Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021816.1 Corchorus olitorius cultivar O-4 contig21849, 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: 93230
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:5414 original size:29 final size:29
Alignment explanation
Indices: 5372--5430 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5362 CACCGTGGGT
5372 TTTCCTTTTAGCAATATCAGAAATCTTCA
1 TTTCCTTTTAGCAATATCAGAAATCTTCA
5401 TTTCCTTTTAGCAATATCAGAAATCTTCA
1 TTTCCTTTTAGCAATATCAGAAATCTTCA
5430 T
1 T
5431 CCACCACTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (29 bp):
TTTCCTTTTAGCAATATCAGAAATCTTCA
Found at i:6158 original size:52 final size:52
Alignment explanation
Indices: 6070--6173 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
6060 TGTACTGCAT
**
6070 AAGCATGGAGGTTGCAGGTTGGTTCTTCAATCATCTGCGATACATATGCAGA
1 AAGCATGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGATACATATGCAGA
* *
6122 AAGCCTGGAGGTTGCAGGCCGGTTCTTCAATTATCTGCGATACATATGCAGA
1 AAGCATGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGATACATATGCAGA
6174 GGCCAGTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (52 bp):
AAGCATGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGATACATATGCAGA
Found at i:7423 original size:3 final size:3
Alignment explanation
Indices: 7415--7439 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7405 AAGCATGGAC
7415 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
7440 AAGATCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:14454 original size:21 final size:22
Alignment explanation
Indices: 14430--14503 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 22
14420 TTGGGCATAA
14430 AGATTT-ATTTGAATTGTAATG
1 AGATTTCATTTGAATTGTAATG
* * ** *
14451 AGATTTCACTAGGTTTGT-TTG
1 AGATTTCATTTGAATTGTAATG
**
14472 TTATTT-ATTTGAATTGTAATG
1 AGATTTCATTTGAATTGTAATG
*
14493 AGATTTGATTT
1 AGATTTCATTT
14504 CACGAGATGT
Statistics
Matches: 36, Mismatches: 14, Indels: 5
0.65 0.25 0.09
Matches are distributed among these distances:
20 7 0.19
21 18 0.50
22 11 0.31
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (22 bp):
AGATTTCATTTGAATTGTAATG
Found at i:16778 original size:144 final size:144
Alignment explanation
Indices: 16518--16803 Score: 563
Period size: 144 Copynumber: 2.0 Consensus size: 144
16508 TTTTTTGTCG
16518 AAAATTACATTGTGAATACTTCATATACTTTAGTGAGTAATTGCAAATTATCCTTTTGTTGCCTT
1 AAAATTACATTGTGAATACTTCATATACTTTAGTGAGTAATTGCAAATTATCCTTTTGTTGCCTT
*
16583 TGAGAGGTCTTGTTATGCTTGCATTGGATGATGTATCTTTGGCTATACAATCCTCATTTTTTTTT
66 TGAGAGGTCTTGTTATGCTTGCATTGGATGATGTATCTTTGGCTATACAATCCTCATTCTTTTTT
16648 GGTATGTATAAACC
131 GGTATGTATAAACC
16662 AAAATTACATTGTGAATACTTCATATACTTTAGTGAGTAATTGCAAATTATCCTTTTGTTGCCTT
1 AAAATTACATTGTGAATACTTCATATACTTTAGTGAGTAATTGCAAATTATCCTTTTGTTGCCTT
16727 TGAGAGGTCTTGTTATGCTTGCATTGGATGATGTATCTTTGGCTATACAATCCTCATTCTTTTTT
66 TGAGAGGTCTTGTTATGCTTGCATTGGATGATGTATCTTTGGCTATACAATCCTCATTCTTTTTT
16792 GGTATGTATAAA
131 GGTATGTATAAA
16804 AAGAATTGTA
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 141 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.44
Consensus pattern (144 bp):
AAAATTACATTGTGAATACTTCATATACTTTAGTGAGTAATTGCAAATTATCCTTTTGTTGCCTT
TGAGAGGTCTTGTTATGCTTGCATTGGATGATGTATCTTTGGCTATACAATCCTCATTCTTTTTT
GGTATGTATAAACC
Found at i:21055 original size:21 final size:21
Alignment explanation
Indices: 21030--21088 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
21020 GACTGGAGTT
* *
21030 GGAGGATTGCCACCGTATGTA
1 GGAGGACTACCACCGTATGTA
21051 GGAGGACTACCACCGTATGTA
1 GGAGGACTACCACCGTATGTA
21072 GGAGGACTACCACCGTA
1 GGAGGACTACCACCGTA
21089 GTTGGGATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.19
Consensus pattern (21 bp):
GGAGGACTACCACCGTATGTA
Found at i:21206 original size:12 final size:12
Alignment explanation
Indices: 21167--21208 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
21157 AATATCCACC
21167 GTGTGAAGGAGT
1 GTGTGAAGGAGT
*
21179 GTGGGAAGGAGT
1 GTGTGAAGGAGT
*
21191 GTGTGAAGGTGT
1 GTGTGAAGGAGT
21203 GTGTGA
1 GTGTGA
21209 TGGTGTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.52, T:0.26
Consensus pattern (12 bp):
GTGTGAAGGAGT
Found at i:21213 original size:12 final size:12
Alignment explanation
Indices: 21167--21214 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
21157 AATATCCACC
*
21167 GTGTGAAGGAGT
1 GTGTGAAGGTGT
* *
21179 GTGGGAAGGAGT
1 GTGTGAAGGTGT
21191 GTGTGAAGGTGT
1 GTGTGAAGGTGT
*
21203 GTGTGATGGTGT
1 GTGTGAAGGTGT
21215 TGATGGAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (12 bp):
GTGTGAAGGTGT
Found at i:24228 original size:7 final size:7
Alignment explanation
Indices: 24213--24246 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
24203 AGAAAAGGGT
*
24213 TTGCTAA
1 TTGCCAA
24220 TTGCCAA
1 TTGCCAA
24227 TTGCCAA
1 TTGCCAA
24234 TTGCCAA
1 TTGCCAA
24241 TTGCCA
1 TTGCCA
24247 TGCAACACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (7 bp):
TTGCCAA
Found at i:33895 original size:29 final size:29
Alignment explanation
Indices: 33849--33925 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
33839 CTGAATATGC
* *
33849 AAATGACTAAAATGCCCCTGGAACGTGAA
1 AAATGACCAAAATACCCCTGGAACGTGAA
**** *
33878 AAATGACCAAAATACCCCTGGGTTTTTAA
1 AAATGACCAAAATACCCCTGGAACGTGAA
*
33907 AAATGACCAAAATTCCCCT
1 AAATGACCAAAATACCCCT
33926 AGGTGATCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.22
Consensus pattern (29 bp):
AAATGACCAAAATACCCCTGGAACGTGAA
Found at i:34580 original size:16 final size:16
Alignment explanation
Indices: 34539--34573 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
34529 TTTGGCCTTT
*
34539 GGTCACTCGGGTTTTG
1 GGTCATTCGGGTTTTG
34555 GGTCATTCGGGTTTTG
1 GGTCATTCGGGTTTTG
34571 GGT
1 GGT
34574 TTTTCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.14, G:0.40, T:0.40
Consensus pattern (16 bp):
GGTCATTCGGGTTTTG
Found at i:37050 original size:17 final size:17
Alignment explanation
Indices: 37028--37067 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
37018 TCCTTTTTCC
**
37028 CCTTTTTTTTTCCTTTT
1 CCTTTTTTTCCCCTTTT
37045 CCTTTTTTTCCCCTTTT
1 CCTTTTTTTCCCCTTTT
37062 CCTTTT
1 CCTTTT
37068 CCTTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
CCTTTTTTTCCCCTTTT
Found at i:37080 original size:29 final size:28
Alignment explanation
Indices: 37021--37080 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
37011 TCTTATTTCC
* **
37021 TTTTTCCCCTTTTTTTTTCCTTTTCCTT
1 TTTTTCCCCTTTTCTTTTCCTTTTCAAT
*
37049 TTTTTCCCCTTTTCCTTTTCCTTTTTAAT
1 TTTTTCCCCTTTT-CTTTTCCTTTTCAAT
37078 TTT
1 TTT
37081 CCTTCCTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTTCCCCTTTTCTTTTCCTTTTCAAT
Found at i:38753 original size:348 final size:345
Alignment explanation
Indices: 38119--38810 Score: 1134
Period size: 348 Copynumber: 2.0 Consensus size: 345
38109 ATTATTTTTA
* * *
38119 GTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGCGTCTTCTTTTGGCTTTTTT
1 GTGACTATGAAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGCGCCTCCTTTTGGCTTTTTT
*
38184 TGGTCTTTTCGCACTTTTCGTGTGACTAAAAAAGCCCTCGATGAATTTTCTCCCTTACTTTTCCT
66 TGGTCTTTTCGCACTTTTCGGGTGACTAAAAAAGCCCTCGATGAATTTTCTCCCTTACTTTTCCT
* *
38249 GTTGTTCTTTTCGGTAATTTACTATTTTTATATTTATGATGAAGTGTGTTTTAATTACATATTAA
131 GTTGTCCTTTTCGGTAATTTACTATTTTTATATTTATGATGAAGTGTATTTTAATTACATATTAA
*** *
38314 TTGTGTGTGGATATTTGGATTTACCGCTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGTTA
196 TTGTGTGTGGATATTAAAAATTACCGCTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGTTA
* *
38379 TAAATGTATCTGTAATAATGGTTGATTCATGGTTAAACTATTGACATTCCAGTTCTGTTTTCCTT
261 TAAATGTATCTATAATAATGGTTGATTCATGGGTAAACTATTGACATTCCAGTTCTGTTTTCCTT
38444 TCATCTTCATTTCTATTTGC
326 TCATCTTCATTTCTATTTGC
* *
38464 GTGACTATGAAAATTACTTAAAGGCCAAATTGAGGATTAATGTTGTGCCTCCTTTTGGCTTTTTT
1 GTGACTATGAAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGCGCCTCCTTTTGGC---TTT
* * *
38529 TTTTTGTCTTTTCGCACTTTTCGGGTGACTAAAAAGGCCTTCGATGAATTTTCTCCCTTACTTTT
63 TTTTGGTCTTTTCGCACTTTTCGGGTGACTAAAAAAGCCCTCGATGAATTTTCTCCCTTACTTTT
* *
38594 CCTGTTG-CCATTTTCGGTAATTTATTATTTTTATATTTATGATTAAGTGTATTTTAATTACATA
128 CCTGTTGTCC-TTTTCGGTAATTTACTATTTTTATATTTATGATGAAGTGTATTTTAATTACATA
* * *
38658 TTAATTGTGTGTGGATATTAAAAATTACCGGTTCAATTCCTCTGTCGGAATTCCAAAGGATTGGT
192 TTAATTGTGTGTGGATATTAAAAATTACCGCTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGT
38723 GTTATAAATGTATCTATAATAATGGTTGATTCATGGGTAAACTATTGACATTCCAGTTCTGTTTT
257 GTTATAAATGTATCTATAATAATGGTTGATTCATGGGTAAACTATTGACATTCCAGTTCTGTTTT
*
38788 TCTTTCATCTTCATTTCTATTTG
322 CCTTTCATCTTCATTTCTATTTG
38811 GGTGGGTTTC
Statistics
Matches: 320, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
345 54 0.17
347 1 0.00
348 265 0.83
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.45
Consensus pattern (345 bp):
GTGACTATGAAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGCGCCTCCTTTTGGCTTTTTT
TGGTCTTTTCGCACTTTTCGGGTGACTAAAAAAGCCCTCGATGAATTTTCTCCCTTACTTTTCCT
GTTGTCCTTTTCGGTAATTTACTATTTTTATATTTATGATGAAGTGTATTTTAATTACATATTAA
TTGTGTGTGGATATTAAAAATTACCGCTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGTTA
TAAATGTATCTATAATAATGGTTGATTCATGGGTAAACTATTGACATTCCAGTTCTGTTTTCCTT
TCATCTTCATTTCTATTTGC
Found at i:40642 original size:27 final size:27
Alignment explanation
Indices: 40612--40665 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
40602 AAAATTATAA
40612 CAATAATAAAGATTTTATTGAATAAAT
1 CAATAATAAAGATTTTATTGAATAAAT
40639 CAATAATAAAGATTTTATTGAATAAAT
1 CAATAATAAAGATTTTATTGAATAAAT
40666 GATAATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (27 bp):
CAATAATAAAGATTTTATTGAATAAAT
Found at i:41678 original size:26 final size:26
Alignment explanation
Indices: 41649--41699 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41639 TATATATATA
41649 TATATATATATGCTATTGAGACATGG
1 TATATATATATGCTATTGAGACATGG
* * *
41675 TATATATGTGTGTTATTGAGACATG
1 TATATATATATGCTATTGAGACATG
41700 CATGGGTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (26 bp):
TATATATATATGCTATTGAGACATGG
Found at i:42299 original size:27 final size:29
Alignment explanation
Indices: 42269--42328 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
42259 ACCGTAATAG
*
42269 CCCTAG-TAT-GCAAAATTACCGTTTTGC
1 CCCTAGATATGGCAAAATTACAGTTTTGC
* *
42296 CCCT-GATCTGGTAAAATTACAGTTTTGC
1 CCCTAGATATGGCAAAATTACAGTTTTGC
42324 CCCTA
1 CCCTA
42329 AAGGCTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.04
27 6 0.22
28 20 0.74
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (29 bp):
CCCTAGATATGGCAAAATTACAGTTTTGC
Found at i:42474 original size:5 final size:5
Alignment explanation
Indices: 42464--42488 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42454 GTTTCTTGTG
42464 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
42489 TCTCATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:42762 original size:13 final size:13
Alignment explanation
Indices: 42709--42763 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
42699 TTGAGGAACT
*
42709 ATTTTATT-ACTG
1 ATTTTATTAAATG
42721 -TTTTATTAAATTG
1 ATTTTATTAAA-TG
* *
42734 TTTTTA-TAAATA
1 ATTTTATTAAATG
42746 ATTTTATTAAATG
1 ATTTTATTAAATG
42759 ATTTT
1 ATTTT
42764 GGGTGCATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 7 0.20
12 7 0.20
13 16 0.46
14 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (13 bp):
ATTTTATTAAATG
Found at i:48648 original size:16 final size:16
Alignment explanation
Indices: 48623--48663 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
48613 GTCAACGTCT
*
48623 CGAACCCGAAATTACC
1 CGAACCCGAAAATACC
*
48639 CGAGCCCGAAAATACC
1 CGAACCCGAAAATACC
48655 CGAACCCGA
1 CGAACCCGA
48664 GGCAGCCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.39, G:0.17, T:0.07
Consensus pattern (16 bp):
CGAACCCGAAAATACC
Found at i:49481 original size:13 final size:12
Alignment explanation
Indices: 49445--49491 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
49435 TCAATCTTTA
*
49445 TATATATTGATAA
1 TATATATT-ATAT
*
49458 TA-ATGTTATAT
1 TATATATTATAT
49469 TATATTATTATAT
1 TATA-TATTATAT
49482 TATATATTAT
1 TATATATTAT
49492 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:49734 original size:32 final size:32
Alignment explanation
Indices: 49667--49735 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
49657 ATCAAATCCA
* * * *
49667 AAAATACCCAAACCTGACATAATTCGAGCCTG
1 AAAATACCCAAACCCGACATAATCCGAACCCG
*
49699 AAAATACCCAAACCCGAC-TTATCCCGAACCCG
1 AAAATACCCAAACCCGACATAAT-CCGAACCCG
49731 AAAAT
1 AAAAT
49736 CCGACCCGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.42, C:0.32, G:0.10, T:0.16
Consensus pattern (32 bp):
AAAATACCCAAACCCGACATAATCCGAACCCG
Found at i:49749 original size:15 final size:15
Alignment explanation
Indices: 49722--49760 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
49712 CCGACTTATC
*
49722 CCGAACCCG-AAAAT
1 CCGAACCCGAAAAAA
49736 CCG-ACCCGAAAAAA
1 CCGAACCCGAAAAAA
49750 CCGAACCCGAA
1 CCGAACCCGAA
49761 CCCACTCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 10 0.45
15 7 0.32
ACGTcount: A:0.44, C:0.38, G:0.15, T:0.03
Consensus pattern (15 bp):
CCGAACCCGAAAAAA
Found at i:50021 original size:27 final size:28
Alignment explanation
Indices: 49960--50021 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
49950 AATAGCAAAG
49960 AAAAAGAAAATAAAAGTTATTCTTCTTT
1 AAAAAGAAAATAAAAGTTATTCTTCTTT
*
49988 AACAAAGAAGA-AAAA-TTA-TCTTCCTCTT
1 AA-AAAGAAAATAAAAGTTATTCTT-CT-TT
50016 AAAAAG
1 AAAAAG
50022 GTCTCAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 4 0.13
27 9 0.30
28 10 0.33
29 7 0.23
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (28 bp):
AAAAAGAAAATAAAAGTTATTCTTCTTT
Found at i:57371 original size:13 final size:13
Alignment explanation
Indices: 57355--57379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57345 GTATCATCAC
57355 TTTGTTTTTTTTG
1 TTTGTTTTTTTTG
57368 TTTGTTTTTTTT
1 TTTGTTTTTTTT
57380 TTTTATTAGG
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTGTTTTTTTTG
Found at i:58699 original size:19 final size:19
Alignment explanation
Indices: 58672--58710 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
58662 TTTTCAAATG
*
58672 TTTTCTTTACTCTTTTAAT
1 TTTTCTTTACTCTTATAAT
*
58691 TTTTTTTTACTCTTATAAT
1 TTTTCTTTACTCTTATAAT
58710 T
1 T
58711 ACACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTCTTTACTCTTATAAT
Found at i:67843 original size:21 final size:21
Alignment explanation
Indices: 67817--67858 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
67807 TTTAACCCAG
67817 TTTTATGTGTATACATTTTTA
1 TTTTATGTGTATACATTTTTA
67838 TTTTATGTGTATACATTTTTA
1 TTTTATGTGTATACATTTTTA
67859 ACCCAGTTTT
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:0.24, C:0.05, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTTATGTGTATACATTTTTA
Found at i:67876 original size:27 final size:27
Alignment explanation
Indices: 67804--67879 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
67794 CCTAAGCCTT
67804 ATTTTTAACCCAGTTTTATGTGTATAC
1 ATTTTTAACCCAGTTTTATGTGTATAC
67831 ATTTTT-----A-TTTTATGTGTATAC
1 ATTTTTAACCCAGTTTTATGTGTATAC
67852 ATTTTTAACCCAGTTTTATGTGTATAC
1 ATTTTTAACCCAGTTTTATGTGTATAC
67879 A
1 A
67880 AAGGAAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
21 20 0.47
22 1 0.02
26 1 0.02
27 21 0.49
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (27 bp):
ATTTTTAACCCAGTTTTATGTGTATAC
Done.