGCGTTGAACCGGGAAACTTTGAATTTGTATT
66 TGTGTTGAACCGGGAAACTTTGAATTTGTATT
* *
70281 TCTTTATTGGTACAAGCCCCCAATATCTTATAGTCACGTTGGATTTTAACTAATCTGGATCAAGT
1 TCTTTATTGGTACAAGCCCCCAATATCTTATAGTCACATTGGATTTTAACTAATCCGGATCAAGT
70346 TGTGTTGAACC-GGAAACTT
66 TGTGTTGAACCGGGAAACTT
70365 CACACATTTA
Statistics
Matches: 164, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
96 12 0.07
97 152 0.93
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (97 bp):
TCTTTATTGGTACAAGCCCCCAATATCTTATAGTCACATTGGATTTTAACTAATCCGGATCAAGT
TGTGTTGAACCGGGAAACTTTGAATTTGTATT
Found at i:76342 original size:22 final size:22
Alignment explanation
Indices: 76219--76444 Score: 149
Period size: 22 Copynumber: 10.4 Consensus size: 22
76209 CGTAGAACTA
* *
76219 TTGATAACCAAAC--TGAAAAT
1 TTGATAACCACACTATGAAATT
** *
76239 TTGATAACCTTATTATGAAATT
1 TTGATAACCACACTATGAAATT
** ** * *
76261 TCAATAACTTCCCTATGAAAAT
1 TTGATAACCACACTATGAAATT
76283 TTGATAACCACACTATGAAATT
1 TTGATAACCACACTATGAAATT
76305 TTGATAACCACACTATGAAATT
1 TTGATAACCACACTATGAAATT
* *
76327 TTGATAATCC-CCCTATGATATT
1 TTGATAA-CCACACTATGAAATT
* *
76349 TTGATAATCATACTATG-AA-T
1 TTGATAACCACACTATGAAATT
* * *
76369 TTGGTAACAACACAATGAAAGTT
1 TTGATAACCACACTATGAAA-TT
* **
76392 TTGATAACCTC-CTCAAAAAATT
1 TTGATAACCACACT-ATGAAATT
* * * *
76414 ATGATAAACACACCAGGAAATT
1 TTGATAACCACACTATGAAATT
*
76436 TCGATAACC
1 TTGATAACC
76445 TTCTTATGAG
Statistics
Matches: 154, Mismatches: 43, Indels: 16
0.72 0.20 0.08
Matches are distributed among these distances:
20 23 0.15
21 4 0.03
22 111 0.72
23 16 0.10
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.32
Consensus pattern (22 bp):
TTGATAACCACACTATGAAATT
Found at i:76419 original size:65 final size:65
Alignment explanation
Indices: 76278--76443 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 65
76268 CTTCCCTATG
* *
76278 AAAATTTGATAACCACACTATGAAATTTTGATAACCACACTATGAAATTTTGATAATCCCCCTAT
1 AAAATTTGATAACCACACTATGAAATTTTGATAACAACACAATGAAATTTTGATAATCCCCCTA-
*
76343 G
65 A
* * * * * *
76344 ATATTTTGATAATCATACTATG-AA-TTTGGTAACAACACAATGAAAGTTTTGATAA-CCTCCTC
1 AAAATTTGATAACCACACTATGAAATTTTGATAACAACACAATGAAA-TTTTGATAATCCCCCT-
76406 AA
64 AA
* * * *
76408 AAAATTATGATAAACACACCAGGAAATTTCGATAAC
1 AAAATT-TGATAACCACACTATGAAATTTTGATAAC
76444 CTTCTTATGA
Statistics
Matches: 78, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
64 27 0.35
65 24 0.31
66 20 0.26
67 7 0.09
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (65 bp):
AAAATTTGATAACCACACTATGAAATTTTGATAACAACACAATGAAATTTTGATAATCCCCCTAA
Found at i:76496 original size:22 final size:22
Alignment explanation
Indices: 76465--76846 Score: 145
Period size: 22 Copynumber: 17.1 Consensus size: 22
76455 AATAAAACTC
* * *
76465 TGATATCCTCTCTATGTAATTT
1 TGATAACCTCCCTATGAAATTT
*
76487 TGATAACCTCTCC-ATAAAATTT
1 TGATAACCTC-CCTATGAAATTT
* *
76509 TCATAACCTCCATATGAAATTT
1 TGATAACCTCCCTATGAAATTT
76531 TGTTAATTAACCTCCCTATGAAATTT
1 TG---A-TAACCTCCCTATGAAATTT
76557 TGTTAATTAACCTCCCTATGAAATTT
1 TG---A-TAACCTCCCTATGAAATTT
* *
76583 TGATAA----GC-A-CAAATTT
1 TGATAACCTCCCTATGAAATTT
76599 TGATAACCTCCCTCCCTATGAAATTT
1 TGATAA----CCTCCCTATGAAATTT
* * * *
76625 CGATAACCACACTATAAAATTT
1 TGATAACCTCCCTATGAAATTT
** * * * *
76647 CAATAACATTCATATGAGATTT
1 TGATAACCTCCCTATGAAATTT
* *
76669 TGTTAACCTCCCTAAGAAATTT
1 TGATAACCTCCCTATGAAATTT
** ***
76691 TGATAAATTTTTTATGAAATTT
1 TGATAACCTCCCTATGAAATTT
** ***
76713 TGATAAATTTTTTATGAAATTT
1 TGATAACCTCCCTATGAAATTT
*** *
76735 TGATAACCTTTGTATGAAATTA
1 TGATAACCTCCCTATGAAATTT
* * *
76757 TGATAA-CTACACGAT-AAAGTGT
1 TGATAACCT-CCCTATGAAA-TTT
*
76779 TGATAACCTCCATATGAAATTT
1 TGATAACCTCCCTATGAAATTT
* * **
76801 TGGT-AGCTATACTATGAAATTT
1 TGATAACCT-CCCTATGAAATTT
* * *
76823 TAATAACCTTCCTATGTAATTT
1 TGATAACCTCCCTATGAAATTT
76845 TG
1 TG
76847 GTTTGATTGT
Statistics
Matches: 273, Mismatches: 65, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
16 12 0.04
17 1 0.00
18 1 0.00
21 9 0.03
22 180 0.66
23 10 0.04
24 1 0.00
25 2 0.01
26 57 0.21
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TGATAACCTCCCTATGAAATTT
Found at i:76550 original size:26 final size:26
Alignment explanation
Indices: 76512--76584 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
76502 AAAATTTTCA
*
76512 TAACCTCCATATGAAATTTTGTTAAT
1 TAACCTCCCTATGAAATTTTGTTAAT
76538 TAACCTCCCTATGAAATTTTGTTAAT
1 TAACCTCCCTATGAAATTTTGTTAAT
76564 TAACCTCCCTATGAAATTTTG
1 TAACCTCCCTATGAAATTTTG
76585 ATAAGCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (26 bp):
TAACCTCCCTATGAAATTTTGTTAAT
Found at i:76713 original size:11 final size:11
Alignment explanation
Indices: 76684--76760 Score: 61
Period size: 11 Copynumber: 7.0 Consensus size: 11
76674 ACCTCCCTAA
76684 GAAATTTTGAT
1 GAAATTTTGAT
*
76695 -AAATTTTTTAT
1 GAAA-TTTTGAT
76706 GAAATTTTGAT
1 GAAATTTTGAT
*
76717 -AAATTTTTTAT
1 GAAA-TTTTGAT
76728 GAAATTTTGAT
1 GAAATTTTGAT
**
76739 -AACCTTTGTAT
1 GAAATTTTG-AT
*
76750 GAAATTATGAT
1 GAAATTTTGAT
76761 AACTACACGA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
10 12 0.24
11 28 0.55
12 11 0.22
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (11 bp):
GAAATTTTGAT
Found at i:79103 original size:13 final size:13
Alignment explanation
Indices: 79085--79113 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
79075 ATATAATAGT
79085 ATAGTAAGATAAG
1 ATAGTAAGATAAG
79098 ATAGTAAGATAAG
1 ATAGTAAGATAAG
79111 ATA
1 ATA
79114 AGATATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (13 bp):
ATAGTAAGATAAG
Found at i:79103 original size:18 final size:18
Alignment explanation
Indices: 79080--79118 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
79070 ATTTTATATA
79080 ATAGTATAG-TAAGATAAG
1 ATAGTA-AGATAAGATAAG
79098 ATAGTAAGATAAGATAAG
1 ATAGTAAGATAAGATAAG
79116 ATA
1 ATA
79119 TATGAATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.26
Consensus pattern (18 bp):
ATAGTAAGATAAGATAAG
Found at i:81558 original size:11 final size:11
Alignment explanation
Indices: 81542--81583 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
81532 CAGCACAACA
81542 AAAACAAAACG
1 AAAACAAAACG
81553 AAAACAAAACG
1 AAAACAAAACG
*
81564 AAAACAAAACA
1 AAAACAAAACG
81575 AAAACAAAA
1 AAAACAAAA
81584 AACAGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAACAAAACG
Found at i:81584 original size:6 final size:5
Alignment explanation
Indices: 81542--81583 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
81532 CAGCACAACA
81542 AAAAC AAAAC GAAAAC AAAAC GAAAAC AAAAC AAAAAC AAAA
1 AAAAC AAAAC -AAAAC AAAAC -AAAAC AAAAC -AAAAC AAAA
81584 AACAGAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 19 0.56
6 15 0.44
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:83912 original size:2 final size:2
Alignment explanation
Indices: 83905--83936 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83895 GAAGATGAAC
83905 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
83937 ACTAGTAAGT
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
Found at i:93228 original size:16 final size:17
Alignment explanation
Indices: 93202--93233 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
93192 ACATGTAATT
93202 TATTCAATTTAATTATG
1 TATTCAATTTAATTATG
93219 TATT-AATTTAATTAT
1 TATTCAATTTAATTAT
93234 TTAATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTCAATTTAATTATG
Found at i:93237 original size:8 final size:8
Alignment explanation
Indices: 93208--93254 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
93198 AATTTATTCA
93208 ATTTAATT
1 ATTTAATT
*
93216 ATGT-ATT
1 ATTTAATT
93223 AATTTAATT
1 -ATTTAATT
93232 ATTTAATT
1 ATTTAATT
93240 ATATTATATT
1 AT-TTA-ATT
93250 ATTTA
1 ATTTA
93255 TATATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 3 0.09
8 16 0.48
9 9 0.27
10 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:98640 original size:13 final size:12
Alignment explanation
Indices: 98619--98653 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
98609 AATAAAGTAA
98619 TAATACTATTAT
1 TAATACTATTAT
98631 TAATTACTATTAT
1 TAA-TACTATTAT
98644 TAATACTATT
1 TAATACTATT
98654 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Found at i:100813 original size:27 final size:27
Alignment explanation
Indices: 100781--100833 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
100771 TCAACGTATA
100781 TTTTTATAATATGAATATGAATACATT
1 TTTTTATAATATGAATATGAATACATT
100808 TTTTTATAATATGAATATGAATACAT
1 TTTTTATAATATGAATATGAATACAT
100834 CTGTATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTTATAATATGAATATGAATACATT
Found at i:102733 original size:23 final size:23
Alignment explanation
Indices: 102703--102747 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
102693 AAGAAAGAAA
102703 TAGCCGAATGGTAGTAGGTTTGC
1 TAGCCGAATGGTAGTAGGTTTGC
102726 TAGCCGAATGGTAGTAGGTTTG
1 TAGCCGAATGGTAGTAGGTTTG
102748 ACAACTGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.36, T:0.31
Consensus pattern (23 bp):
TAGCCGAATGGTAGTAGGTTTGC
Found at i:103330 original size:26 final size:28
Alignment explanation
Indices: 103292--103347 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
103282 CAGGAAGATC
*
103292 TGGAGAATCAATT-ACCGCATGAAAAAT
1 TGGAGAATCAATTCACCGCAGGAAAAAT
*
103319 TGGA-AATGAATTCACCGCAGGAAAAAT
1 TGGAGAATCAATTCACCGCAGGAAAAAT
103346 TG
1 TG
103348 AGATGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (28 bp):
TGGAGAATCAATTCACCGCAGGAAAAAT
Done.