Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013146.1 Corchorus olitorius cultivar O-4 contig13179, 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: 25426
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3447 original size:38 final size:38
Alignment explanation
Indices: 3401--3510 Score: 148
Period size: 38 Copynumber: 2.9 Consensus size: 38
3391 TATTTTTCAA
*
3401 TTCTGTGTTGAAGTTTTTGTTTTACTTTTCAATTGCAT
1 TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATTGCAT
* * ***
3439 TTTTGTGTTGAAGTTTCTGTTTTACTTCTGTTTTGCAT
1 TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATTGCAT
* *
3477 TTCTGTGTTGAAGTTTCTGTTTTGCATTTCAATT
1 TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATT
3511 TTGTTTAGTG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (38 bp):
TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATTGCAT
Found at i:3482 original size:13 final size:13
Alignment explanation
Indices: 3433--3506 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
3423 TACTTTTCAA
* *
3433 TTGCATTTTTGTG
1 TTGCATTTCTGTT
*
3446 TTGAAGTTTCTGTT
1 TTGCA-TTTCTGTT
*
3460 TT--ACTTCTGTT
1 TTGCATTTCTGTT
*
3471 TTGCATTTCTGTG
1 TTGCATTTCTGTT
*
3484 TTGAAGTTTCTGTT
1 TTGCA-TTTCTGTT
3498 TTGCATTTC
1 TTGCATTTC
3507 AATTTTGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
11 9 0.19
12 1 0.02
13 19 0.40
14 19 0.40
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (13 bp):
TTGCATTTCTGTT
Found at i:3542 original size:27 final size:25
Alignment explanation
Indices: 3494--3543 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
3484 TTGAAGTTTC
*
3494 TGTTTTGCATTTCAATTTTGTTTAG
1 TGTTTTGCATTTCAATTCTGTTTAG
3519 TGTTTTGCATTTTTCAATTCTGTTT
1 TGTTTTGCA--TTTCAATTCTGTTT
3544 TTCAATTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62
Consensus pattern (25 bp):
TGTTTTGCATTTCAATTCTGTTTAG
Found at i:3546 original size:13 final size:13
Alignment explanation
Indices: 3528--3557 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3518 GTGTTTTGCA
3528 TTTTTCAATTCTG
1 TTTTTCAATTCTG
3541 TTTTTCAATTCTG
1 TTTTTCAATTCTG
3554 TTTT
1 TTTT
3558 GCATTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (13 bp):
TTTTTCAATTCTG
Found at i:3583 original size:32 final size:33
Alignment explanation
Indices: 3519--3595 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 33
3509 TTTTGTTTAG
*
3519 TGTTTTGCATTTTTCAATTCTGTTTTTCAATTC
1 TGTTTTGCATTTTTCAATTCAGTTTTTCAATTC
*
3552 TGTTTTGCATTTTTCAATT-AGTTTTTGAATTC
1 TGTTTTGCATTTTTCAATTCAGTTTTTCAATTC
3584 TGTTTTGCATTT
1 TGTTTTGCATTT
3596 AACTCACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 23 0.55
33 19 0.45
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.61
Consensus pattern (33 bp):
TGTTTTGCATTTTTCAATTCAGTTTTTCAATTC
Found at i:7891 original size:9 final size:9
Alignment explanation
Indices: 7853--7893 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
7843 TAAATTAAAA
7853 ATATATATT
1 ATATATATT
7862 ATA-A-ATT
1 ATATATATT
*
7869 ATATTTATT
1 ATATATATT
*
7878 TTATATATT
1 ATATATATT
7887 ATATATA
1 ATATATA
7894 ATTTCCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
7 6 0.23
8 1 0.04
9 19 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATATATT
Found at i:9174 original size:43 final size:42
Alignment explanation
Indices: 9126--9411 Score: 304
Period size: 41 Copynumber: 6.8 Consensus size: 42
9116 CCCAATAACT
* *
9126 AAAAGTCCCCAAACACATGTACAACACAGGA-GCACCTCTATTC
1 AAAAGTCCCCAAACACATTTATAACACAGGAGGCA--TCTATTC
* * *
9169 AAAAGTCCTCAAACACATTTATAACACA-GAGGCATCAATAC
1 AAAAGTCCCCAAACACATTTATAACACAGGAGGCATCTATTC
9210 AAAAGTCCCCAAACACATTTATAACACAGG-GGCACCTCTATTC
1 AAAAGTCCCCAAACACATTTATAACACAGGAGGCA--TCTATTC
* *
9253 CAAAGTCCTCAAACACATTTATAACACA-GAGGCATCTATATC
1 AAAAGTCCCCAAACACATTTATAACACAGGAGGCATCTAT-TC
*
9295 -AAAGTCCCCAAACACATTTATAACACAGG-GGCAATTCT-CTC
1 AAAAGTCCCCAAACACATTTATAACACAGGAGGC-A-TCTATTC
** *
9336 TAAAAGTCCTTAAACACATTTATAACACA-AAGGCATCTATATC
1 -AAAAGTCCCCAAACACATTTATAACACAGGAGGCATCTAT-TC
* *
9379 AAAA-TCCCCAAACACAATTATAACATAGG-GGCA
1 AAAAGTCCCCAAACACATTTATAACACAGGAGGCA
9412 AGTCACTCTA
Statistics
Matches: 207, Mismatches: 21, Indels: 32
0.80 0.08 0.12
Matches are distributed among these distances:
41 98 0.47
42 13 0.06
43 96 0.46
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (42 bp):
AAAAGTCCCCAAACACATTTATAACACAGGAGGCATCTATTC
Found at i:9214 original size:84 final size:85
Alignment explanation
Indices: 9126--9411 Score: 427
Period size: 84 Copynumber: 3.4 Consensus size: 85
9116 CCCAATAACT
* * *
9126 AAAAGTCCCCAAACACATGTACAACACAGGAGCACCTCTATTCAAAAGTCCTCAAACACATTTAT
1 AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCAAAAGTCCTCAAACACATTTAT
*
9191 AACACAGAGGCATCAATA-C
66 AACACAGAGGCATCTATATC
*
9210 AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTAT
1 AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCAAAAGTCCTCAAACACATTTAT
9275 AACACAGAGGCATCTATATC
66 AACACAGAGGCATCTATATC
** * *
9295 -AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCT-CTCTAAAAGTCCTTAAACACATTTA
1 AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTC-AAAAGTCCTCAAACACATTTA
*
9358 TAACACAAAGGCATCTATATC
65 TAACACAGAGGCATCTATATC
* *
9379 AAAA-TCCCCAAACACAATTATAACATAGGGGCA
1 AAAAGTCCCCAAACACATTTATAACACAGGGGCA
9412 AGTCACTCTA
Statistics
Matches: 186, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
83 2 0.01
84 180 0.97
85 4 0.02
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (85 bp):
AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCAAAAGTCCTCAAACACATTTAT
AACACAGAGGCATCTATATC
Found at i:9225 original size:41 final size:42
Alignment explanation
Indices: 9126--9403 Score: 300
Period size: 43 Copynumber: 6.6 Consensus size: 42
9116 CCCAATAACT
* * *
9126 AAAAGTCCCCAAACACATGTACAACACAG-GAGCACCTCTATTC
1 AAAAGTCCCCAAACACATTTATAACACAGAG-GCA-CTCTATAC
* *
9169 AAAAGTCCTCAAACACATTTATAACACAGAGGCA-TCAATAC
1 AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATAC
* *
9210 AAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTC
1 AAAAGTCCCCAAACACATTTATAACACAGAGGCA-CTCTATAC
* *
9253 CAAAGTCCTCAAACACATTTATAACACAGAGGCA-TCTATATC
1 AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATA-C
* * *
9295 -AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCT-C
1 AAAAGTCCCCAAACACATTTATAACACAGAGGC-ACTCTATAC
** *
9336 TAAAAGTCCTTAAACACATTTATAACACAAAGGCA-TCTATATC
1 -AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATA-C
*
9379 AAAA-TCCCCAAACACAATTATAACA
1 AAAAGTCCCCAAACACATTTATAACA
9404 TAGGGGCAAG
Statistics
Matches: 201, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
41 95 0.47
42 7 0.03
43 98 0.49
44 1 0.00
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.21
Consensus pattern (42 bp):
AAAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATAC
Found at i:12306 original size:72 final size:72
Alignment explanation
Indices: 12206--13337 Score: 1599
Period size: 72 Copynumber: 15.8 Consensus size: 72
12196 CCTCTTCTTC
* * * **
12206 ATTGCGATTGTAACCGAGGCAGTTCCCACATTTCGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
12271 CTCCCAT
66 CTTCCAT
* * * *
12278 ATTGCGGTTGTAGCCAAGGCAGTTCCCACATTTAGCAGTCCTTCGCACAATTCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
12343 CTTCCTT
66 CTTCCAT
* * * * **
12350 ATTGCGGTTGTAGCCGAGGCAGTTCCCAAATTTGGTAGTCTTTCACACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
12415 C-TCCTAT
66 CTTCC-AT
*
12422 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
12487 CTTCCTT
66 CTTCCAT
** * **
12494 ATTAAGGTTGTAGCCGAGGTAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
12559 CTTCCAT
66 CTTCCAT
* * *
12566 ATTACGGTTGTAGCCGAGGCAGTTCCCACATTTGGTAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
12631 CTTCCTT
66 CTTCCAT
* * *
12638 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAATCCTTCACACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
12703 CTTCCTT
66 CTTCCAT
* **
12710 TTTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
12775 CTTCCAT
66 CTTCCAT
* * * * *
12782 AATGCGGTTGTAGCCCAGACAGTTCTCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
12847 CTTCCTT
66 CTTCCAT
* * **
12854 ACTGCGGTTGTAGCCGAGGTAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
12919 CTTCTAT
66 CTTCCAT
** * *
12926 ATTGCGGTTGTAGCCGATACAGTTCCCACATTTGGTAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
12991 CTTCCAT
66 CTTCCAT
* ** **
12998 ATTGCGGTTGTAGCCGAGGCAGTTCTCACATTTGGCAGTGTTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
13063 CTTCCAT
66 CTTCCAT
13070 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTG-T-AT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
*
13133 CTTCCTT
66 CTTCCAT
* **
13140 ATTGCGGGTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
13205 CTTCCAT
66 CTTCCAT
* * *
13212 ATTGCGGTTGTAGCCGAGGAAGTTCCCACATTTGGCAGTCCTTCGCATAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
13277 CTTCC-T
66 CTTCCAT
* * * * * *
13283 CATAGCGATTATAGTCGAGGTAGTTCCCACA-TTGGTAGTCCTTCGCACAATCCTT
1 -ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
13338 GCTACTAATC
Statistics
Matches: 941, Mismatches: 114, Indels: 11
0.88 0.11 0.01
Matches are distributed among these distances:
70 65 0.07
71 28 0.03
72 845 0.90
73 3 0.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (72 bp):
ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATAAT
CTTCCAT
Found at i:14003 original size:16 final size:17
Alignment explanation
Indices: 13982--14021 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
13972 CTTGCCACAA
*
13982 CAGAATGTTACC-GCAG
1 CAGAATGTCACCTGCAG
*
13998 CAGAATGTCCCCTGCAG
1 CAGAATGTCACCTGCAG
14015 CAGAATG
1 CAGAATG
14022 ATAGCAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (17 bp):
CAGAATGTCACCTGCAG
Found at i:16694 original size:43 final size:41
Alignment explanation
Indices: 16646--16924 Score: 294
Period size: 41 Copynumber: 6.7 Consensus size: 41
16636 CCAATAACTG
*
16646 AAAGTCCCCAAACACATTTATAACATAGGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCA--TCTATTCC
* * * * *
16689 AAAGTCCTCAAACACATTTATAACACAGAGGCATCAATACA
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTATTCC
*
16730 AAAGTCCCCAAATACATTTATAACACAGGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCA--TCTATTCC
* * *
16773 AAACTCCTCAAACACATTTATAACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTAT-TCC
* *
16814 AAAGTGCCCAAACACATTTATAACACAGGGGCAATTCTA-TCTA
1 AAAGTCCCCAAACACATTTATAACACAGGGGC-A-TCTATTC-C
* **
16857 AAAGTCCTCAAACACATTTATAACACAAAGGCATCTATAT-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTAT-TCC
* * *
16898 AAAATCCCCGAACACAATTATAACACA
1 AAAGTCCCCAAACACATTTATAACACA
16925 TGGGTAATTC
Statistics
Matches: 197, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
41 97 0.49
42 3 0.02
43 97 0.49
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (41 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCATCTATTCC
Found at i:16736 original size:84 final size:85
Alignment explanation
Indices: 16646--16924 Score: 422
Period size: 84 Copynumber: 3.3 Consensus size: 85
16636 CCAATAACTG
*
16646 AAAGTCCCCAAACACATTTATAACATAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
*
16711 ACACAGAGGCATCAATA-CA
66 ACACAGAGGCATCTATATCA
* *
16730 AAAGTCCCCAAATACATTTATAACACAGGGGCACCTCTATTCCAAACTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
16795 ACACAGAGGCATCTATATC-
66 ACACAGAGGCATCTATATCA
* ** *
16814 AAAGTGCCCAAACACATTTATAACACAGGGGCAATTCTA-TCTAAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTC-CAAAGTCCTCAAACACATTTAT
*
16878 AACACAAAGGCATCTATATCA
65 AACACAGAGGCATCTATATCA
* *
16899 AAA-TCCCCGAACACAATTATAACACA
1 AAAGTCCCCAAACACATTTATAACACA
16925 TGGGTAATTC
Statistics
Matches: 178, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
83 2 0.01
84 172 0.97
85 4 0.02
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (85 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
ACACAGAGGCATCTATATCA
Found at i:16747 original size:41 final size:42
Alignment explanation
Indices: 16646--16924 Score: 291
Period size: 43 Copynumber: 6.6 Consensus size: 42
16636 CCAATAACTG
* * * *
16646 AAAGTCCCCAAACACATTTATAACATAGGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGAGGCA-CTCTATACA
* *
16689 AAAGTCCTCAAACACATTTATAACACAGAGGCA-TCAATACA
1 AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATACA
* * * *
16730 AAAGTCCCCAAATACATTTATAACACAGGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGAGGCA-CTCTATACA
* *
16773 AAACTCCTCAAACACATTTATAACACAGAGGCA-TCTATATC-
1 AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATA-CA
* * *
16814 AAAGTGCCCAAACACATTTATAACACAGGGGCAATTCTAT-CTA
1 AAAGTCCCCAAACACATTTATAACACAGAGGC-ACTCTATAC-A
* *
16857 AAAGTCCTCAAACACATTTATAACACAAAGGCA-TCTATATCA
1 AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATA-CA
* *
16899 AAA-TCCCCGAACACAATTATAACACA
1 AAAGTCCCCAAACACATTTATAACACA
16925 TGGGTAATTC
Statistics
Matches: 199, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
41 94 0.47
42 7 0.04
43 98 0.49
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (42 bp):
AAAGTCCCCAAACACATTTATAACACAGAGGCACTCTATACA
Found at i:21229 original size:10 final size:9
Alignment explanation
Indices: 21205--21262 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
21195 ATTTCTTACC
*
21205 CTTATCTTT
1 CTTATTTTT
21214 -TTATTTTT
1 CTTATTTTT
21222 CGTTATTTTT
1 C-TTATTTTT
21232 CTT-TTTCTT
1 CTTATTT-TT
21241 -TTATTTTT
1 CTTATTTTT
*
21249 GTTTATTTTT
1 -CTTATTTTT
21259 CTTA
1 CTTA
21263 GTTACTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (9 bp):
CTTATTTTT
Found at i:21236 original size:16 final size:17
Alignment explanation
Indices: 21211--21248 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21201 TACCCTTATC
21211 TTTTTATTTTTC-GTTA
1 TTTTTATTTTTCTGTTA
* *
21227 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTGTTA
21244 TTTTT
1 TTTTT
21249 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTCTGTTA
Found at i:21836 original size:36 final size:37
Alignment explanation
Indices: 21778--21853 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 37
21768 TTTACCCTTA
21778 TGGATCATGCAAAGGATTGGTTGTACTACATGCCTAG
1 TGGATCATGCAAAGGATTGGTTGTACTACATGCCTAG
21815 TGGATCATGC-AAGGATTGGTTGTACTACATGCCTAG
1 TGGATCATGCAAAGGATTGGTTGTACTACATGCCTAG
21851 TGG
1 TGG
21854 TTCAATCACA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
36 29 0.74
37 10 0.26
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (37 bp):
TGGATCATGCAAAGGATTGGTTGTACTACATGCCTAG
Found at i:23757 original size:22 final size:21
Alignment explanation
Indices: 23705--23758 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
23695 TGCTTCTTGA
23705 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
23726 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
23745 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
23759 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:24635 original size:20 final size:20
Alignment explanation
Indices: 24599--24636 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
24589 TCCTCTTGTC
*
24599 ATGAAAACACTTCTTTTTTT
1 ATGAAAACACATCTTTTTTT
24619 ATGAAAACAACAT-TTTTT
1 ATGAAAAC-ACATCTTTTT
24637 AATTACCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
ATGAAAACACATCTTTTTTT
Found at i:24949 original size:29 final size:28
Alignment explanation
Indices: 24857--24950 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 28
24847 TAGGTCATTT
* *
24857 AGGGGGATTTTGGTCATTTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCACAT-C
** *
24886 AGGGGCATTTTAATCATTTTTACAC-T-
1 AGGGGCATTTTGGTCATTTTTGCACATC
* *
24912 AAGGGCATTTTGGTCATTTTGGCACATC
1 AGGGGCATTTTGGTCATTTTTGCACATC
24940 AGGGGGCATTT
1 A-GGGGCATTT
24951 GAGTCAATTC
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
26 20 0.39
27 1 0.02
28 2 0.04
29 28 0.55
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTGCACATC
Done.