Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015552.1 Corchorus olitorius cultivar O-4 contig15585, 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: 34438
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Found at i:280 original size:4 final size:4
Alignment explanation
Indices: 271--307 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
261 GAAGAAGAAG
271 AAGA AAGA AAGA AAG- AAGA AAGA AAGA AA-A AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
308 TAAGGCCTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 9 0.29
4 22 0.71
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:286 original size:15 final size:15
Alignment explanation
Indices: 268--299 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
258 GGAGAAGAAG
268 AAGAAGAAAGAAAGA
1 AAGAAGAAAGAAAGA
283 AAGAAGAAAGAAAGA
1 AAGAAGAAAGAAAGA
298 AA
1 AA
300 AAAAAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAGAAAGA
Found at i:440 original size:5 final size:5
Alignment explanation
Indices: 425--487 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
415 GGGAAAAAGG
425 GAAAA GAAAAA GAAAA GAAAA GAAAA GAAAGA GGAAAA -AGAAA -AAAA
1 GAAAA G-AAAA GAAAA GAAAA GAAAA GAAA-A -GAAAA GA-AAA GAAAA
*
472 GAAAA AAATAA GAAAA
1 GAAAA GAA-AA GAAAA
488 TAAGAAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 31 0.62
6 11 0.22
7 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (5 bp):
GAAAA
Found at i:472 original size:8 final size:8
Alignment explanation
Indices: 426--530 Score: 68
Period size: 8 Copynumber: 12.1 Consensus size: 8
416 GGAAAAAGGG
426 AAAAGAAA
1 AAAAGAAA
*
434 AAGAA-AAG
1 AA-AAGAAA
442 AAAAGAAA
1 AAAAGAAA
*
450 AGAAAGAGGA
1 A-AAAGA-AA
460 AAAAGAAA
1 AAAAGAAA
468 AAAAGAAAAA
1 AAAAG--AAA
478 AATAAGAAA
1 AA-AAGAAA
*
487 ATAAGAAA
1 AAAAGAAA
*
495 ATAAGAAA
1 AAAAGAAA
*
503 AAAATAAGA
1 AAAAGAA-A
512 AATAAGAGAA
1 AA-AAGA-AA
*
522 AATAGAAA
1 AAAAGAAA
530 A
1 A
531 TTATGGATAA
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
7 2 0.03
8 37 0.47
9 22 0.28
10 13 0.17
11 4 0.05
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (8 bp):
AAAAGAAA
Found at i:505 original size:27 final size:26
Alignment explanation
Indices: 428--530 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 26
418 AAAAAGGGAA
*
428 AAGAAA-AAGAAAAGAAAAGAAAAGAAAG
1 AAGAAATAAG-AAA-AAAAGAAAA-AAAT
*
456 AGGAAA-AAGAAAAAAAGAAAAAAAT
1 AAGAAATAAGAAAAAAAGAAAAAAAT
*
481 AAGAAAATAAGAAAATAAGAAAAAAAT
1 AAG-AAATAAGAAAAAAAGAAAAAAAT
*
508 AAGAAATAAGAGAAAATAGAAAA
1 AAGAAATAAGA-AAAAAAGAAAA
531 TTATGGATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
25 5 0.08
26 20 0.30
27 33 0.50
28 8 0.12
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (26 bp):
AAGAAATAAGAAAAAAAGAAAAAAAT
Found at i:624 original size:27 final size:28
Alignment explanation
Indices: 574--628 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
564 GGAGTTAAAG
* *
574 ACGATTTTACCCTTAGATACATTAAATT
1 ACGAATTTACCCCTAGATACATTAAATT
*
602 ACGAATTTACCCCTAGAT-GATTAAATT
1 ACGAATTTACCCCTAGATACATTAAATT
629 GACAATCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (28 bp):
ACGAATTTACCCCTAGATACATTAAATT
Found at i:4851 original size:34 final size:34
Alignment explanation
Indices: 4812--4880 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
4802 TAATTGGGTC
4812 GAATTATGTTTGGTGTGGAGTTCATTGTAATCCG
1 GAATTATGTTTGGTGTGGAGTTCATTGTAATCCG
4846 GAATTATGTTTGGTGTGGAGTTCATTGTAATCCG
1 GAATTATGTTTGGTGTGGAGTTCATTGTAATCCG
4880 G
1 G
4881 TTAATTGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.41
Consensus pattern (34 bp):
GAATTATGTTTGGTGTGGAGTTCATTGTAATCCG
Found at i:5277 original size:26 final size:27
Alignment explanation
Indices: 5235--5309 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 27
5225 TAGTATTATT
*
5235 GGATTCTACC--CATAGCGTCACCAGG
1 GGATTCTACCGACTTAGCGTCACCAGG
*
5260 GGATT-TACCGACTTAGCGTCACCCGG
1 GGATTCTACCGACTTAGCGTCACCAGG
* *
5286 GGATTCTACTGACTTAGCATCACC
1 GGATTCTACCGACTTAGCGTCACC
5310 GGAGTTTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.09
25 5 0.12
26 18 0.42
27 16 0.37
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.24
Consensus pattern (27 bp):
GGATTCTACCGACTTAGCGTCACCAGG
Found at i:7402 original size:11 final size:11
Alignment explanation
Indices: 7382--7425 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
7372 ATGTATATTC
*
7382 ATAATAAATTT
1 ATAATTAATTT
7393 ATAATTAATTT
1 ATAATTAATTT
7404 ATAATT-ATTT
1 ATAATTAATTT
*
7414 GATAATTTATTT
1 -ATAATTAATTT
7426 TATATAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
ATAATTAATTT
Found at i:7640 original size:31 final size:30
Alignment explanation
Indices: 7599--7763 Score: 119
Period size: 29 Copynumber: 5.5 Consensus size: 30
7589 TTAGGCTAAT
7599 TGCTCAAATAAGGGCCTAACGTTTGGCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-GCAAAA
* * * * **
7630 TGTTCAAATAAGGGCATGATC-TTT-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCAAAA
*
7659 TGGTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTG-CAAAA
* * * **
7690 TGCTCAAATAAGGGCCCGATC-TTT-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCAAAA
7719 TGGC-CAAATAAGGGCCTAACG--TGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTG-CAAAA
7748 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
7764 CGGCGTCGAA
Statistics
Matches: 101, Mismatches: 23, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
27 1 0.01
28 8 0.08
29 48 0.48
30 2 0.02
31 36 0.36
32 6 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTGCAAAA
Found at i:7670 original size:60 final size:60
Alignment explanation
Indices: 7602--7762 Score: 263
Period size: 60 Copynumber: 2.7 Consensus size: 60
7592 GGCTAATTGC
* * *
7602 TCAAATAAGGGCCTAACGTTTGGCAAAATGTTCAAATAAGGGCATGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTTAATTTGG
*
7662 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTTAATTTGG
*
7722 CCAAATAAGGGCCTAACG--TGCCAAAATGCTCAAATAAGGGC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
7763 CCGGCGTCGA
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
58 23 0.24
60 73 0.76
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTTAATTTGG
Found at i:7841 original size:31 final size:30
Alignment explanation
Indices: 7803--7970 Score: 89
Period size: 31 Copynumber: 5.6 Consensus size: 30
7793 CACTGATGCC
7803 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GATAACGTT
** * *
7834 AGGCCCTTATTTG-GCTAAATT-A-AAAGATC
1 AGGCCCTTATTTGAGC-ATTTTGATAACG-TT
* *
7863 GGGCCCTTATTTGAGCATTTTTGATGACGTT
1 AGGCCCTTATTTGAGCA-TTTTGATAACGTT
* ** * *
7894 AGACCCTTATTTG-GCCAAATT-A-AAAGATC
1 AGGCCCTTATTTGAG-CATTTTGATAACG-TT
* **
7923 GGGCCCTTATTTGAGCATTTTGGCA-AATATT
1 AGGCCCTTATTTGAGCATTTT-G-ATAACGTT
7954 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
7971 ATTAGCCTTT
Statistics
Matches: 100, Mismatches: 25, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
28 5 0.05
29 32 0.32
30 10 0.10
31 48 0.48
32 5 0.05
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGATAACGTT
Found at i:7935 original size:29 final size:29
Alignment explanation
Indices: 7835--7935 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
7825 GATAACGTTA
*
7835 GGCCCTTATTTGGCTAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
** ** *
7864 GGCCCTTATTTGAG-CATTTTTGATGA-CG
1 GGCCCTTATTTG-GCCAAATTAAAAGATCG
*
7892 TTAGACCCTTATTTGGCCAAATTAAAAGATCG
1 ---GGCCCTTATTTGGCCAAATTAAAAGATCG
7924 GGCCCTTATTTG
1 GGCCCTTATTTG
7936 AGCATTTTGG
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 2 0.04
29 29 0.55
30 2 0.04
31 18 0.34
32 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:7961 original size:60 final size:60
Alignment explanation
Indices: 7804--7966 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
7794 ACTGATGCCA
*
7804 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCTAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * *
7864 GGCCCTTATTTGAGCATTTTTGATGACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* **
7924 GGCCCTTATTTGAGCATTTTGGCA-AATATTAGGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
7967 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:11770 original size:165 final size:164
Alignment explanation
Indices: 11527--11846 Score: 389
Period size: 166 Copynumber: 1.9 Consensus size: 164
11517 TTTTTTGTGG
* * * * *
11527 ATTTTGGGTAAAAACTGATTTTCGGTTATGGGTTTTGGAAATAAATGTTGTATTATAATTCTTTT
1 ATTTTGGGTAAAAACTGATTATCGGTTATGGGTTTTGAAAAAAAATGTTGTATTATAAGTCTATT
* * * *
11592 GTTTGAATTGTTTTTGGGTTTTTGCGATA-TTTCAG-GAATTTTAAGGTTTGTTCATAAGATGAA
66 GTATGAATTGTTTTTGGGTATTTG-GAAAGTTTCAGCAAATTTTAAGGTTTGTTCATAAGAT-AA
* *
11655 -TTGGGAATTAGTGTTTCTGAGTTAAAATGATTGTC
129 TTTGGGAATTAGGGTTTCCGAGTTAAAATGATTGTC
* * *
11690 ATTTTGGGTCAAAA-TAGATTATCTGTTATGGGTATTTGAAAAAAAAGTGTTGTATTATGAGT-T
1 ATTTTGGGTAAAAACT-GATTATCGGTTATGGGT-TTTGAAAAAAAA-TGTTGTATTATAAGTCT
* * * *
11753 ATTGCTATGAATTGTTTTTGGGTATTTGGAAAGTTTCTGCAAATTTTAGGGTTTGTTCATTAGGT
63 ATTG-TATGAATTGTTTTTGGGTATTTGGAAAGTTTCAGCAAATTTTAAGGTTTGTTCATAAGAT
11818 AATTTGGGAATTAGGGTTTCCGAGTTAAA
127 AATTTGGGAATTAGGGTTTCCGAGTTAAA
11847 TTAACATGGA
Statistics
Matches: 132, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
162 1 0.01
163 28 0.21
164 17 0.13
165 41 0.31
166 45 0.34
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (164 bp):
ATTTTGGGTAAAAACTGATTATCGGTTATGGGTTTTGAAAAAAAATGTTGTATTATAAGTCTATT
GTATGAATTGTTTTTGGGTATTTGGAAAGTTTCAGCAAATTTTAAGGTTTGTTCATAAGATAATT
TGGGAATTAGGGTTTCCGAGTTAAAATGATTGTC
Found at i:15288 original size:20 final size:20
Alignment explanation
Indices: 15250--15289 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15240 ATACTATTAT
15250 CTTTTGAATTTAATATTTTA
1 CTTTTGAATTTAATATTTTA
*
15270 CTTTT-AATTTCAATTTTTTA
1 CTTTTGAATTT-AATATTTTA
15290 AATGTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (20 bp):
CTTTTGAATTTAATATTTTA
Found at i:15512 original size:22 final size:21
Alignment explanation
Indices: 15458--15632 Score: 145
Period size: 22 Copynumber: 7.9 Consensus size: 21
15448 CTCTGTGTAA
*
15458 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAGGA-GG
* *
15480 TTATTATAATTTCATGAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
15502 TTATCAAAA-TTCTATAGTGTGG
1 TTATCAAAATTTC-ATAG-GAGG
* *
15524 TTACCAAAATTTCATATGGAAG
1 TTATCAAAATTTCATA-GGAGG
*
15546 TTATCAAAATTTCATGGGTAGG
1 TTATCAAAATTTCATAGG-AGG
*
15568 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* *
15590 TTACCAAAATTTTATAGGATCAGG
1 TTATCAAAATTTCATAGG---AGG
* *
15614 TTATTAAAATTTCTTAGGA
1 TTATCAAAATTTCATAGGA
15633 AAATTATTGA
Statistics
Matches: 122, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
21 9 0.07
22 89 0.73
23 8 0.07
24 16 0.13
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:15714 original size:22 final size:21
Alignment explanation
Indices: 15689--16768 Score: 346
Period size: 22 Copynumber: 49.5 Consensus size: 21
15679 ATCCAAGAGA
*
15689 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
15711 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
15733 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
15755 -TAACTAATATTTCATGAGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
15777 TTATCAAAATTTCATAGG-GTAG
1 TTATCAAAATTTCATAGGAG--G
* * *
15799 TTATCAAAAATTT-TTATTGTGG
1 TTATC-AAAATTTCATA-GGAGG
* *
15821 TTATCAAAATTTCGTATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
15843 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
15868 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
15890 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
15910 ATTATCGAAATTTCATAGAGATCGA
1 -TTATCAAAATTTCATAG-GA--GG
*
15935 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGG-AGG
**
15956 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* *
15978 TTATCAAAATTTCAAAGCAAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
16000 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
*
16022 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * * *
16044 TCAACAAAATTTTATTGAGAAG
1 TTATCAAAATTTCATAG-GAGG
*
16066 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
* * * * *
16088 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTC-ATAGGAGG
* *
16110 TTACCAAAATTTCATAGTACGG
1 TTATCAAAATTTCATAGGA-GG
16132 TTA-CAAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* * *
16149 TTATTAAACTTTTATTATGGA-G
1 TTATCAAAATTTCA-TA-GGAGG
* *
16171 TAATCAAAATTTCA-GGGAGG
1 TTATCAAAATTTCATAGGAGG
* * *
16191 ATATGAAAATTTCAT-GTGAAGA
1 TTATCAAAATTTCATAG-G-AGG
* *
16213 TTATTAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG--GAGG
* *
16235 TTTTCAAAATTTCATAAGAGGG
1 TTATCAAAATTTCATAGGA-GG
* *
16257 TTATC-AAATTTCATA-TATG
1 TTATCAAAATTTCATAGGAGG
* * **
16276 TAGATCAAAATTTGATAGGGAAA
1 T-TATCAAAATTTCATA-GGAGG
* *
16299 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCAT-AGGAGG
**
16321 TTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
16343 TTATCAAAA-TT--T-GTA-G
1 TTATCAAAATTTCATAGGAGG
*
16359 TTATCAAGATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
16381 TTATCAAAATTTTATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* **
16403 TTTATCAAAATTTTATAAAAAGG
1 -TTATCAAAATTTCAT-AGGAGG
*
16426 TTTATCAAAATTTCATAGCAAGG
1 -TTATCAAAATTTCATAG-GAGG
* * *
16449 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
* * *
16471 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
*
16493 TTA-CTAACAA-TTCATATGGTGG
1 TTATC-AA-AATTTCATA-GGAGG
* * * * *
16515 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCAT-AGGAGG
* *
16537 TTATCAATATATCATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
16559 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-G-AGG
* * *
16582 TTATTAAAATTTCATCGGGAAAG
1 TTATCAAAATTTCAT-AGG-AGG
16605 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
16627 TCT-TCAAAATTCCTTAGGGAGG
1 T-TATCAAAATTTCATA-GGAGG
* * *
16649 TTAACAAAATTTCATAAGAAAG
1 TTATCAAAATTTCAT-AGGAGG
** * ** **
16671 TTAAAAAAAATT-ATAAAAAAC
1 TTATCAAAATTTCAT-AGGAGG
* * *
16692 TTCTCAAAATTTCATAGTATCG
1 TTATCAAAATTTCATAGGA-GG
** *
16714 TTATTGAAATTTCACAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
16736 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
16758 TCATCCAAAAT
1 TTAT-CAAAAT
16769 AGTGTAATTA
Statistics
Matches: 792, Mismatches: 181, Indels: 169
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.01
17 12 0.02
18 4 0.01
19 10 0.01
20 37 0.05
21 92 0.12
22 474 0.60
23 120 0.15
24 18 0.02
25 5 0.01
26 3 0.00
28 8 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:16411 original size:23 final size:23
Alignment explanation
Indices: 16359--16438 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
16349 AAATTTGTAG
* *
16359 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAAGGAGGT
16381 TTATCAAAATTTTATAAGGAGGT
1 TTATCAAAATTTTATAAGGAGGT
**
16404 TTATCAAAATTTTATAAAAAGGT
1 TTATCAAAATTTTATAAGGAGGT
16427 TTATCAAAATTT
1 TTATCAAAATTT
16439 CATAGCAAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 20 0.38
23 33 0.62
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAAGGAGGT
Found at i:22334 original size:87 final size:87
Alignment explanation
Indices: 22231--22404 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
22221 AAAAGAGAGA
22231 ACGCACTTTCTCTCTTGGTTTTCTCTATTCTTAGTTCTTTTGTAATTTTTCCTTTTTAGTTAATT
1 ACGCACTTTCTCTCTTGGTTTTCTCTATTCTTAGTTCTTTTGTAATTTTTCCTTTTTAGTTAATT
22296 TAATTTTGAGGCTTTCAATCTC
66 TAATTTTGAGGCTTTCAATCTC
22318 ACGCACTTTCTCTCTTGGTTTTCTCTATTCTTAGTTCTTTTGTAATTTTTCCTTTTTAGTTAATT
1 ACGCACTTTCTCTCTTGGTTTTCTCTATTCTTAGTTCTTTTGTAATTTTTCCTTTTTAGTTAATT
22383 TAATTTTGAGGCTTTCAATCTC
66 TAATTTTGAGGCTTTCAATCTC
22405 TTGTGTATTT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.16, C:0.18, G:0.10, T:0.55
Consensus pattern (87 bp):
ACGCACTTTCTCTCTTGGTTTTCTCTATTCTTAGTTCTTTTGTAATTTTTCCTTTTTAGTTAATT
TAATTTTGAGGCTTTCAATCTC
Found at i:23204 original size:20 final size:19
Alignment explanation
Indices: 23170--23226 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
23160 TTTCCTTTAC
* *
23170 TTTTGTTTCTATTTTTCGTA
1 TTTTGTTTTTGTTTTT-GTA
*
23190 TTTTGTTTTTGTTTTTGTG
1 TTTTGTTTTTGTTTTTGTA
23209 TTTGTGTTTTTGTGTTTT
1 TTT-TGTTTTTGT-TTTT
23227 TGTTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.72
21 4 0.12
ACGTcount: A:0.04, C:0.04, G:0.18, T:0.75
Consensus pattern (19 bp):
TTTTGTTTTTGTTTTTGTA
Found at i:23210 original size:14 final size:14
Alignment explanation
Indices: 23193--23230 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
23183 TTTCGTATTT
23193 TGTTTTTGTTTTTG
1 TGTTTTTGTTTTTG
*
23207 TGTTTGTGTTTTTG
1 TGTTTTTGTTTTTG
23221 TGTTTTTGTT
1 TGTTTTTGTT
23231 AATTTTGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (14 bp):
TGTTTTTGTTTTTG
Found at i:23230 original size:6 final size:6
Alignment explanation
Indices: 23170--23226 Score: 51
Period size: 6 Copynumber: 8.7 Consensus size: 6
23160 TTTCCTTTAC
* *
23170 TTTTGT TTCTAT TTTTCGT ATTTTGT TTTTGT TTTTGT GTTTGTGT TTTTGT
1 TTTTGT TTTTGT TTTT-GT -TTTTGT TTTTGT TTTTGT -TTT-TGT TTTTGT
23222 GTTTT
1 -TTTT
23227 TGTTAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
6 22 0.52
7 13 0.31
8 7 0.17
ACGTcount: A:0.04, C:0.04, G:0.18, T:0.75
Consensus pattern (6 bp):
TTTTGT
Found at i:24759 original size:1 final size:1
Alignment explanation
Indices: 24755--24780 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
24745 AACCAAAAAG
24755 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
24781 AAAAACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27565 original size:23 final size:21
Alignment explanation
Indices: 27526--27568 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
27516 AAAAAAATAT
27526 ATTTTTGATTTTGCGTTTTTA
1 ATTTTTGATTTTGCGTTTTTA
27547 ATTTTTGAGTGTTTGCGTTTTT
1 ATTTTTGA-T-TTTGCGTTTTT
27569 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.12, C:0.05, G:0.19, T:0.65
Consensus pattern (21 bp):
ATTTTTGATTTTGCGTTTTTA
Found at i:27619 original size:19 final size:19
Alignment explanation
Indices: 27595--27634 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
27585 GTTTTGTGTT
27595 TTGCGTCA-AAGAAAAAAAA
1 TTGCGTCATAA-AAAAAAAA
27614 TTGCGTCATAAAAAAAAAA
1 TTGCGTCATAAAAAAAAAA
27633 TT
1 TT
27635 TTGTCTCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (19 bp):
TTGCGTCATAAAAAAAAAA
Found at i:29809 original size:21 final size:21
Alignment explanation
Indices: 29785--29861 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
29775 CCTGGCCACA
* * *
29785 GCCCGGCCACCCGAGCCATAT
1 GCCCGGCCATCCGCGCCATCT
29806 GCCCGGCCATCCGCGCCATCT
1 GCCCGGCCATCCGCGCCATCT
*
29827 TCCCGGCCATCCGCGCCATCT
1 GCCCGGCCATCCGCGCCATCT
*
29848 TCCCGGCCATCCGC
1 GCCCGGCCATCCGC
29862 ACTATCCTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.12, C:0.52, G:0.22, T:0.14
Consensus pattern (21 bp):
GCCCGGCCATCCGCGCCATCT
Found at i:30088 original size:21 final size:21
Alignment explanation
Indices: 30062--30111 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
30052 CGCCCATTCA
*
30062 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
*
30083 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
30104 CCGTGCCA
1 CCGTGCCA
30112 TCGCCATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.46, G:0.24, T:0.14
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:30305 original size:2 final size:2
Alignment explanation
Indices: 30298--30322 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30288 TGATTGCAAG
30298 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30323 AATCTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33997 original size:190 final size:190
Alignment explanation
Indices: 33669--34051 Score: 748
Period size: 190 Copynumber: 2.0 Consensus size: 190
33659 GCTTAAGTTT
*
33669 AGTTTTTCTTTAAGTTGTTAGTCTTTGTTTTGTTTTCTAGCTTGCTAGGGACTAGCAAGATCTAA
1 AGTTTTTCTTTAAGTTGTTAGTCTTTGTTTTGTTATCTAGCTTGCTAGGGACTAGCAAGATCTAA
33734 GTGTGGGGGAATTTGTTAGGCACATATTTTCTTATATTTTATATGTCAATTTGATTTGATTATGT
66 GTGTGGGGGAATTTGTTAGGCACATATTTTCTTATATTTTATATGTCAATTTGATTTGATTATGT
*
33799 GTCTATTTCTATGTACTTGATGCTTAATTTATTCATATTTGTGTTTTAGGTACATATTGG
131 GCCTATTTCTATGTACTTGATGCTTAATTTATTCATATTTGTGTTTTAGGTACATATTGG
33859 AGTTTTTCTTTAAGTTGTTAGTCTTTGTTTTGTTATCTAGCTTGCTAGGGACTAGCAAGATCTAA
1 AGTTTTTCTTTAAGTTGTTAGTCTTTGTTTTGTTATCTAGCTTGCTAGGGACTAGCAAGATCTAA
33924 GTGTGGGGGAATTTGTTAGGCACATATTTTCTTATATTTTATATGTCAATTTGATTTGATTATGT
66 GTGTGGGGGAATTTGTTAGGCACATATTTTCTTATATTTTATATGTCAATTTGATTTGATTATGT
33989 GCCTATTTCTATGTACTTGATGCTTAATTTATTCATATTTGTGTTTTAGGTACATATTGG
131 GCCTATTTCTATGTACTTGATGCTTAATTTATTCATATTTGTGTTTTAGGTACATATTGG
34049 AGT
1 AGT
34052 GCTTCAAGGC
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 191 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.49
Consensus pattern (190 bp):
AGTTTTTCTTTAAGTTGTTAGTCTTTGTTTTGTTATCTAGCTTGCTAGGGACTAGCAAGATCTAA
GTGTGGGGGAATTTGTTAGGCACATATTTTCTTATATTTTATATGTCAATTTGATTTGATTATGT
GCCTATTTCTATGTACTTGATGCTTAATTTATTCATATTTGTGTTTTAGGTACATATTGG
Done.