Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020659.1 Corchorus olitorius cultivar O-4 contig20692, 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: 46507
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:3126 original size:24 final size:25
Alignment explanation
Indices: 3085--3133 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
3075 TTCGTGAATG
3085 GTTCAAAAGGGAACTTTTATGTTTC
1 GTTCAAAAGGGAACTTTTATGTTTC
*
3110 GTTCAAAA-GGAATTTTTATGTTTC
1 GTTCAAAAGGGAACTTTTATGTTTC
3134 AAGATCTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (25 bp):
GTTCAAAAGGGAACTTTTATGTTTC
Found at i:6114 original size:23 final size:24
Alignment explanation
Indices: 6088--6133 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
6078 GCGCCACCTC
*
6088 CTTC-TCCTTGTATGGAGTTTTCT
1 CTTCTTCCTTGTAAGGAGTTTTCT
*
6111 CTTCTTTCTTGTAAGGAGTTTTC
1 CTTCTTCCTTGTAAGGAGTTTTC
6134 CATGAGCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.52
Consensus pattern (24 bp):
CTTCTTCCTTGTAAGGAGTTTTCT
Found at i:7486 original size:21 final size:21
Alignment explanation
Indices: 7462--7505 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
7452 TAAGAACCCT
7462 AATTTGAACCACTTAAATCCA
1 AATTTGAACCACTTAAATCCA
* *
7483 AATTTGTACCACTTGAATCCA
1 AATTTGAACCACTTAAATCCA
7504 AA
1 AA
7506 AGGTTCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (21 bp):
AATTTGAACCACTTAAATCCA
Found at i:8907 original size:19 final size:18
Alignment explanation
Indices: 8883--8929 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
8873 GGTCAACGAT
8883 ATCTCCATG-TTCTTCTTGC
1 ATCTCCATGCTTC--CTTGC
8902 ATCTCCATGCTTCCTTGC
1 ATCTCCATGCTTCCTTGC
8920 A-CTCCATGCT
1 ATCTCCATGCT
8930 CATCCTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.33
18 6 0.22
19 9 0.33
20 3 0.11
ACGTcount: A:0.13, C:0.36, G:0.11, T:0.40
Consensus pattern (18 bp):
ATCTCCATGCTTCCTTGC
Found at i:11728 original size:130 final size:124
Alignment explanation
Indices: 11501--11755 Score: 379
Period size: 130 Copynumber: 2.0 Consensus size: 124
11491 CATTGTTTAA
* *
11501 ACTTTTATAGTTTTACTCAACTAAAACCTCTAATGTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATCTTTATAAT
11566 TTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
11625 ACTTTTACAG-TTTACTCAACTAAAAACTCTATTTTTATTTAATTAAAT-TAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATAT-CTT-TA--
*
11688 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAAACTTATATATATTAGAATTTTTTAAAT
62 TA----ATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
11753 AT
123 AT
11755 A
1 A
11756 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 5, Indels: 10
0.89 0.04 0.08
Matches are distributed among these distances:
122 6 0.05
123 38 0.32
124 11 0.09
126 2 0.02
130 61 0.52
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (124 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATCTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:11777 original size:14 final size:13
Alignment explanation
Indices: 11741--11779 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
11731 TATATATTAG
11741 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
11754 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
11768 AATTTTTTAAAT
1 AATTTTTTAAAT
11780 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:13614 original size:21 final size:22
Alignment explanation
Indices: 13590--13630 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
13580 GTGTATAATA
*
13590 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
13611 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
13631 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:15295 original size:22 final size:22
Alignment explanation
Indices: 15258--15309 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
15248 GCTTACAAGA
*
15258 TTACT-AAAATTTTAATAAAGG
1 TTACTAAAAATTGTAATAAAGG
15279 TTACTAAAAATTGTAATAAAGG
1 TTACTAAAAATTGTAATAAAGG
15301 TTACTAAAA
1 TTACTAAAA
15310 CGTTTAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (22 bp):
TTACTAAAAATTGTAATAAAGG
Found at i:15642 original size:20 final size:22
Alignment explanation
Indices: 15597--15644 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
15587 AAAACACTCA
15597 ATAAGGTTACTAAAAAAAACTTC
1 ATAAGGTTACT-AAAAAAACTTC
*
15620 ATAAGGTTACT-ATAAAA-TTC
1 ATAAGGTTACTAAAAAAACTTC
15640 ATAAG
1 ATAAG
15645 TTAACGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 5 0.21
23 11 0.46
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (22 bp):
ATAAGGTTACTAAAAAAACTTC
Found at i:15654 original size:20 final size:21
Alignment explanation
Indices: 15612--15655 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
15602 GTTACTAAAA
*
15612 AAAACTTCATAAGGTTACTAT
1 AAAACTTCATAAGGTTACGAT
15633 AAAA-TTCATAA-GTTAACGAT
1 AAAACTTCATAAGGTT-ACGAT
15653 AAA
1 AAA
15656 TCTTACAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAACTTCATAAGGTTACGAT
Found at i:15882 original size:85 final size:86
Alignment explanation
Indices: 15718--15895 Score: 313
Period size: 86 Copynumber: 2.1 Consensus size: 86
15708 TAAGATCACT
*
15718 AAAAATCTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAATTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAATTTAAT
*
15783 GAAAAATTTATAAGCTTACTA
66 GAAAAATTTATAAGCTTACGA
*
15804 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAA-CTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAATTTAAT
15868 GAAAAATTTATAAGCTTACGA
66 GAAAAATTTATAAGCTTACGA
15889 AGAAAAT
1 A-AAAAT
15896 TTACAAGGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
85 34 0.39
86 54 0.61
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.33
Consensus pattern (86 bp):
AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAATTTAAT
GAAAAATTTATAAGCTTACGA
Found at i:15948 original size:21 final size:20
Alignment explanation
Indices: 15924--15962 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15914 GTTTTACCAA
*
15924 TTACAATAAAATTTAAATAGT
1 TTACAA-AAAAGTTAAATAGT
*
15945 TTACTAAAAAGTTAAATA
1 TTACAAAAAAGTTAAATA
15963 AGATTACCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
TTACAAAAAAGTTAAATAGT
Found at i:15975 original size:21 final size:19
Alignment explanation
Indices: 15930--15978 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
15920 CCAATTACAA
* *
15930 TAAAATTTAAATAGTTTAC
1 TAAAAGTTAAATAGATTAC
15949 TAAAAAGTTAAATAAGATTACC
1 T-AAAAGTTAAAT-AGATTA-C
15971 TAAAAGTT
1 TAAAAGTT
15979 TTCAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 12 0.48
22 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (19 bp):
TAAAAGTTAAATAGATTAC
Found at i:16855 original size:16 final size:16
Alignment explanation
Indices: 16834--16864 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16824 AGAATTAATT
16834 ATAAAGACTTAGTAAA
1 ATAAAGACTTAGTAAA
*
16850 ATAAAGATTTAGTAA
1 ATAAAGACTTAGTAA
16865 TATTTTTCAA
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:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (16 bp):
ATAAAGACTTAGTAAA
Found at i:23237 original size:3 final size:3
Alignment explanation
Indices: 23229--23263 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
23219 TTTGGGTAAC
23229 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
23264 GTGAAGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:24074 original size:38 final size:38
Alignment explanation
Indices: 24023--24097 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
24013 CTTGCAACCA
*
24023 GGCCTGCTAGCGGCCCAGCGTGCTAGGCCAGGCGCGCG
1 GGCCTGCAAGCGGCCCAGCGTGCTAGGCCAGGCGCGCG
*
24061 GGCCTGCAAGCGGCCCAGCGTGCTAGGCCTGGCGCGC
1 GGCCTGCAAGCGGCCCAGCGTGCTAGGCCAGGCGCGC
24098 TCGGCCCGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.11, C:0.37, G:0.41, T:0.11
Consensus pattern (38 bp):
GGCCTGCAAGCGGCCCAGCGTGCTAGGCCAGGCGCGCG
Found at i:25216 original size:16 final size:17
Alignment explanation
Indices: 25197--25231 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
25187 ATAAAGGAAA
25197 AAAATAATAATAA-AAT
1 AAAATAATAATAATAAT
*
25213 AAAATAATATTAATAAT
1 AAAATAATAATAATAAT
25230 AA
1 AA
25232 TAATTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAATAATAATAAT
Found at i:25216 original size:19 final size:20
Alignment explanation
Indices: 25194--25234 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
25184 GAAATAAAGG
25194 AAAAAAATAATAATAA-AAT
1 AAAAAAATAATAATAATAAT
* *
25213 AAAATAATATTAATAATAAT
1 AAAAAAATAATAATAATAAT
25233 AA
1 AA
25235 TTTGAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAAAATAATAATAATAAT
Found at i:25254 original size:3 final size:3
Alignment explanation
Indices: 25199--25235 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
25189 AAAGGAAAAA
*
25199 AAT AAT AAT AA- AAT AA- AAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25236 TTGAAGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25908 original size:28 final size:28
Alignment explanation
Indices: 25840--25914 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
25830 TATGGGCATA
* *
25840 AAATTACCGTTTTACCCTAAGAATGAAT
1 AAATTACAGTTTTACCCTTAGAATGAAT
**
25868 AAATTACCA-TTTTACCCTTAGAA-GGTT
1 AAATTA-CAGTTTTACCCTTAGAATGAAT
*
25895 AAATTTACAGTTTTAACCTT
1 AAA-TTACAGTTTTACCCTT
25915 GTACTTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.18
28 31 0.79
29 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (28 bp):
AAATTACAGTTTTACCCTTAGAATGAAT
Found at i:26409 original size:13 final size:12
Alignment explanation
Indices: 26391--26434 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 12
26381 TTTTATTACC
26391 GTTTTATTAAATT
1 GTTTTA-TAAATT
*
26404 GTTTTATAAATG
1 GTTTTATAAATT
26416 GTTTTAAATAAATT
1 GTTTT--ATAAATT
26430 GTTTT
1 GTTTT
26435 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 11 0.41
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (12 bp):
GTTTTATAAATT
Found at i:31284 original size:58 final size:58
Alignment explanation
Indices: 31185--31334 Score: 273
Period size: 58 Copynumber: 2.6 Consensus size: 58
31175 AGATTTAGTC
*
31185 AAATGAAGATTTAGTAATATTTTTCTACAAATTGTAAAGGTTTTACACAGTATGAGTA
1 AAATAAAGATTTAGTAATATTTTTCTACAAATTGTAAAGGTTTTACACAGTATGAGTA
*
31243 AAATAAAGGTTTAGTAATATTTTTCTACAAATTGTAAAGGTTTTACACAGTATGAGTA
1 AAATAAAGATTTAGTAATATTTTTCTACAAATTGTAAAGGTTTTACACAGTATGAGTA
31301 AAATAAAGATTTAGTAATATTCTTTCTACAAATT
1 AAATAAAGATTTAGTAATATT-TTTCTACAAATT
31335 ATATTGCAAC
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 76 0.86
59 12 0.14
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (58 bp):
AAATAAAGATTTAGTAATATTTTTCTACAAATTGTAAAGGTTTTACACAGTATGAGTA
Found at i:31555 original size:21 final size:21
Alignment explanation
Indices: 31531--31587 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
31521 AAAAATATTA
* * *
31531 AAAAAGCTTAATAAGGTTTCT
1 AAAAATCTTAATAAGCTTACT
* * *
31552 AAAATTCATGATAAGCTTACT
1 AAAAATCTTAATAAGCTTACT
31573 AAAAATCTTAATAAG
1 AAAAATCTTAATAAG
31588 TTAAGGTAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (21 bp):
AAAAATCTTAATAAGCTTACT
Found at i:32308 original size:13 final size:13
Alignment explanation
Indices: 32290--32314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32280 TTCAATGTTC
32290 TAAATATTATTTA
1 TAAATATTATTTA
32303 TAAATATTATTT
1 TAAATATTATTT
32315 GGAATTCCAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:33149 original size:276 final size:266
Alignment explanation
Indices: 32488--33284 Score: 1009
Period size: 276 Copynumber: 3.0 Consensus size: 266
32478 GAAACTTAAC
* * *
32488 TAATTAAGTAAAAGGCAAAATAATGTTACTTAAAACTTAAAAGTGTTTGTGGTTATTACGAAAAG
1 TAATTAAGTAAAAGCCATAATAATGTTACTTAAAACTTAAAAGTGTTTATGGTTATTACGAAAAG
* * * * * * * * *
32553 AAAAATCACCATATCCACAATTAGTGTAGTTT-C--GTAGATTGTACAAACGGGATCAAAGGATT
66 TAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACGGGGTTAAAGGATT
* * * *
32615 GACACATGTGCCTTTTTAGTGTATTTTTTAAGAAAAATTATCTTATTCACCGTTAGTGAAGTTTA
131 GACAC--GTGTCTTTTTAGTGTATTTTTTAAGGAAAATTATCTTATCCACCATTAGTGAAGTTTA
* * * *
32680 GCGGACTGTACATGCATTGTTAGGGTTATAGGGTTGGCATGTGTTCCCTTAGGGAATA-----G-
194 GCAGACTGAACATGCATTGTTAGGGTTAAAGGGTTGACATGTG-TCCCTTAGGGAATAGTTTTGA
32739 TTTGAACAT
258 TTTGAACAT
*
32748 TAATTAAGTAAAAGTCATAATAATGTTACTTAAAACTTAAAAAGTGTTTATGGTTATTACGAAAA
1 TAATTAAGTAAAAGCCATAATAATGTTACTTAAAACTT-AAAAGTGTTTATGGTTATTACGAAAA
* * ***
32813 GTAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTGCAAACGAGGTTAAAATTT
65 GTAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACGGGGTTAAAGGAT
* * *
32878 TGACACGTATCTTCTCAGTGTATGTCTTTTAAGGAAAATTATCTTATCCACCATTAGTGAAGTTT
130 TGACACGTGTCTTTTTAGTGTAT-T-TTTTAAGGAAAATTATCTTATCCACCATTAGTGAAGTTT
* * ** *
32943 AGCAGACTGCATATGCAGGGTTAGGGTTAAAGGGTTGACATGTGTACCCTTAGGAAATAGTTTTG
193 AGCAGACTGAACATGCATTGTTAGGGTTAAAGGGTTGACATGTGT-CCCTTAGGGAATAGTTTTG
33008 ATTTTTGAACAT
257 A--TTTGAACAT
33020 TAATTAAGTAAAAAGCCATAATAATGTTACTTAAACTAAACTTAAAAGTGTTTATGGTTATTACG
1 TAATTAAGT-AAAAGCCATAATAATGTTACTT--A--AAACTTAAAAGTGTTTATGGTTATTACG
33085 AAAAGTAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACGGGGTTAAA
61 AAAAGTAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACGGGGTTAAA
* * *
33150 GGATTGACATGTGTCTTTTTGGTGTATATTTTTTAAGGATAATTATCTTATCCACCATTAGTGAA
126 GGATTGACACGTGTCTTTTTAGTG--TATTTTTTAAGGAAAATTATCTTATCCACCATTAGTGAA
* * * *
33215 GTTTAGCAGACTGAACATGCATTATTAGGGTTAAAAGGTCGACATGTGTCTTCTTAGGGAATAGT
189 GTTTAGCAGACTGAACATGCATTGTTAGGGTTAAAGGGTTGACATGTGTC-CCTTAGGGAATAGT
33280 TTTGA
253 TTTGA
33285 ACATTATATA
Statistics
Matches: 461, Mismatches: 53, Indels: 30
0.85 0.10 0.06
Matches are distributed among these distances:
260 36 0.08
261 52 0.11
262 14 0.03
263 2 0.00
264 111 0.24
269 1 0.00
272 18 0.04
273 21 0.05
275 2 0.00
276 194 0.42
277 7 0.02
278 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (266 bp):
TAATTAAGTAAAAGCCATAATAATGTTACTTAAAACTTAAAAGTGTTTATGGTTATTACGAAAAG
TAAAATTATCACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACGGGGTTAAAGGATT
GACACGTGTCTTTTTAGTGTATTTTTTAAGGAAAATTATCTTATCCACCATTAGTGAAGTTTAGC
AGACTGAACATGCATTGTTAGGGTTAAAGGGTTGACATGTGTCCCTTAGGGAATAGTTTTGATTT
GAACAT
Found at i:41805 original size:3 final size:3
Alignment explanation
Indices: 41797--41826 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41787 ATATCATTAC
41797 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41827 GTTAGGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43363 original size:3 final size:3
Alignment explanation
Indices: 43357--43391 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43347 TACAACAATA
43357 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
43392 ATCCGGATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44470 original size:2 final size:2
Alignment explanation
Indices: 44463--44494 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44453 GATTTCGTAC
44463 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
44495 CTAAATGATT
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
Done.