Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016401.1 Corchorus olitorius cultivar O-4 contig16434, 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: 112790
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:205 original size:41 final size:42
Alignment explanation
Indices: 148--227 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
138 CCCACAATAT
*
148 TTTGGTCACGTGGCTTTTT-GCCACGTGGGA-AGATGACGTGG
1 TTTGGCCACGTGGCTTTTTAGCCACGT-GGACAGATGACGTGG
189 TTTGGCCACGTGGCTTTTTGAGCCACGTGGACAGATGAC
1 TTTGGCCACGTGGCTTTTT-AGCCACGTGGACAGATGAC
228 ATGGACAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
41 18 0.51
42 3 0.09
43 14 0.40
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.30
Consensus pattern (42 bp):
TTTGGCCACGTGGCTTTTTAGCCACGTGGACAGATGACGTGG
Found at i:2363 original size:319 final size:320
Alignment explanation
Indices: 1463--3302 Score: 2269
Period size: 319 Copynumber: 5.8 Consensus size: 320
1453 ATTGCTTTTA
*
1463 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATGATTAGTACACGATTTCGACTAAAAACTG
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTG--G--TAGTACACGATTTCGGCTAAAAACTG
* * * * *
1528 ATCC-GAAAATTTTTTTTCCTGAATTTTTTGGCACAATACCCAGGAAAAATATATAATTGAATGC
62 A-CCTGAAAATTTTTTTT-CTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGC
* * * *
1592 CAAAAAGATTGACGGGTTTTTCACGCTTCTATTGACTATTATCATTTTTCCATTTTTTTCCGAAT
125 CAAAAAGATTGACAGGCTTTTCACG---C--TT--CTATTATCGTTTTTCCAATTTTTTCCGAAT
* *
1657 TTATTTATAATTAAATCGAAACAAGATTTTGATAAACGTAAAAATAAATCCTTAAATCCAATGTG
183 TTATTTCTAATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTG
* * * * * * *
1722 GCTAAGATTTGGTTGGATAAATATCGATATTCCAAGGAGTCTTTCTGCCAAAAATAATTCAAAAC
248 GCTGAGATTTAGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAGTAATGCAAAAC
1787 TGAGTCGG
313 TGAGTCGG
* * *
1795 GGCCCCAAAACACGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTG
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATC--G-TGG-TAGTACACGATTTCGGCTAAAAACTG
** * * *
1860 ATTTGAAAAGTTATTTTTC--AATTTTTTGCAACAATACTCAGAAAAATTATATAATTCAAAGCC
62 ACCTGAAAA-TTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCC
* * * * * * *
1923 AAAAA-ATTTAAATGTTTTTCACGCTTCTAATATAGTTTTTCCAATTTTATCCGAATTTATTTCT
126 AAAAAGATTGACAGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTCT
* * *
1987 AATTAAATCGAAACAACATTTTGATACTCGTAAAAATAAATCCTTAAATCTAATGTGGCTGAGAT
191 AATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGAT
*
2052 TTAGTTAGATGAATATAGATATTCCAAGGAGTCTTTCAGCCAAAAGTAATGCAAAACTGAGTCGG
256 TTAGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAGTAATGCAAAACTGAGTCGG
* *
2117 GACCCCGAAACGCGTTTTTAGCTCAAAAATCGTGG-CGTACACGATTTCGGCTAAAAACTGACCT
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGGTAGTACACGATTTCGGCTAAAAACTGACC-
* * * *
2181 TTAAAA-ATTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCGAAA
65 TGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCC-AAA
** * * *
2245 AA-ATTTTCGGGCTTTTCACGCTTCTATTATCGATTTTT-TAATTTTTTCCGAATTTATTTTTAA
129 AAGATTGACAGGCTTTTCACGCTTCTATTATCG-TTTTTCCAATTTTTTCCGAATTTATTTCTAA
* **
2308 TTAAATCGGAACAAGATTCAGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTT
193 TTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTT
*
2373 AGTTAGATGAATATAGATATTCCAAGGAGTCTTTCAGCCAAAAGTAATGCAAAACTGAGTCGG
258 AGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAGTAATGCAAAACTGAGTCGG
* *
2436 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGT--AACGTACACTATTTCGGCTAAAAACTGACC
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGGTA-GTACACGATTTCGGCTAAAAACTGACC
* * * * *
2499 CGAAAATTTTTTTTTCTGAATTTTTTGCCACAATACCCAGAAAAAACATATAATTGAATGCCAAA
65 TGAAAA-TTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAA
* * *
2564 AAGATTGACAGGCTTTTCACGCTTCTATTATCGTTTTTCCAA-TTTTCCCAAATTTAATTCTAAT
129 AAGATTGACAGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTCTAAT
* *
2628 TAAATCGAAAGAAGATTTTGATACTCGTAAAAATAAATCCTT--A---AA--T--CT-A-A--T-
194 TAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTA
* * * **
2679 G-T-G-T--CTA-AGATATTCCCATGAGTCTTTCTGCCAAAAACAATGCAAAACTGAGTCGG
259 GTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAGTAATGCAAAACTGAGTCGG
*
2735 GGCCCCGAAACGCGTTTTTAGCCCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAAACTG
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTG--G--TAGTACACGATTTCGGCTAAAAACTG
* * *
2800 ACTTGAAAATTTTTTTTCTGGA-TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
62 ACCTGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCA
*
2864 AAAAGATTGACGGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTCTA
127 AAAAGATTGACAGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTCTA
* *
2929 ATTAAATCGAAACAAGATTTTGATACTCGTAAAAATACATCCTTAAATCCAATGTGGCTGAGATT
192 ATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATT
* *
2994 TGGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCC-AAAGATAATGCAAAACTGAGTCGA
257 TAGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAG-TAATGCAAAACTGAGTCGG
* *
3058 GGCCCTGAAACGCGTTTTTAGCTCAAAAATCGTGATGGTTAGTACACGATTTCGGCTGAAAACTG
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATC--G-TGG-TAGTACACGATTTCGGCTAAAAACTG
* * **
3123 ACCTGAAAAGTTTTTTTC--AAATTTTTGCCACAATACTCAGAAAATTTATATAATTCAAAGCCA
62 ACCTGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCA
* * * * * * * *
3186 AAAAAATTTAAATGTTTTTCACGCTTCTAATATAGTTTTTCCAATTTTTTCCGAATTTATTT-TG
127 AAAAGATTGACAGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTCTA
** *
3250 ATTAAATCGAAACAAGATTCAGATACACAT-AAAATAAATCCTTAAATCCAATG
192 ATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATG
3303 CAAAAATAAT
Statistics
Matches: 1320, Mismatches: 140, Indels: 108
0.84 0.09 0.07
Matches are distributed among these distances:
299 76 0.06
300 2 0.00
302 82 0.06
303 72 0.05
304 31 0.02
305 3 0.00
306 1 0.00
308 3 0.00
309 1 0.00
310 3 0.00
312 3 0.00
313 1 0.00
314 3 0.00
316 7 0.01
317 27 0.02
318 51 0.04
319 299 0.23
320 106 0.08
321 28 0.02
322 275 0.21
323 111 0.08
324 3 0.00
325 1 0.00
326 3 0.00
329 14 0.01
330 42 0.03
332 61 0.05
333 8 0.01
334 1 0.00
335 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (320 bp):
GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGGTAGTACACGATTTCGGCTAAAAACTGACCT
GAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAA
GATTGACAGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTCTAATTA
AATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTAGT
TAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAGTAATGCAAAACTGAGTCGG
Found at i:3078 original size:622 final size:624
Alignment explanation
Indices: 1463--3302 Score: 2413
Period size: 622 Copynumber: 2.9 Consensus size: 624
1453 ATTGCTTTTA
*
1463 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATGATTAGTACACGATTTCGACTAAAAACTG
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAAACTG
* * * * * *
1528 A-TCCGAAAATTTTTTTTCCTGAATTTTTTGGCACAATACCCAGGAAAAATATATAATTGAATGC
66 ACT-TGAAAATTTTTTTT-CTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC
* * *
1592 CAAAAAGATTGACGGGTTTTTCACGCTTCTATTGACTATTATCATTTTTCCATTTTTTTCCGAAT
129 CAAAAAGATTGACGGGCTTTTCACG---C--TT--CTATTATCGTTTTTCCAATTTTTTCCGAAT
*
1657 TTATTTATAATTAAATCGAAACAAGATTTTGATAAACGTAAAAATAAATCCTTAAATCCAATGTG
187 TTATTTATAATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTG
* * * * *
1722 GCTAAGATTTGGTTGGATAAATATCGATATTCCAAGGAGTCTTTCTGCCAAAAATAATTCAAAAC
252 GCTGAGATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCC-AAAATAATGCAAAAC
* * *
1787 TGAGTCGGGGCCCCAAAACACGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCT
316 TGAGTCGGGGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGA----TAGTACACGATTTCGGCT
** * *
1852 AAAAACTGATTTGAAAAGTTATTTTTCAATTTTTTGCAACAATACTCAGAAAAATTATATAATTC
377 AAAAACTGACCTGAAAA-TTTTTTTTCAATTTTTTGCCACAATACTCAGAAAAATTATATAATTC
1917 AAAGCCAAAAAATTTAAATGTTTTTCACGCTTCTAATATAGTTTTTCCAATTTTATCCGAATTTA
441 AAAGCCAAAAAATTTAAATGTTTTTCACGCTTCTAATATAGTTTTTCCAATTTT-TCCGAATTTA
* *
1982 TTTCTAATTAAATCGAAACAACATTTTGATACTCGTAAAAATAAATCCTTAAATCTAATGTGGCT
505 ATTCTAATTAAATCGAAACAAGATTTTGATACTCGTAAAAATAAATCCTT--A---AA--T--CT
**
2047 GAGATTTAGTTAGATGAATATAGATATTCCAAGGAGTCTTTCAGCCAAAAGTAATGCAAAACTGA
561 -A-A--T-GTTAGAT-AATATAGATATTCCAAGGAGTCTTTCAGCCAAAAACAATGCAAAACTGA
2112 GTCGG
620 GTCGG
* *
2117 GACCCCGAAACGCGTTTTTAGCTCAAAAATCGTG--G---CGTACACGATTTCGGCTAAAAACTG
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAAACTG
* * *
2177 ACCTTTAAAA-ATTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC
66 A-CTTGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC
** *
2241 GAAAAA-ATTTTCGGGCTTTTCACGCTTCTATTATCGATTTTT-TAATTTTTTCCGAATTTATTT
130 -AAAAAGATTGACGGGCTTTTCACGCTTCTATTATCG-TTTTTCCAATTTTTTCCGAATTTATTT
* * **
2304 TTAATTAAATCGGAACAAGATTCAGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAG
193 ATAATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAG
* *
2369 ATTTAGTTAGATGAATATAGATATTCCAAGGAGTCTTTCAGCCAAAAGTAATGCAAAACTGAGTC
258 ATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAA-TAATGCAAAACTGAGTC
*
2434 GGGGCCCCGAAACGCGTTTTTAGCTCAAAAATCGT-A-ACGTACACTATTTCGGCTAAAAACTGA
322 GGGGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATA-GTACACGATTTCGGCTAAAAACTGA
* * ** * *
2497 CCCGAAAATTTTTTTTTCTGAATTTTTTGCCACAATACCCAGAAAAAACATATAATTGAATGCCA
386 CCTGAAAA-TTTTTTTTC--AATTTTTTGCCACAATACTCAGAAAAATTATATAATTCAAAGCCA
* * * * * * * *
2562 AAAAGATTGACAGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTCCCAAATTTAATTCTAA
448 AAAA-ATTTAAATGTTTTTCACGCTTCTAATATAGTTTTTCCAATTTTTCCGAATTTAATTCTAA
* *
2627 TTAAATCGAAAGAAGATTTTGATACTCGTAAAAATAAATCCTTAAATCTAATG-T-G-T-CTA-A
512 TTAAATCGAAACAAGATTTTGATACTCGTAAAAATAAATCCTTAAATCTAATGTTAGATAATATA
* * *
2687 GATATTCCCATGAGTCTTTCTGCCAAAAACAATGCAAAACTGAGTCGG
577 GATATTCCAAGGAGTCTTTCAGCCAAAAACAATGCAAAACTGAGTCGG
*
2735 GGCCCCGAAACGCGTTTTTAGCCCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAAACTG
1 GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAAACTG
*
2800 ACTTGAAAATTTTTTTTCTGGA-TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
66 ACTTGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
*
2864 AAAAGATTGACGGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTCTA
131 AAAAGATTGACGGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTATA
* *
2929 ATTAAATCGAAACAAGATTTTGATACTCGTAAAAATACATCCTTAAATCCAATGTGGCTGAGATT
196 ATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATT
*
2994 TGGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAGATAATGCAAAACTGAGTCGAG
261 TGGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAA-ATAATGCAAAACTGAGTCGGG
* *
3059 GCCCTGAAACGCGTTTTTAGCTCAAAAATCGTGATGGTTAGTACACGATTTCGGCTGAAAACTGA
325 GCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGA----TAGTACACGATTTCGGCTAAAAACTGA
* * *
3124 CCTGAAAAGTTTTTTTCAAATTTTTGCCACAATACTCAGAAAATTTATATAATTCAAAGCCAAAA
386 CCTGAAAATTTTTTTTCAATTTTTTGCCACAATACTCAGAAAAATTATATAATTCAAAGCC-AAA
* *
3189 AAATTTAAATGTTTTTCACGCTTCTAATATAGTTTTTCCAATTTTTTCCGAATTT-ATTTTGATT
450 AAATTTAAATGTTTTTCACGCTTCTAATATAGTTTTTCCAA-TTTTTCCGAATTTAATTCTAATT
** * * *
3253 AAATCGAAACAAGATTCAGATACACAT-AAAATAAATCCTTAAATCCAATG
514 AAATCGAAACAAGATTTTGATACTCGTAAAAATAAATCCTTAAATCTAATG
3303 CAAAAATAAT
Statistics
Matches: 1051, Mismatches: 109, Indels: 83
0.85 0.09 0.07
Matches are distributed among these distances:
618 76 0.07
619 2 0.00
620 1 0.00
621 11 0.01
622 250 0.24
623 59 0.06
624 100 0.10
625 17 0.02
626 8 0.01
627 31 0.03
628 2 0.00
629 2 0.00
631 1 0.00
633 2 0.00
635 1 0.00
636 38 0.04
638 98 0.09
639 37 0.04
640 5 0.00
641 172 0.16
642 5 0.00
643 2 0.00
645 1 0.00
648 56 0.05
649 35 0.03
650 4 0.00
651 1 0.00
652 1 0.00
654 33 0.03
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (624 bp):
GGCCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATGATTAGTACACGATTTCGGCTAAAAACTG
ACTTGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
AAAAGATTGACGGGCTTTTCACGCTTCTATTATCGTTTTTCCAATTTTTTCCGAATTTATTTATA
ATTAAATCGAAACAAGATTTTGATACACGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATT
TGGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAATAATGCAAAACTGAGTCGGGG
CCCCGAAACGCGTTTTTAGCTCAAAAATCGTGATAGTACACGATTTCGGCTAAAAACTGACCTGA
AAATTTTTTTTCAATTTTTTGCCACAATACTCAGAAAAATTATATAATTCAAAGCCAAAAAATTT
AAATGTTTTTCACGCTTCTAATATAGTTTTTCCAATTTTTCCGAATTTAATTCTAATTAAATCGA
AACAAGATTTTGATACTCGTAAAAATAAATCCTTAAATCTAATGTTAGATAATATAGATATTCCA
AGGAGTCTTTCAGCCAAAAACAATGCAAAACTGAGTCGG
Found at i:3635 original size:17 final size:16
Alignment explanation
Indices: 3595--3644 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
3585 CATGTAATCT
*
3595 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
3611 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
3628 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
3645 CGGGGTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:23992 original size:25 final size:24
Alignment explanation
Indices: 23947--24003 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
23937 ATTTTAAGGA
*
23947 AGAAATAAGAAGAAAACGAAAGAG
1 AGAAATAAAAAGAAAACGAAAGAG
**
23971 AGAAATAATAAAGAAATTGAAAGAG
1 AGAAATAA-AAAGAAAACGAAAGAG
23996 -GAAA-AAAA
1 AGAAATAAAA
24004 GTATGATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 12 0.41
25 13 0.45
ACGTcount: A:0.68, C:0.02, G:0.21, T:0.09
Consensus pattern (24 bp):
AGAAATAAAAAGAAAACGAAAGAG
Found at i:30504 original size:15 final size:16
Alignment explanation
Indices: 30480--30512 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30470 AACTAATTTG
30480 AGCTTATATT-AGGGA
1 AGCTTATATTAAGGGA
*
30495 AGCTTCTATTAAGGGA
1 AGCTTATATTAAGGGA
30511 AG
1 AG
30513 ATCAATACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (16 bp):
AGCTTATATTAAGGGA
Found at i:32290 original size:6 final size:6
Alignment explanation
Indices: 32279--32317 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
32269 ACAAGCCAAA
*
32279 ACCTCC ACCTCC ACCTCC ACCTCC ACCTGC ACCTCC ACC
1 ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACC
32318 AAGTGGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.64, G:0.03, T:0.15
Consensus pattern (6 bp):
ACCTCC
Found at i:37496 original size:20 final size:21
Alignment explanation
Indices: 37457--37500 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
37447 AACAAGCACT
37457 TTTTGACAGCAAAAAAAAGGG
1 TTTTGACAGCAAAAAAAAGGG
*
37478 TTTTGACAGC-AAAAGAAGGG
1 TTTTGACAGCAAAAAAAAGGG
37498 TTT
1 TTT
37501 CAGCTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (21 bp):
TTTTGACAGCAAAAAAAAGGG
Found at i:59028 original size:23 final size:23
Alignment explanation
Indices: 59002--59046 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
58992 TGATCAAACA
59002 AAGAATCAAATGCTATTGGTATC
1 AAGAATCAAATGCTATTGGTATC
59025 AAGAATCAAATGCTATTGGTAT
1 AAGAATCAAATGCTATTGGTAT
59047 AATTTTCGTT
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:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (23 bp):
AAGAATCAAATGCTATTGGTATC
Found at i:90778 original size:20 final size:20
Alignment explanation
Indices: 90753--90805 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
90743 GCTGGGAGAG
90753 TTTTAAAATTTTGGAACATA
1 TTTTAAAATTTTGGAACATA
*
90773 TTTTAAAATTTTAGAACATA
1 TTTTAAAATTTTGGAACATA
90793 TTTTAAAATTTTG
1 TTTTAAAATTTTG
90806 AAGTATTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTTAAAATTTTGGAACATA
Found at i:91949 original size:12 final size:11
Alignment explanation
Indices: 91930--91960 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
91920 CACCAACAAC
91930 AAAAAGAAAAA
1 AAAAAGAAAAA
91941 AAGAAAGAAAAA
1 AA-AAAGAAAAA
91953 AAAAAGAA
1 AAAAAGAA
91961 GTTGGTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:92188 original size:17 final size:19
Alignment explanation
Indices: 92166--92211 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
92156 TTTCCGGTTG
92166 TCTCCTCCT-C-TTACTCT
1 TCTCCTCCTCCGTTACTCT
* *
92183 TCTCCTTCTCCGTTTTCTCT
1 TCTCCTCCTCCG-TTACTCT
92203 TCTCCTCCT
1 TCTCCTCCT
92212 GCCGCCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 8 0.35
18 1 0.04
20 14 0.61
ACGTcount: A:0.02, C:0.46, G:0.02, T:0.50
Consensus pattern (19 bp):
TCTCCTCCTCCGTTACTCT
Found at i:96611 original size:23 final size:23
Alignment explanation
Indices: 96581--96625 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
96571 CCATTGGAAA
96581 TGATCAGAGTTCAATTCAAACTG
1 TGATCAGAGTTCAATTCAAACTG
96604 TGATCAGAGTTCAATTCAAACT
1 TGATCAGAGTTCAATTCAAACT
96626 ATGAAATGGA
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:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (23 bp):
TGATCAGAGTTCAATTCAAACTG
Found at i:105480 original size:3 final size:3
Alignment explanation
Indices: 105472--105500 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
105462 ATACTATTAA
105472 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
105501 ATTTCAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.