Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022101.1 Corchorus olitorius cultivar O-4 contig22134, 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: 32318
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2510 original size:492 final size:488
Alignment explanation
Indices: 1498--2409 Score: 1110
Period size: 492 Copynumber: 1.8 Consensus size: 488
1488 TAATGGAAAT
* ** * ** * *
1498 TTAGATTATCCTCATTAATTAGAATCCAACGTGGCCAATAGGGATGCCCCACATCATCTTTAGCA
1 TTAGATTATCTTCACGAATTAG-ATCTAACGTGATCAATAGGAATGCCCCACATCATCTGTAGCA
* * *
1563 TCTGAATTTTCGTCCAAAACAGTCTCCAAGTCGGTTTAGGAGAAGATCAATTTTGTCCAGAAATT
65 TCTGAATTTTCGTCCAAAACAGTCTCCAAGTCGGTTTAGGAGAAGATCAATTCTATCCAGAAACT
* * * * *
1628 TCAAGGGCAAAATCGTCCACCGAAACAGCAGAATTAGGTCTTGAGATAAACATAAAAGTTGTAAA
130 TCAAGGGAAAAATCGTCCAACGAAACAGAAGAATTAGGCCTCGAGATAAACATAAAAGTTGTAAA
* * *
1693 TCTCAAAATCCTCTTTCCAATGGTAACTCATTTGAATTTTTCTTAGTTCTAGTTCAAAAGTTATG
195 TATCAAAATCCTCTTTCCAATGGTAACTCATTTGAATTTTTCTGAG-TCTAGATCAAAAGTTATG
* * * * * *
1758 AATTCCAAAACTGCTCTTGTAAAGTTCTCCTTTAAATAGGATTTAACAATGTTGTATCATGCCTG
259 AATTCCAAAACTGCTCTTATAAACTCCTCATTTAAATAGGATTTAACAATGTTGCATCAGGCCTG
* *
1823 AATCATTACTACATCATAATTACTGATTGGACTTGGAGTCCTTTTTTGGGCTTCCATATTAACGA
324 AATCATTACTACATCATAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTTCCATATTAACGA
*
1888 ATTGGGCCTAAAAATATCAGAGTTAGACTTCAATGGCTTAACATTCTAAATTGCCATTATTAAAA
389 ATTGGGCCTAAAAATATCAGAGTTAGACTTCAATGACTTAACATTCTAAATTGCCATTATTAAAA
* *** * *** * * *
1953 AATATTTTAATTATTTCATTATTAAAATAATGAAAA
454 AAGAGCCTAACTAGGCCATAATGAAAAAAAT-AAAA
** *
1989 TTTAGATTATCTTCATTAATTAGGATCTAACGTGATCAATAGGAATGCTCCACATCATCTGTAGC
1 -TTAGATTATCTTCACGAATTA-GATCTAACGTGATCAATAGGAATGCCCCACATCATCTGTAGC
* * *
2054 ATCTGAATTTTCGTCCAAAACATTCTTCAAGTCGGTTTAGGGGAAGATCAATTCTATCCAGAAAC
64 ATCTGAATTTTCGTCCAAAACAGTCTCCAAGTCGGTTTAGGAGAAGATCAATTCTATCCAGAAAC
* * * *
2119 TTCAAGGGAAAAAT-GATCTAACTAAACGGAAGAATTAGGCCTCGAGGTAAACATAAAAGTTGTA
129 TTCAAGGGAAAAATCG-TCCAACGAAACAGAAGAATTAGGCCTCGAGATAAACATAAAAGTTGTA
** *** * *
2183 GGTATTGGAATCCTCTTTCCAATGGTATCTCATTTGCATTTTTCTGAG-CTATGATCAAAAGTTA
193 AATATCAAAATCCTCTTTCCAATGGTAACTCATTTGAATTTTTCTGAGTCTA-GATCAAAAGTTA
*
2247 TGAATTTTCTTCCAAAACTGCTCTTATGAACTCCTCATTTAAATAGGATTTAACAATGTTGCATC
257 TGAA-----TTCCAAAACTGCTCTTATAAACTCCTCATTTAAATAGGATTTAACAATGTTGCATC
** * * * *
2312 AGGGTTGAATCATTACTGCATCATAATTACTGATTGGACTTGGACTCCTTCTTTGGGTTTCTATG
317 AGGCCTGAATCATTACTACATCATAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTTCCATA
*
2377 TTAACGAATTAGGG-CTAAAAATATCAGATTTAG
382 TTAACGAATT-GGGCCTAAAAATATCAGAGTTAG
2410 GATTCAAGAC
Statistics
Matches: 363, Mismatches: 48, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
490 3 0.01
491 16 0.04
492 206 0.57
493 1 0.00
496 134 0.37
497 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (488 bp):
TTAGATTATCTTCACGAATTAGATCTAACGTGATCAATAGGAATGCCCCACATCATCTGTAGCAT
CTGAATTTTCGTCCAAAACAGTCTCCAAGTCGGTTTAGGAGAAGATCAATTCTATCCAGAAACTT
CAAGGGAAAAATCGTCCAACGAAACAGAAGAATTAGGCCTCGAGATAAACATAAAAGTTGTAAAT
ATCAAAATCCTCTTTCCAATGGTAACTCATTTGAATTTTTCTGAGTCTAGATCAAAAGTTATGAA
TTCCAAAACTGCTCTTATAAACTCCTCATTTAAATAGGATTTAACAATGTTGCATCAGGCCTGAA
TCATTACTACATCATAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTTCCATATTAACGAAT
TGGGCCTAAAAATATCAGAGTTAGACTTCAATGACTTAACATTCTAAATTGCCATTATTAAAAAA
GAGCCTAACTAGGCCATAATGAAAAAAATAAAA
Found at i:3072 original size:22 final size:23
Alignment explanation
Indices: 3027--3132 Score: 98
Period size: 22 Copynumber: 4.9 Consensus size: 23
3017 TACTTTTGGA
*
3027 GGTTA-TCAAAA-TTCATTGTGT
1 GGTTACTCAAAATTTCATAGTGT
*
3048 GGTTACT-AAAATTTTATAGTGT
1 GGTTACTCAAAATTTCATAGTGT
* *
3070 GGTT-CTCAAAATTTCATACTCT
1 GGTTACTCAAAATTTCATAGTGT
* *
3092 GGTTA-TCAAAATTTCATAGGGA
1 GGTTACTCAAAATTTCATAGTGT
* *
3114 AGTTA-ACAAAATTTCATAG
1 GGTTACTCAAAATTTCATAG
3133 GGCAATTGTC
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
21 11 0.16
22 59 0.84
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (23 bp):
GGTTACTCAAAATTTCATAGTGT
Found at i:3133 original size:22 final size:22
Alignment explanation
Indices: 3093--3197 Score: 117
Period size: 22 Copynumber: 4.8 Consensus size: 22
3083 TCATACTCTG
3093 GTTATCAAAATTTCATAGGGAA
1 GTTATCAAAATTTCATAGGGAA
*
3115 GTTAACAAAATTTCATAGGGCAA
1 GTTATCAAAATTTCATAGGG-AA
* * * * *
3138 -TTGTCGAAATTTTATATGGAG
1 GTTATCAAAATTTCATAGGGAA
3159 GTTATCAAAATTTCATA--GAA
1 GTTATCAAAATTTCATAGGGAA
3179 GATTATCAAAATTTCATAG
1 G-TTATCAAAATTTCATAG
3198 TGTGCTTATA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 3 0.04
21 17 0.25
22 46 0.68
23 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAA
Found at i:3285 original size:22 final size:22
Alignment explanation
Indices: 3237--3316 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
3227 GAGTGAGCTT
** *
3237 ATCAAAATTTCA-AGTGTCGTT
1 ATCAAAATTTCATAGTGTAATA
*
3258 ACCAAAATTTCATAGTGTAATA
1 ATCAAAATTTCATAGTGTAATA
*
3280 ATCAAAATTTCATAGAGGTTAATTA
1 ATCAAAATTTCATAG-TG-TAA-TA
3305 A-CAAAATTTCAT
1 ATCAAAATTTCAT
3317 GCGGAGGTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
21 11 0.22
22 20 0.41
23 1 0.02
24 14 0.29
25 3 0.06
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGTAATA
Found at i:3309 original size:24 final size:22
Alignment explanation
Indices: 3260--3316 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
3250 GTGTCGTTAC
*
3260 CAAAATTTCATAGTGTAATAAT
1 CAAAATTTCATAGGGTAATAAT
3282 CAAAATTTCATAGAGGTTAATTAA-
1 CAAAATTTCATAG-GG-TAA-TAAT
3306 CAAAATTTCAT
1 CAAAATTTCAT
3317 GCGGAGGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 13 0.42
23 1 0.03
24 14 0.45
25 3 0.10
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGGTAATAAT
Found at i:3344 original size:22 final size:22
Alignment explanation
Indices: 3319--3381 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
3309 AATTTCATGC
*
3319 GGAGGTTATCGAAATTTTAGAG
1 GGAGGTTATCAAAATTTTAGAG
* * *
3341 GGAGATTATCAAAATTTCATAG
1 GGAGGTTATCAAAATTTTAGAG
* *
3363 TGTGGTTATCAAAATTTTA
1 GGAGGTTATCAAAATTTTA
3382 TAATATGTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTTAGAG
Found at i:3370 original size:44 final size:44
Alignment explanation
Indices: 3260--3381 Score: 122
Period size: 44 Copynumber: 2.7 Consensus size: 44
3250 GTGTCGTTAC
** * *
3260 CAAAATTTCATAGTGTAATAATCAAAATTTCATAGAGGTTAATTAA
1 CAAAATTTCATAGTGTGGTTATCAAAATTT--TAGAGGTGAATTAA
* * * *
3306 CAAAATTTCAT-GCGGAGGTTATCGAAATTTTAGAGG-GAGATTAT
1 CAAAATTTCATAG-TGTGGTTATCAAAATTTTAGAGGTGA-ATTAA
3350 CAAAATTTCATAGTGTGGTTATCAAAATTTTA
1 CAAAATTTCATAGTGTGGTTATCAAAATTTTA
3382 TAATATGTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
43 1 0.02
44 37 0.60
45 2 0.03
46 22 0.35
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAGTGTGGTTATCAAAATTTTAGAGGTGAATTAA
Found at i:3478 original size:21 final size:22
Alignment explanation
Indices: 3433--3487 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
3423 TGTGGTAACT
* * *
3433 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAGTGAGATTAGC
3455 AAAATTT-ATAGTGAGATTAGC
1 AAAATTTCATAGTGAGATTAGC
*
3476 AAAATTTGATAG
1 AAAATTTCATAG
3488 AGTGGTTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTAGC
Found at i:6018 original size:19 final size:20
Alignment explanation
Indices: 5982--6019 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5972 TTACTATTAT
5982 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
6002 TTTT-AATTTCAAT-TTTTA
1 TTTTGAATTT-AATATTTTA
6020 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:6213 original size:22 final size:22
Alignment explanation
Indices: 6185--6417 Score: 120
Period size: 22 Copynumber: 10.5 Consensus size: 22
6175 TGTCTCTGTG
6185 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
6207 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
6230 -AGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
6251 TGGTTAACAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
6274 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
*
6295 AGGTTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* * *
6315 TGTACTTACCAAAATTTCATAGGA
1 TG--GTTATCAAAATTTCATAAGA
* * * *
6339 TCAAGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* **
6363 AGGTTATTGAAATTTCAT-AGAA
1 TGGTTATCAAAATTTCATAAG-A
* *
6385 TGGTTATCACAATTTTATATA-A
1 TGGTTATCAAAATTTCATA-AGA
*
6407 AGGTTATCAAA
1 TGGTTATCAAA
6418 GAGATTATCA
Statistics
Matches: 158, Mismatches: 38, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.01
21 5 0.03
22 128 0.81
23 4 0.03
24 19 0.12
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:6255 original size:44 final size:44
Alignment explanation
Indices: 6187--6335 Score: 151
Period size: 44 Copynumber: 3.4 Consensus size: 44
6177 TCTCTGTGTG
** *
6187 GTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGAA
1 GTTATCAAAATTTCATAAGATGGTTAACAAAATTTCAT-ATGGAA
*
6231 GTTATCAAAATTTCAT-AGTGTGGTTAACAAAATTTCATATGGAA
1 GTTATCAAAATTTCATAAG-ATGGTTAACAAAATTTCATATGGAA
** * * *
6275 GTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATA-GTGTA
1 GTTATCAAAATTTCATAAGATGGTTAACAAAATTTCATATG-GAA
* *
6319 CTTACCAAAATTTCATA
1 GTTATCAAAATTTCATA
6336 GGATCAAGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
43 4 0.04
44 84 0.94
45 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (44 bp):
GTTATCAAAATTTCATAAGATGGTTAACAAAATTTCATATGGAA
Found at i:6265 original size:66 final size:67
Alignment explanation
Indices: 6182--6568 Score: 281
Period size: 66 Copynumber: 5.6 Consensus size: 67
6172 TCTTGTCTCT
* * * *
6182 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAA-GTTATCAAAATTTCA
1 GTGTGGTTAACAAAATTTCATAGGATAGTTATTAAAATTTCATGAGGAAGGTTATCAAAATTTCA
6246 TA
66 TA
*
6248 GTGTGGTTAACAAAATTTCATATGGA-AGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTC
1 GTGTGGTTAACAAAATTTCATA-GGATAGTTATTAAAATTTCATGAGGAAGGTTATCAAAATTTC
6311 ATA
65 ATA
** * * **
6314 GTGTACTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTT
1 GTGTGGTTAACAAAATTTCATAGGAT--AGTTATTAAAATTTCATGAGGAAGGTTATCAAAATTT
6378 CATA
64 CATA
** * * * * * *
6382 GAATGGTTATCACAATTTTATATAAAGGTTATCAAAGAGATTATCAAAATGTCAT-AGCG-AGAT
1 GTGTGGTTAACA-AAATTT-CAT--AGG--AT-----AG-TTATTAAAATTTCATGAG-GAAGGT
6445 TAT-AAGAATTTCATA
53 TATCAA-AATTTCATA
* * * * * *
6460 GTGTGGTTAACGAAATTTCATAAGGA-GGTTACTAATATTTCATGAGG-AGGTTATCACACTTTC
1 GTGTGGTTAACAAAATTTCAT-AGGATAGTTATTAAAATTTCATGAGGAAGGTTATCAAAATTTC
6523 ATA
65 ATA
* * *
6526 GTGTGGTTATCAAAATTTCTTAGTG-TAGTTATCAAAATTTCAT
1 GTGTGGTTAACAAAATTTCATAG-GATAGTTATTAAAATTTCAT
6569 TCGAAGGTTA
Statistics
Matches: 252, Mismatches: 46, Indels: 46
0.73 0.13 0.13
Matches are distributed among these distances:
65 9 0.04
66 130 0.52
67 7 0.03
68 41 0.16
69 5 0.02
70 2 0.01
72 3 0.01
73 1 0.00
74 2 0.01
75 4 0.02
76 2 0.01
77 8 0.03
78 36 0.14
79 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (67 bp):
GTGTGGTTAACAAAATTTCATAGGATAGTTATTAAAATTTCATGAGGAAGGTTATCAAAATTTCA
TA
Found at i:6361 original size:24 final size:22
Alignment explanation
Indices: 6187--6382 Score: 121
Period size: 22 Copynumber: 8.8 Consensus size: 22
6177 TCTCTGTGTG
* * **
6187 GTTATCAAAATTTCATAAGATG
1 GTTATTAAAATTTCATAGGAAA
*
6209 GTTATTATAATTTCATGAGG-AA
1 GTTATTAAAATTTCAT-AGGAAA
* **
6231 GTTATCAAAATTTCATAGTG-TG
1 GTTATTAAAATTTCATAG-GAAA
**
6253 GTTAACAAAATTTCATATGG-AA
1 GTTATTAAAATTTCATA-GGAAA
* * *
6275 GTTATCAAAATTTCATGGGAAG
1 GTTATTAAAATTTCATAGGAAA
* *
6297 GTTATCAAAATTTCATAGTG-TA
1 GTTATTAAAATTTCATAG-GAAA
* **
6319 CTTACCAAAATTTCATAGGATCAA
1 GTTATTAAAATTTCATAGGA--AA
* *
6343 GTTATTAAAATTTCTTAGGAAG
1 GTTATTAAAATTTCATAGGAAA
*
6365 GTTATTGAAATTTCATAG
1 GTTATTAAAATTTCATAG
6383 AATGGTTATC
Statistics
Matches: 138, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
21 5 0.04
22 112 0.81
23 4 0.03
24 17 0.12
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTATTAAAATTTCATAGGAAA
Found at i:6476 original size:22 final size:22
Alignment explanation
Indices: 6422--6840 Score: 162
Period size: 22 Copynumber: 18.8 Consensus size: 22
6412 ATCAAAGAGA
* * * *
6422 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATAGTGTGG
6444 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGTGG
* * *
6466 TTAACGAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGTGG
* *
6488 TTA-CTAATATTTCATGAG-GAGG
1 TTATC-AAAATTTCAT-AGTGTGG
* *
6510 TTATCACACTTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *
6532 TTATCAAAATTTCTTAGTGTAG
1 TTATCAAAATTTCATAGTGTGG
*
6554 TTATCAAAATTTCAT--TCGAAGG
1 TTATCAAAATTTCATAGT-G-TGG
* *
6576 TTATAAAAGTCTCAATTTCATA-AG-GAG
1 TTAT-CAA-----AATTTCATAGTGTG-G
* * **
6603 -TACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
6623 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGTGG
* *
6644 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTG-T-GG
*
6668 ATTATCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGTGTGG
* * *
6691 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
6713 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGTGG
*
6735 TTAAT-AAAATTTCATAGAG-GG
1 TT-ATCAAAATTTCATAGTGTGG
* * * * *
6756 ATCAACAAAATTTTATAGAGAGG
1 -TTATCAAAATTTCATAGTGTGG
** * *
6779 TTATCAAAATTTCATAAAGAGA
1 TTATCAAAATTTCATAGTGTGG
* * * *
6801 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGTGG
*
6823 TTACCAAAATTTCATAGT
1 TTATCAAAATTTCATAGT
6841 AGTATTTCTG
Statistics
Matches: 301, Mismatches: 68, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
20 19 0.06
21 18 0.06
22 218 0.72
23 12 0.04
24 2 0.01
25 19 0.06
26 3 0.01
27 1 0.00
28 9 0.03
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:7010 original size:22 final size:20
Alignment explanation
Indices: 6985--7183 Score: 109
Period size: 22 Copynumber: 9.2 Consensus size: 20
6975 AGTTTAATTT
6985 TCAAAATTTCATTAGAGGTTTA
1 TCAAAATTTCA-TAGAGG-TTA
* *
7007 TCAAAATTTCATAGTATGTAGA
1 TCAAAATTTCATAG-AGGT-TA
*
7029 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATA--GAGGTTA
*
7051 ACAAAATTTCATAATGAGGTTA
1 TCAAAATTTCAT-A-GAGGTTA
**
7073 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATA--GAGGTTA
*
7095 TCAAAATTT-GT--A-GTTA
1 TCAAAATTTCATAGAGGTTA
* *
7111 TCAAGATTTCATAAGGAAGTTA
1 TCAAAATTTCAT-A-GAGGTTA
*
7133 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA--GAGG-TTA
*
7156 TCAAAATTTTATAGGAAGGTTTA
1 TCAAAATTTCATA-G-AGG-TTA
7179 TCAAA
1 TCAAA
7184 TTATTACAAT
Statistics
Matches: 142, Mismatches: 20, Indels: 29
0.74 0.10 0.15
Matches are distributed among these distances:
16 12 0.08
17 2 0.01
21 8 0.06
22 88 0.62
23 31 0.22
24 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.35
Consensus pattern (20 bp):
TCAAAATTTCATAGAGGTTA
Found at i:7076 original size:44 final size:44
Alignment explanation
Indices: 6985--7103 Score: 125
Period size: 44 Copynumber: 2.7 Consensus size: 44
6975 AGTTTAATTT
* * * *
6985 TCAAAATTTCATTAGAG-GTTTATCAAAATTTCATAGTATGTAGA
1 TCAAAATTTCA-TAGGGAGATTATCAAAATTTCATAATAGGTAGA
* *
7029 TCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT-TA
1 TCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT-AGGTAGA
** *
7073 TCAAAAAATCATAGGGAGGTTATCAAAATTT
1 TCAAAATTTCATAGGGAGATTATCAAAATTT
7104 GTAGTTATCA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 4 0.06
44 56 0.89
45 3 0.05
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (44 bp):
TCAAAATTTCATAGGGAGATTATCAAAATTTCATAATAGGTAGA
Found at i:7158 original size:23 final size:23
Alignment explanation
Indices: 7108--7183 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
7098 AAATTTGTAG
* * * *
7108 TTATCAAGATTTCATAAGGAAG-
1 TTATCAAAATTTTATAGGGAGGT
7130 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
7153 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
7176 TTATCAAA
1 TTATCAAA
7184 TTATTACAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 18 0.38
23 30 0.62
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:8928 original size:23 final size:22
Alignment explanation
Indices: 8913--8968 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
8903 CATAGTGTTG
* *
8913 GTTATCAAAATTTCATTGAGAA
1 GTTATCAAAATTTCATAGTGAA
*
8935 GTTATCAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATAGTGAA
8957 GTCT-TCAAAATT
1 GT-TATCAAAATT
8969 CCTTTGGGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAA
Found at i:9078 original size:22 final size:22
Alignment explanation
Indices: 9019--9081 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
9009 AATGTATAAA
* * *
9019 AAGGTTCTCGAAATTCCATAGT
1 AAGGTTATCGAAATTTCATAGG
** *
9041 ATCGTTAT-TAAATTTCATAGG
1 AAGGTTATCGAAATTTCATAGG
9062 AAGGTTATCGAAATTTCATA
1 AAGGTTATCGAAATTTCATA
9082 AGGAGGTCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (22 bp):
AAGGTTATCGAAATTTCATAGG
Found at i:9098 original size:23 final size:22
Alignment explanation
Indices: 9050--9096 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
9040 TATCGTTATT
* *
9050 AAATTTCATAGGAAGGTTATCG
1 AAATTTCATAGGAAGGTCATCA
9072 AAATTTCATAAGG-AGGTCATCA
1 AAATTTCAT-AGGAAGGTCATCA
9094 AAA
1 AAA
9097 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (22 bp):
AAATTTCATAGGAAGGTCATCA
Found at i:12085 original size:48 final size:49
Alignment explanation
Indices: 12030--12132 Score: 129
Period size: 49 Copynumber: 2.1 Consensus size: 49
12020 AATTTTGTAC
* * * *
12030 AAAAATTGATAAAAAG-AGCAATG-AAAAGTAAATATTCAATTTTGTCTT
1 AAAAATTGAGAAAAAGTAGCAA-GAAAAAATAAAGATTCAATTTTGTCGT
* *
12078 AAAAATTGAGAAAAAGTTGCAAGAAAAAATAAAGATTTAATTTTGTCGT
1 AAAAATTGAGAAAAAGTAGCAAGAAAAAATAAAGATTCAATTTTGTCGT
12127 AAAAAT
1 AAAAAT
12133 CTTACTACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 16 0.34
49 31 0.66
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (49 bp):
AAAAATTGAGAAAAAGTAGCAAGAAAAAATAAAGATTCAATTTTGTCGT
Found at i:12294 original size:43 final size:41
Alignment explanation
Indices: 12247--12357 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 41
12237 TCATTCAACT
12247 TTTTTTATTAATTATGGAAAGATATTGTAAATCCAATAT-TTAA
1 TTTTTTATTAATTATGGAAAGATATTGTAAAT-C--TATCTTAA
* * *
12290 TTTTTTA-AAATTATGAAAAGATATTTTAAATCTATCTTAA
1 TTTTTTATTAATTATGGAAAGATATTGTAAATCTATCTTAA
* *
12330 TTTTATTTTTGAATTATGGAAATATATT
1 TTTT-TTATT-AATTATGGAAAGATATT
12358 TTTAAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 3 0.05
40 8 0.14
41 3 0.05
42 21 0.37
43 22 0.39
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.50
Consensus pattern (41 bp):
TTTTTTATTAATTATGGAAAGATATTGTAAATCTATCTTAA
Found at i:13284 original size:20 final size:20
Alignment explanation
Indices: 13231--13285 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
13221 GTTGAATTTG
* **
13231 TTAATACCATTATAACTTTT
1 TTAATAACATTATAACTTCC
*
13251 TTGATAATCATTATAACTTCC
1 TTAATAA-CATTATAACTTCC
13272 TTAATAACATTATA
1 TTAATAACATTATA
13286 TTAAAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAATAACATTATAACTTCC
Found at i:14297 original size:30 final size:30
Alignment explanation
Indices: 14258--14342 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
14248 TAGTAGGGCC
* * *
14258 AATACTATAAAATTTTGATTTTA-ATGGGGTT
1 AATA-TATAAAACTTTCATTTTAGA-AGGGTT
14289 AATATATAAAACTTTCATTTTAGAAGGGTT
1 AATATATAAAACTTTCATTTTAGAAGGGTT
*
14319 AATATTGTAAAAC-TTCAATTTTAG
1 AATA-TATAAAACTTTC-ATTTTAG
14343 TGGAGTCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 28 0.60
31 19 0.40
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (30 bp):
AATATATAAAACTTTCATTTTAGAAGGGTT
Found at i:14333 original size:31 final size:30
Alignment explanation
Indices: 14284--14342 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
14274 GATTTTAATG
14284 GGGTTAATATATAAAACTTTC-ATTTTAGAA
1 GGGTTAATATATAAAAC-TTCAATTTTAGAA
*
14314 GGGTTAATATTGTAAAACTTCAATTTTAG
1 GGGTTAATA-TATAAAACTTCAATTTTAG
14343 TGGAGTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (30 bp):
GGGTTAATATATAAAACTTCAATTTTAGAA
Found at i:14976 original size:22 final size:22
Alignment explanation
Indices: 14951--15067 Score: 73
Period size: 22 Copynumber: 5.3 Consensus size: 22
14941 ACAATCAAAC
14951 CAAAATTACATAGGAAGGTTAT
1 CAAAATTACATAGGAAGGTTAT
* * *
14973 CAAAATTTA-GTAGTG-TGGTTAC
1 CAAAA-TTACATAG-GAAGGTTAT
*
14995 CAAAATTTCATATGG-AGGTTAT
1 CAAAATTACATA-GGAAGGTTAT
*
15017 CAAAACTT-CATAGTATA-GTTAT
1 CAAAA-TTACATAGGA-AGGTTAT
** **
15039 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTACATAGGAAGGTTAT
15061 CAAAATT
1 CAAAATT
15068 TCTTAGACTC
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
21 6 0.08
22 61 0.81
23 8 0.11
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAATTACATAGGAAGGTTAT
Found at i:15014 original size:44 final size:42
Alignment explanation
Indices: 14949--15068 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 42
14939 TGACAATCAA
* * *
14949 ACCAAAATTACATAGGAAGGTTATCAAAATTTAGTAGTGTGGTT
1 ACCAAAATTTCATAGG-AGGTTATCAAAATTTA-TAGTATAGTT
*
14993 ACCAAAATTTCATATGGAGGTTATCAAAACTTCATAGTATAGTT
1 ACCAAAATTTCATA-GGAGGTTATCAAAA-TTTATAGTATAGTT
* * **
15037 ATCAAAATTTTATAAAAAGGTTATCAAAATTT
1 ACCAAAATTTCAT-AGGAGGTTATCAAAATTT
15069 CTTAGACTCC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 2 0.03
44 56 0.88
45 6 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (42 bp):
ACCAAAATTTCATAGGAGGTTATCAAAATTTATAGTATAGTT
Found at i:15434 original size:22 final size:22
Alignment explanation
Indices: 15391--15487 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
15381 ATATTCGTGC
*
15391 TTATCAAAATTTCCT--GGAGG
1 TTATCAAAATTTCATAGGGAGG
*
15411 TTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
15433 TTATGAAAATTTCAT-GGAGAAG
1 TTATCAAAATTTCATAGG-GAGG
* *
15455 TTATCAAAATTACATAGAGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
15477 ATATCACAATT
1 TTATCAAAATT
15488 CACAATTTCA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 13 0.21
21 2 0.03
22 46 0.74
23 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:15443 original size:42 final size:43
Alignment explanation
Indices: 15391--15487 Score: 115
Period size: 44 Copynumber: 2.3 Consensus size: 43
15381 ATATTCGTGC
* * *
15391 TTATCAAAATTTCCTGGAG-GTTAACAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATGGAGAGTTAACAAAATTACATAGAGAGG
* *
15433 TTATGAAAATTTCATGGAGAAGTTATCAAAATTACATAGAGAGG
1 TTATCAAAATTTCATGGAG-AGTTAACAAAATTACATAGAGAGG
* *
15477 ATATCACAATT
1 TTATCAAAATT
15488 CACAATTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
42 17 0.38
44 28 0.62
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (43 bp):
TTATCAAAATTTCATGGAGAGTTAACAAAATTACATAGAGAGG
Found at i:15599 original size:22 final size:22
Alignment explanation
Indices: 15576--15783 Score: 226
Period size: 22 Copynumber: 9.6 Consensus size: 22
15566 TATAATTTGA
* *
15576 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGAGG
* *
15598 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
15620 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGAGG
* *
15642 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
15664 TTATCAAAATTT-ATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
15685 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
15707 TTATCAAACTTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
*
15729 TTATCAAAA-TTCTATAATGAGG
1 TTATCAAAATTTC-ATAGTGAGG
* *
15751 TTATCAAATTTTCA-A-TGTGG
1 TTATCAAAATTTCATAGTGAGG
*
15771 TTATCAATATTTC
1 TTATCAAAATTTC
15784 TACGTTGGAG
Statistics
Matches: 156, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.10
21 22 0.14
22 116 0.74
23 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:15626 original size:44 final size:44
Alignment explanation
Indices: 15576--15764 Score: 265
Period size: 44 Copynumber: 4.3 Consensus size: 44
15566 TATAATTTGA
15576 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
15620 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
* * * * *
15664 TTATCAAAATTT-ATAGTGTGGTTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
* * * *
15707 TTATCAAACTTTCATAGGGAGGTTATCAAAA-TTCTATAATGAGG
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTC-ACACTGAGG
*
15751 TTATCAAATTTTCA
1 TTATCAAAATTTCA
15765 ATGTGGTTAT
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
43 40 0.31
44 91 0.69
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
Found at i:15709 original size:87 final size:87
Alignment explanation
Indices: 15576--15783 Score: 269
Period size: 87 Copynumber: 2.4 Consensus size: 87
15566 TATAATTTGA
* * *
15576 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGGTTATCAAAATTTCATAGGGAG
1 TTATCAAAATTT-ATAGTGTGGTTATCAAAATTTCACACTGAGGTTATCAAAATTTCATAGGGAG
*
15641 ATTATCAAAATT-TCACACTGAGG
65 ATTATCAAAATTCT-ACAATGAGG
* * * *
15664 TTATCAAAATTTATAGTGTGGTTATCAAAATTTCACAGTGTGGTTATCAAACTTTCATAGGGAGG
1 TTATCAAAATTTATAGTGTGGTTATCAAAATTTCACACTGAGGTTATCAAAATTTCATAGGGAGA
*
15729 TTATCAAAATTCTATAATGAGG
66 TTATCAAAATTCTACAATGAGG
* *
15751 TTATC-AAATTT-TCAATGTGGTTATCAATATTTC
1 TTATCAAAATTTAT-AGTGTGGTTATCAAAATTTC
15784 TACGTTGGAG
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
85 1 0.01
86 24 0.22
87 69 0.64
88 13 0.12
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (87 bp):
TTATCAAAATTTATAGTGTGGTTATCAAAATTTCACACTGAGGTTATCAAAATTTCATAGGGAGA
TTATCAAAATTCTACAATGAGG
Found at i:18791 original size:45 final size:45
Alignment explanation
Indices: 18736--18822 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
18726 GTAAATTTTG
*
18736 GACTCCACAAGCGGGTTGTGGAGTTGACACATGTCCATTTTTTAA
1 GACTCCACAAGCGGGTTATGGAGTTGACACATGTCCATTTTTTAA
18781 GACTCCACAAGCGGGTTATGGAGTTGACACATGTCCATTTTT
1 GACTCCACAAGCGGGTTATGGAGTTGACACATGTCCATTTTT
18823 GAATTAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (45 bp):
GACTCCACAAGCGGGTTATGGAGTTGACACATGTCCATTTTTTAA
Done.