Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017621.1 Corchorus olitorius cultivar O-4 contig17654, 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: 41987
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:2820 original size:21 final size:21
Alignment explanation
Indices: 2796--2868 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
2786 GGCACTGAAT
*
2796 GGTGATGGCACGGGCATAGCC
1 GGTGATGGCACGGGCATAACC
* *
2817 GGTGGTGGCACGGGCTTAACC
1 GGTGATGGCACGGGCATAACC
* * * *
2838 GGTGGTGTCACGGTGAATACCC
1 GGTGATGGCACGG-GCATAACC
*
2860 GGTAATGGC
1 GGTGATGGC
2869 TTGGTAGTGG
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 30 0.73
22 11 0.27
ACGTcount: A:0.18, C:0.22, G:0.41, T:0.19
Consensus pattern (21 bp):
GGTGATGGCACGGGCATAACC
Found at i:5985 original size:29 final size:28
Alignment explanation
Indices: 5952--6028 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
5942 AAAATATATA
*
5952 TTTTTTTAAAAAAACGCAAGAACAAGTTT
1 TTTTTTTAAAAAAACGCAA-AACAAATTT
* *
5981 TTTTTTTTAGAAAACGCAAAACAAA-TT
1 TTTTTTTAAAAAAACGCAAAACAAATTT
*
6008 TTTTTTT-CAAAAACGCAAAAC
1 TTTTTTTAAAAAAACGCAAAAC
6029 TAATAAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.28
27 9 0.21
28 5 0.12
29 17 0.40
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (28 bp):
TTTTTTTAAAAAAACGCAAAACAAATTT
Found at i:6009 original size:26 final size:26
Alignment explanation
Indices: 5951--6028 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 26
5941 AAAAATATAT
**
5951 ATTTTTTTAAAAAAACGCAAGAACAAG
1 ATTTTTTTTTAAAAACGCAA-AACAAG
*
5978 TTTTTTTTTTTAGAAAACGCAAAACAA-
1 -ATTTTTTTTTA-AAAACGCAAAACAAG
6005 ATTTTTTTTTCAAAAACGCAAAAC
1 ATTTTTTTTT-AAAAACGCAAAAC
6029 TAATAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 21 0.48
27 1 0.02
28 13 0.30
29 9 0.20
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.35
Consensus pattern (26 bp):
ATTTTTTTTTAAAAACGCAAAACAAG
Found at i:6098 original size:26 final size:26
Alignment explanation
Indices: 6042--6127 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 26
6032 TAAATTAAAA
* ** *
6042 ACGCAAGAAAACTTTTTTTTTATGAAAG
1 ACGCAA-AAAGCTTTTTTTTT-TTTATG
6070 ACGCAAAAAGCTTTTTTTTTTTTATG
1 ACGCAAAAAGCTTTTTTTTTTTTATG
6096 ACGC-AAAAG-TTTTTTTTTTTT-TCG
1 ACGCAAAAAGCTTTTTTTTTTTTAT-G
6120 ACGCAAAA
1 ACGCAAAA
6128 CACAAAACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
23 1 0.02
24 17 0.33
25 8 0.15
26 7 0.13
27 13 0.25
28 6 0.12
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (26 bp):
ACGCAAAAAGCTTTTTTTTTTTTATG
Found at i:12750 original size:82 final size:82
Alignment explanation
Indices: 12648--12809 Score: 272
Period size: 82 Copynumber: 2.0 Consensus size: 82
12638 CTCAATTTAC
*
12648 AATTGAGGGTAAATTGGTCTTCA-CATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAA
1 AATTGAGGATAAATTGGTCTT-ATCATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAA
*
12712 ATCCTGGTGAAACATGTA
65 ATCCTAGTGAAACATGTA
*
12730 AATTGAGGATAAATTGGTCTTATCATAAATAATATTAAGATGTGTGGTCAAGATTTGATTAAAAA
1 AATTGAGGATAAATTGGTCTTATCATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAAA
*
12795 TTCTAGTGAAACATG
66 TCCTAGTGAAACATG
12810 GTTTCTGCAC
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 1 0.01
82 74 0.99
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (82 bp):
AATTGAGGATAAATTGGTCTTATCATAAATAATATTAAGATGTGTGGTCAAGAATTGATTAAAAA
TCCTAGTGAAACATGTA
Found at i:12916 original size:19 final size:18
Alignment explanation
Indices: 12881--12925 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12871 TAAAATTAAT
*
12881 TAATTAATTATTAAATAA
1 TAATTATTTATTAAATAA
*
12899 TAATTATTTTTTAGAATAA
1 TAATTATTTATTA-AATAA
*
12918 TTATTATT
1 TAATTATT
12926 AAAATTCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:20246 original size:122 final size:127
Alignment explanation
Indices: 20102--20352 Score: 377
Period size: 131 Copynumber: 2.0 Consensus size: 127
20092 CATTGTTTAA
* *
20102 ACTTTTATAGGTTTATTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-TA-T
1 ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATACT
20163 A-ATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
20224 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATA-C
* *
20289 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 TA---TATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
20353 TTTACAATTT
Statistics
Matches: 114, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
122 52 0.46
123 1 0.01
124 1 0.01
125 2 0.02
127 2 0.02
131 56 0.49
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:21478 original size:316 final size:315
Alignment explanation
Indices: 20905--21528 Score: 1160
Period size: 316 Copynumber: 2.0 Consensus size: 315
20895 AGACTAGTAC
20905 TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT
1 TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT
*
20970 ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAGCTCTAATGTTATTTA
66 ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA
21035 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATT
131 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAAC-TATATATATT
21100 AGAATTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAAT
195 AGAATTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAAT
*
21165 CTAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTTCTACACTA
260 ATAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTTCTACACTA
* *
21221 TATTAAAAAGTATGTTCACCTGTAAAACTTTTGAATCGTCCATTATACCCTTATTTTTCGAATAT
1 TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT
*
21286 ATTTCTTAAATGTCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA
66 ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA
21351 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAAAC-ATATATATT
131 ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATT-AAAAAACTATATATATT
*
21415 AGAATTTTTTTAAATATACTTTTACTGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAA
195 AGAA-TTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAA
21480 TATAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTT
259 TATAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTT
21529 TAAAAAACTT
Statistics
Matches: 300, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
315 13 0.04
316 280 0.93
317 7 0.02
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (315 bp):
TATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATAT
ATTTCTTAAATGCCATTGTTTAAACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTA
ATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTATATATATTA
GAATTTTTTAAATATACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATA
TAATATCCTTATACCTATTTTATTTTTACCATTTTACTATTTTATTTCTACACTA
Found at i:21586 original size:14 final size:13
Alignment explanation
Indices: 21550--21588 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
21540 TATATATTAG
21550 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
21563 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
21577 AATTTTTTAAAT
1 AATTTTTTAAAT
21589 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:22760 original size:188 final size:188
Alignment explanation
Indices: 22446--23011 Score: 976
Period size: 188 Copynumber: 3.0 Consensus size: 188
22436 GACATTAGAG
* * * *
22446 TGAATAACCCAATATGGCAGAGAAATGCCGTGGTAA-T-TAAGGA-TTTCTTATGATTGAGCACC
1 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC
* * *
22508 CAAAGTAACTGTTGAACTTTGAGAAAGGTTGGTGTTTGCCATATCCACTTCCAACTTGTCACAAG
66 CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG
22573 TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA
131 TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA
22631 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC
1 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC
22696 CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG
66 CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG
*
22761 TTCAAAGGTCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA
131 TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA
* *
22819 TGAATAACTCAATCTGACAGAAAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC
1 TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC
** *
22884 CAAAGTCTCATCTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAA
66 CAAAGTAAC-TGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAA
*
22949 GTTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCATTGAACTTGTAAGAAA
130 GTTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA
23008 TGAA
1 TGAA
23012 CAATTTAATC
Statistics
Matches: 362, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
185 32 0.09
186 1 0.00
187 6 0.02
188 208 0.57
189 115 0.32
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (188 bp):
TGAATAACCCAATCTGACAGAGAAATGCCCTAGTAATTATAAGGATTTTCTTATGATTGAGCACC
CAAAGTAACTGTCGGACTTTGAGAAAGGTTGGTGTTTTCCATATCCACTTCCAACTTGTCACAAG
TTCAAAGGCCTTTAGCAATCGGTTTAATAGACATTTTGACCCTTGAACTTGTAAGAAA
Found at i:26412 original size:13 final size:14
Alignment explanation
Indices: 26394--26429 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
26384 TTTTATTTTA
26394 TTTTGTATTTT-GT
1 TTTTGTATTTTCGT
26407 TTTTGT-TTTTCGT
1 TTTTGTATTTTCGT
26420 TTTTGTATTT
1 TTTTGTATTT
26430 CATTAGGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 14 0.67
14 3 0.14
ACGTcount: A:0.06, C:0.03, G:0.14, T:0.78
Consensus pattern (14 bp):
TTTTGTATTTTCGT
Found at i:29422 original size:11 final size:10
Alignment explanation
Indices: 29397--29421 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29387 TTCAAAAGGA
29397 TTTTTAATTT
1 TTTTTAATTT
29407 TTTTTAATTT
1 TTTTTAATTT
29417 TTTTT
1 TTTTT
29422 TTTTTGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:36233 original size:21 final size:21
Alignment explanation
Indices: 36201--36292 Score: 68
Period size: 22 Copynumber: 4.4 Consensus size: 21
36191 GAAATATTTA
*
36201 TATGAAACTATGATAACCTCC
1 TATGAAATTATGATAACCTCC
*
36222 TATTAAATTATGATAA-CTACAC
1 TATGAAATTATGATAACCT-C-C
* *
36244 TAT----TTTTGATGACCTCC
1 TATGAAATTATGATAACCTCC
*
36261 TTATGAAATTTTGATAACCTTCC
1 -TATGAAATTATGATAACC-TCC
36284 TATGAAATT
1 TATGAAATT
36293 TTAATAACGA
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
17 1 0.02
18 11 0.19
19 2 0.04
20 2 0.04
21 15 0.26
22 23 0.40
23 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
TATGAAATTATGATAACCTCC
Found at i:36272 original size:22 final size:21
Alignment explanation
Indices: 36247--36952 Score: 374
Period size: 22 Copynumber: 32.3 Consensus size: 21
36237 ACTACACTAT
*
36247 TTTTGATGACCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
36269 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACC-TCCTATGAAA
* * * *
36291 TTTTAATAACGATACTATGGAA
1 TTTTGATAAC-CTCCTATGAAA
* * **
36313 TTTCGAGAACCTTTTTAT-AAA
1 TTTTGATAACC-TCCTATGAAA
** *
36334 TTTTTTTTAACCTTCTTATGAAA
1 -TTTTGATAACC-TCCTATGAAA
* *
36357 TTTTGTTAACCTCTCTAAGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
36379 TTTTGA-AGACTTCATTATGAAA
1 TTTTGATA-ACCTC-CTATGAAA
* *
36401 TTTTGATAACTTCCCAATGAAA
1 TTTTGATAACCT-CCTATGAAA
* *
36423 TTTTGATAACCAACACTATGAGA
1 TTTTGATAACC-TC-CTATGAAA
* *
36446 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTCC-TATGAAA
* * *
36468 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* * * *
36490 ATTTAAGAACCTCCATATG-GA
1 TTTTGATAACCTCC-TATGAAA
* * *
36511 TTGTT-AGTAATCACACTCTGAAA
1 TT-TTGA-TAACCTC-CTATGAAA
* * *
36534 TATTGATAATCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
36556 TTGTCATAACCTCTCTATGAAA
1 TTTTGATAACCTC-CTATGAAA
*
36578 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACC-TCCTATGAAA
*
36601 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCT-CCTATGAAA
36624 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* *
36646 TCTTGATAA----CTA-CAAA
1 TTTTGATAACCTCCTATGAAA
* **
36662 TTTTTATAACCTCCCTATGATT
1 TTTTGATAACCT-CCTATGAAA
* **
36684 TTTTTATAACCTCCCTATGATT
1 TTTTGATAACCT-CCTATGAAA
* *
36706 TTTTTATAACCTCATTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
36728 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCT-CCTATGAAA
* * *
36750 TTTTGATCTACATACTATGAAA
1 TTTTGAT-AACCTCCTATGAAA
36772 TTTTGATAATCCTCCTATGAAA
1 TTTTGATAA-CCTCCTATGAAA
* *
36794 TTTTGA-AAACTAAGCTATGAAA
1 TTTTGATAACCT--CCTATGAAA
*
36816 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACC-TCCTATGAAA
* * * *
36838 TTTTGATCTACATACTATAAAA
1 TTTTGAT-AACCTCCTATGAAA
*
36860 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAA-CCTCCTATGAAA
* *
36882 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT--CCTATGAAA
*
36904 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACC-TCCTATGAAA
* *
36926 TTTTGATATCCTCC-CTGAAA
1 TTTTGATAACCTCCTATGAAA
36946 TTTTGAT
1 TTTTGAT
36953 TACTCCATAA
Statistics
Matches: 532, Mismatches: 109, Indels: 88
0.73 0.15 0.12
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
18 1 0.00
20 16 0.03
21 23 0.04
22 398 0.75
23 78 0.15
24 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:36625 original size:46 final size:45
Alignment explanation
Indices: 36563--36654 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 45
36553 AAATTGTCAT
* * *
36563 AACCTCTCTATGAAATTTTGATAAACCTTCC-TATAAAATTTTGATA
1 AACCTCCCTATAAAATTTTGAT-AACC-TCCTTATAAAATCTTGATA
*
36609 AACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATA
1 AACCTCCCTATAAAATTTTGATAACCTCCTTATAAAATCTTGATA
36654 A
1 A
36655 CTACAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
44 3 0.07
45 18 0.44
46 20 0.49
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (45 bp):
AACCTCCCTATAAAATTTTGATAACCTCCTTATAAAATCTTGATA
Found at i:37089 original size:22 final size:22
Alignment explanation
Indices: 37064--37285 Score: 107
Period size: 22 Copynumber: 10.0 Consensus size: 22
37054 AATGACATTT
*
37064 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
*
37086 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
37108 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
* * *
37130 TTAAAATTTTGATAATCACAT-TA
1 TGAAAA-TTTGATAACCTC-TCTA
* * * *
37153 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* * ** *
37175 TGAAATTTTCATAACAACACTA
1 TGAAAATTTGATAACCTCTCTA
* *
37197 TGAAATTTTGATAATCT-TCCTA
1 TGAAAATTTGATAACCTCT-CTA
* *
37219 T-AAATTTTGATAATCCGATCTCTG
1 TGAAAATTTGATAA-CC--TCTCTA
* *
37243 TG-AAATTTCGATAATCACTCTA
1 TGAAAATTT-GATAACCTCTCTA
*
37265 TG-AGATTTGATAACCT-TCTA
1 TGAAAATTTGATAACCTCTCTA
37285 T
1 T
37286 CAAATGTTGG
Statistics
Matches: 152, Mismatches: 37, Indels: 24
0.71 0.17 0.11
Matches are distributed among these distances:
20 5 0.03
21 21 0.14
22 91 0.60
23 18 0.12
24 11 0.07
25 6 0.04
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:37204 original size:44 final size:42
Alignment explanation
Indices: 37064--37231 Score: 131
Period size: 44 Copynumber: 3.8 Consensus size: 42
37054 AATGACATTT
* * * *
37064 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCCTT-TGAAATTTTGATAA-CACACTA
* * * * * *
37108 TAAAATTTTGTTGACCCCTCTATTAAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTC-CT-TTGAAATTTTGATAA-CACACTA
* *
37153 TGTAATTTTGATAACCTCGCTTTGAAATTTTCATAACAACACTA
1 TGAAATTTTGATAACCTC-CTTTGAAATTTTGATAAC-ACACTA
* *
37197 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAA
1 TGAAATTTTGATAA-CCTCCTTTGAAATTTTGATAA
37232 TCCGATCTCT
Statistics
Matches: 96, Mismatches: 24, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
43 12 0.12
44 47 0.49
45 36 0.38
46 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (42 bp):
TGAAATTTTGATAACCTCCTTTGAAATTTTGATAACACACTA
Found at i:37391 original size:22 final size:21
Alignment explanation
Indices: 37317--37473 Score: 97
Period size: 22 Copynumber: 7.1 Consensus size: 21
37307 AAATTGAGAC
*
37317 TTTT-ATAACCTTCTTATGAAA
1 TTTTGATAACC-TCCTATGAAA
* *
37338 TTTTGAAAACCTCCCCATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
37360 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCTCC-TATGAAA
* *
37382 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
*
37404 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-CTATGAAA
* *
37426 TTTTGATAATCTTTCTAT-AAA
1 TTTTGATAA-CCTCCTATGAAA
*
37447 GTTTGTGATAACCACACTATGAAA
1 -TTT-TGATAACCTC-CTATGAAA
37471 TTT
1 TTT
37474 CAATCAGTAT
Statistics
Matches: 104, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
21 12 0.12
22 71 0.68
23 18 0.17
24 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:37402 original size:44 final size:44
Alignment explanation
Indices: 37319--37431 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
37309 ATTGAGACTT
* * *
37319 TTATAACCTTCTTATGAAATTTTGAAAACCTCCCCATGAAA-TA
1 TTATAACCTCCTTATGAAATTTTGAAAACCACACCATGAAATTA
** * *
37362 TTAGTAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTC
1 TTA-TAACCTCCTTATGAAATTTTGAAAACCACACCATGAAATTA
*
37407 TTATAACCTCGC-TATGACATTTTGA
1 TTATAACCTC-CTTATGAAATTTTGA
37432 TAATCTTTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 3 0.05
44 50 0.86
45 5 0.09
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (44 bp):
TTATAACCTCCTTATGAAATTTTGAAAACCACACCATGAAATTA
Found at i:41535 original size:16 final size:16
Alignment explanation
Indices: 41516--41559 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
41506 ATCCGCCCGA
*
41516 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
* *
41532 ACCCGAGCTCGAAAAT
1 ACCCGAACCCGAAAAT
41548 ACCCGAACCCGA
1 ACCCGAACCCGA
41560 GGCTGCCTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.39, G:0.16, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Done.