Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014519.1 Corchorus olitorius cultivar O-4 contig14552, 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: 54471
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1112 original size:32 final size:31
Alignment explanation
Indices: 1074--1314 Score: 261
Period size: 32 Copynumber: 7.5 Consensus size: 31
1064 TGTGAAAAGA
*
1074 AAACGCCCTTATTTAGCAGCGTCTATAGAAC-
1 AAACGCCCTTATTTAGCGGCGTCT-TAGAACG
* *
1105 AAGACGCCCTTTTTTAGCGGCGTCTATAGAACA
1 AA-ACGCCCTTATTTAGCGGCGTCT-TAGAACG
* *
1138 AAACGCCCTTATTTGGCGGCGTCTACAGAACG
1 AAACGCCCTTATTTAGCGGCGTCT-TAGAACG
*
1170 AAACGCCAC-TATTTAGCGGCGTCTTAAAAACG
1 AAACGCC-CTTATTTAGCGGCGTCTT-AGAACG
1202 AAACGCCCTTATTTAGCGGCGTCTTCAGAACG
1 AAACGCCCTTATTTAGCGGCGTCTT-AGAACG
* * *
1234 AAACGCCATTATTTAGCGGCGTCTTAAAACCA
1 AAACGCCCTTATTTAGCGGCGTCTTAGAA-CG
* **
1266 AAACGCCCTTATTTAACGGCGTCTTCAGAATA
1 AAACGCCCTTATTTAGCGGCGTCTT-AGAACG
1298 AAACGCCGCTATATTTA
1 AAACGCC-CT-TATTTA
1315 ACTGCTTCAA
Statistics
Matches: 183, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
31 6 0.03
32 163 0.89
33 8 0.04
34 6 0.03
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (31 bp):
AAACGCCCTTATTTAGCGGCGTCTTAGAACG
Found at i:1290 original size:64 final size:63
Alignment explanation
Indices: 1068--1304 Score: 307
Period size: 64 Copynumber: 3.7 Consensus size: 63
1058 AGCATGTGTG
* * * *
1068 AAAAGAAAACGCCCTTATTTAGCAGCGTCTAT-AGAAC-AAGACGCCCTTTTTTAGCGGCGTCTA
1 AAAACAAAACGCCCTTATTTAGCGGCGTCT-TCAGAACGAA-ACGCCATTATTTAGCGGCGTCT-
1131 T
63 T
* * * *
1132 AGAACAAAACGCCCTTATTTGGCGGCGTCTACAGAACGAAACGCCACTATTTAGCGGCGTCTT
1 AAAACAAAACGCCCTTATTTAGCGGCGTCTTCAGAACGAAACGCCATTATTTAGCGGCGTCTT
*
1195 AAAAACGAAACGCCCTTATTTAGCGGCGTCTTCAGAACGAAACGCCATTATTTAGCGGCGTCTT
1 -AAAACAAAACGCCCTTATTTAGCGGCGTCTTCAGAACGAAACGCCATTATTTAGCGGCGTCTT
* **
1259 AAAACCAAAACGCCCTTATTTAACGGCGTCTTCAGAATAAAACGCC
1 AAAA-CAAAACGCCCTTATTTAGCGGCGTCTTCAGAACGAAACGCC
1305 GCTATATTTA
Statistics
Matches: 152, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
63 5 0.03
64 145 0.95
65 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (63 bp):
AAAACAAAACGCCCTTATTTAGCGGCGTCTTCAGAACGAAACGCCATTATTTAGCGGCGTCTT
Found at i:5543 original size:21 final size:21
Alignment explanation
Indices: 5510--5549 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5500 ATTAATGAGT
5510 TAAAATAAAAAAATTGAAAAA
1 TAAAATAAAAAAATTGAAAAA
5531 TAAAA-AAATAAAATTGAAA
1 TAAAATAAA-AAAATTGAAA
5550 GACTAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
TAAAATAAAAAAATTGAAAAA
Found at i:6138 original size:30 final size:31
Alignment explanation
Indices: 6075--6151 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
6065 TAAAAAAGAG
*
6075 TTAGGGACCCAATTGCTCAATTAACTCCACT
1 TTAGGGACCCAATTGCTCAACTAACTCCACT
* * * *
6106 TTAGTGACTCAATTGCTC-ACTAAGTTCACT
1 TTAGGGACCCAATTGCTCAACTAACTCCACT
*
6136 TTAGGGACCCATTTGC
1 TTAGGGACCCAATTGC
6152 ATATTTGCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 22 0.58
31 16 0.42
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (31 bp):
TTAGGGACCCAATTGCTCAACTAACTCCACT
Found at i:7783 original size:20 final size:21
Alignment explanation
Indices: 7745--7784 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
7735 ACGTATTGTT
**
7745 TTGTTTTAGATATCCAAACTA
1 TTGTTTTAGATATAAAAACTA
7766 TTGTTTTA-ATATAAAAACT
1 TTGTTTTAGATATAAAAACT
7785 GAAGGGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
TTGTTTTAGATATAAAAACTA
Found at i:13477 original size:36 final size:36
Alignment explanation
Indices: 13436--13505 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
13426 ATTTTCTCTA
13436 ATTTATTTCATCAATGTCTAAAGACATTGACTAATC
1 ATTTATTTCATCAATGTCTAAAGACATTGACTAATC
* *
13472 ATTTATTTCATCAATGTCTCAAGACATTGGCTAA
1 ATTTATTTCATCAATGTCTAAAGACATTGACTAA
13506 ATCTCCATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (36 bp):
ATTTATTTCATCAATGTCTAAAGACATTGACTAATC
Found at i:13927 original size:2 final size:2
Alignment explanation
Indices: 13920--13946 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13910 TAACCACAAA
13920 AT 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 AT A
13947 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14744 original size:38 final size:40
Alignment explanation
Indices: 14702--14788 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 40
14692 TCATCAGTCA
14702 TAAATGTAG-AAAG-TCAATTATTATAAGCTGAAATAAGG
1 TAAATGTAGAAAAGATCAATTATTATAAGCTGAAATAAGG
14740 TAAATGTAGAAAAGACCCAATCAATTATTATAAGCTGAAATAAGG
1 TAAATGTAGAAAAG-----ATCAATTATTATAAGCTGAAATAAGG
14785 TAAA
1 TAAA
14789 GGAAACTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
38 9 0.21
39 4 0.10
45 29 0.69
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.26
Consensus pattern (40 bp):
TAAATGTAGAAAAGATCAATTATTATAAGCTGAAATAAGG
Found at i:24580 original size:29 final size:30
Alignment explanation
Indices: 24532--24590 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
24522 TTCACATGTA
24532 TTTTATGTAAAACCCTTCTTTGGGCACTTG
1 TTTTATGTAAAACCCTTCTTTGGGCACTTG
24562 TTTTATGT-AAACCCTTCTTTGGGCACTTG
1 TTTTATGTAAAACCCTTCTTTGGGCACTTG
24591 ATAATCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (30 bp):
TTTTATGTAAAACCCTTCTTTGGGCACTTG
Found at i:45197 original size:22 final size:20
Alignment explanation
Indices: 45149--45273 Score: 66
Period size: 22 Copynumber: 6.0 Consensus size: 20
45139 TTAATTTTAG
45149 AGGTTATCAAAA-TTTATTATGT
1 AGGTTAT-AAAATTTTA-TA-GT
45171 A-GTTACTAAAATTTTATAGT
1 AGGTTA-TAAAATTTTATAGT
45191 ATGG-T-T--AATTTTATAGT
1 A-GGTTATAAAATTTTATAGT
45208 -GTAGTTATCAAAATTTTATAGT
1 AG--GTTAT-AAAATTTTATAGT
* *
45230 GAGGTTACCAAAATTTCATAGGT
1 -AGGTTA-TAAAATTTTATA-GT
*
45253 AGGATATTAAAATTTTATAGT
1 AGGTTA-TAAAATTTTATAGT
45274 GTAGTTATCA
Statistics
Matches: 82, Mismatches: 6, Indels: 31
0.69 0.05 0.26
Matches are distributed among these distances:
15 1 0.01
17 12 0.15
18 1 0.01
19 2 0.02
20 3 0.04
21 13 0.16
22 47 0.57
23 2 0.02
24 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (20 bp):
AGGTTATAAAATTTTATAGT
Found at i:45214 original size:17 final size:17
Alignment explanation
Indices: 45180--45214 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45170 TAGTTACTAA
*
45180 AATTTTATAGTATGGTT
1 AATTTTATAGTATAGTT
*
45197 AATTTTATAGTGTAGTT
1 AATTTTATAGTATAGTT
45214 A
1 A
45215 TCAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (17 bp):
AATTTTATAGTATAGTT
Found at i:45383 original size:44 final size:43
Alignment explanation
Indices: 45211--46318 Score: 287
Period size: 44 Copynumber: 25.0 Consensus size: 43
45201 TTATAGTGTA
* *
45211 GTTATCAAAATTTTATA-GTGAGGTTACCAAAATTTCATAGGTAG
1 GTTATCAAAATTTCATATG-GAGGTTATCAAAATTTCATAGG-AG
* * * * * * *
45255 GATATTAAAATTTTATAGTGTA-GTTATCACAATTTCATGGGAT
1 GTTATCAAAATTTCATA-TGGAGGTTATCAAAATTTCATAGGAG
* *
45298 GTTATCAAAATTTCATAAGGAGGTTATTACAATAAAATTTCATGAGGAT
1 GTTATCAAAATTTCATATGGAGGTTA-T-C---AAAATTTCAT-AGGAG
45347 GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCAT-AGGAG
* * *
45391 GTTATCGAAA-TTCAT-GGGAAGGTTATCAAAATTTCACAGCGAG
1 GTTATCAAAATTTCATATGG-AGGTTATCAAAATTTCATAG-GAG
** *
45434 GTTA-CTAAAATTTCATACT-CTGGTTATCAGAATTTCATAGGGAG
1 GTTATC-AAAATTTCATA-TGGAGGTTATCAAAATTTCATA-GGAG
** * * * *
45478 ACTAACAAAATTTCATAGTGTGA--TTATCGAAATTTTATATGAAG
1 GTTATCAAAATTTCATA-TG-GAGGTTATCAAAATTTCATA-GGAG
* * * * *
45522 GTAACCAAAATTTCATATGAAGATTATCAAAATTTCATAGTATG
1 GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGA-G
* * * **
45566 CTTATAAAAATTACATAGTGAGATAGAGTAAGCTTATC-AAATTTCA-AGTGTC
1 GTTATCAAAATTTCATA-T--G---GAG---G-TTATCAAAATTTCATAG-GAG
* * * * * *
45618 GTTACCAAAATCTCATAGTGTA-ATAATCACAATTTCATA-GAG
1 GTTATCAAAATTTCATA-TGGAGGTTATCAAAATTTCATAGGAG
* ** * * * *
45660 GTTAACAAAATTTCATGGGGAGGTTGTCGAAATTTTAGAGGGAG
1 GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATA-GGAG
* * * * *
45704 ATT-TACAAAATTTCATA-GTGTGGTTATCAAGATTTTATA--AT
1 GTTAT-CAAAATTTCATATG-GAGGTTATCAAAATTTCATAGGAG
** * * * * *
45745 GTGGT----ATTTCAGAGGGAGAGGTTATCAAATTTTCATTGTGTG
1 GTTATCAAAATTTCATA-TG-GAGGTTATCAAAATTTCATAG-GAG
* * *
45787 GTAATTAAAATTTCATAAT-GAGTTTATCAAAATTT-ATAGTGAG
1 GTTATCAAAATTTCAT-ATGGAGGTTATCAAAATTTCATAG-GAG
* * * * * *
45830 ATTAACAAAATTTGATA-GTGTGGTTCTCAAAATTTTATAGG-G
1 GTTATCAAAATTTCATATG-GAGGTTATCAAAATTTCATAGGAG
* * ** * *
45872 AGTTAACAAAATTTCATA-GGTAAGTTATCGTAATTTTATGGTGCAG
1 -GTTATCAAAATTTCATATGG-AGGTTATCAAAATTTCATAG-G-AG
* * * * *
45918 TTAATTATAAAAATTTTAT-TGGGGGTTATCTTATCAAAATTTCGTAGGAG
1 ---GTTATCAAAATTTCATATGGAGG-----TTATCAAAATTTCATAGGAG
** * * ** *
45968 GTTAAAAAATATTTTATAAGGAGGTTAAAAAAAATTT-ATAGGGAT
1 GTTATCAAA-ATTTCATATGGAGGTT-ATCAAAATTTCATA-GGAG
**
46013 GTTATCAAAATTTCATA-AAATGGTTATCAAAATTTCAT-GAGATG
1 GTTATCAAAATTTCATATGGA-GGTTATCAAAATTTCATAG-GA-G
* *
46057 GTTTTCAAAATTTC--AT-GAGGTTATCAAAATTTTATAGGCAG
1 GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGG-AG
* * * * * *
46098 GTTTATAAAAATTTCAAAGGGATGTTATCAGAATTTCATAAGATG
1 G-TTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGA-G
* *
46143 GTTATCAAAATTTC--ATGAGATGGTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATATG-GA-GGTTATCAAAATTTCAT-AGGAG
* * * *
46187 ATTACCAATATTT--TATCGGAAAGTTATCAAAATTTCATAATGTGCA-
1 GTTATCAAAATTTCATAT-GG-AGGTTATCAAAATTTCAT-A-G-G-AG
* * * * *
46233 CTTACCAACATTTCAT-TGGGAGATTATCAAAATTTCATAGGGTG
1 GTTATCAAAATTTCATAT-GGAGGTTATCAAAATTTCATA-GGAG
* * * * *
46277 GTTATCAAATTTTCAT-TAGGTGGTTATTACAATTTTATAGGA
1 GTTATCAAAATTTCATAT-GGAGGTTATCAAAATTTCATAGGA
46319 AGCCAGGGAA
Statistics
Matches: 781, Mismatches: 188, Indels: 191
0.67 0.16 0.16
Matches are distributed among these distances:
37 7 0.01
39 16 0.02
41 23 0.03
42 62 0.08
43 139 0.18
44 321 0.41
45 49 0.06
46 36 0.05
47 15 0.02
48 33 0.04
49 33 0.04
50 5 0.01
51 1 0.00
52 28 0.04
53 8 0.01
54 5 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (43 bp):
GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGAG
Found at i:45420 original size:65 final size:64
Alignment explanation
Indices: 45210--45561 Score: 237
Period size: 66 Copynumber: 5.3 Consensus size: 64
45200 TTTATAGTGT
* * * * * *
45210 AGTTATCAAAATTTTATAGTGAGGTTACCAAAATTTCAT-AGGTAGGATATTAAAATTTTATAGT
1 AGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGG-AGGTTATCAAAATTTCAT-G-
*
45274 GT
63 GG
* * *
45276 AGTTATCACAATTTCAT-GGGATGTTATCAAAATTTCATAAGGAGGTTATTACAATAAAATTTCA
1 AGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGGAGGTTA-T-C---AAAATTTCA
45340 TGAGG
61 TG-GG
*
45345 ATGTTATCAAAATTTCATATG-GAGGTTATCAAAATTTCATAAGGAGGTTATCGAAA-TTCATGG
1 A-GTTATCAAAATTTCATA-GCGAGGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATGG
45408 G
64 G
* **** *
45409 AAGGTTATCAAAATTTCACAGCGAGGTTA-CTAAAATTTCATACTCTGGTTATCAGAATTTCATA
1 -A-GTTATCAAAATTTCATAGCGAGGTTATC-AAAATTTCATAAGGAGGTTATCAAAATTTCAT-
45473 GGG
62 GGG
* * * * * * * * * * * *
45476 AGACTAACAAAATTTCATAGTGTGATTATCGAAATTTTATATGAAGGTAACCAAAATTTCATATG
1 AG-TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCAT-GG
*
45541 A
64 G
45542 AGATTATCAAAATTTCATAG
1 AG-TTATCAAAATTTCATAG
45562 TATGCTTATA
Statistics
Matches: 230, Mismatches: 40, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
64 4 0.02
65 74 0.32
66 90 0.39
67 4 0.02
69 4 0.02
70 25 0.11
71 28 0.12
72 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (64 bp):
AGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATGGG
Found at i:45570 original size:22 final size:21
Alignment explanation
Indices: 45211--45584 Score: 189
Period size: 22 Copynumber: 16.9 Consensus size: 21
45201 TTATAGTGTA
*
45211 GTTATCAAAATTTTATAGTGAG
1 GTTATCAAAATTTCATAGT-AG
*
45233 GTTACCAAAATTTCATAGGTAG
1 GTTATCAAAATTTCATA-GTAG
* * *
45255 GATATTAAAATTTTATAGT-G
1 GTTATCAAAATTTCATAGTAG
* * * *
45275 TAGTTATCACAATTTCATGGGAT
1 --GTTATCAAAATTTCATAGTAG
*
45298 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCAT-AGTAG
* *
45320 GTTATTACAATAAAATTTCATGAGGAT
1 GTTA-T-C---AAAATTTCAT-AGTAG
*
45347 GTTATCAAAATTTCATATGGAG
1 GTTATCAAAATTTCATA-GTAG
*
45369 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCAT-AGTAG
* * *
45391 GTTATCGAAA-TTCATGGGAAG
1 GTTATCAAAATTTCAT-AGTAG
* *
45412 GTTATCAAAATTTCACAGCGAG
1 GTTATCAAAATTTCATAG-TAG
* *
45434 GTTA-CTAAAATTTCATACTCTG
1 GTTATC-AAAATTTCATAGT-AG
* *
45456 GTTATCAGAATTTCATAGGGAG
1 GTTATCAAAATTTCATA-GTAG
** *
45478 ACTAACAAAATTTCATAGT-G
1 GTTATCAAAATTTCATAGTAG
* * *
45498 TGATTATCGAAATTTTATATGAAG
1 -G-TTATCAAAATTTCATA-GTAG
* * *
45522 GTAACCAAAATTTCATATGAAG
1 GTTATCAAAATTTCATA-GTAG
*
45544 ATTATCAAAATTTCATAGTATG
1 GTTATCAAAATTTCATAGTA-G
* * *
45566 CTTATAAAAATTACATAGT
1 GTTATCAAAATTTCATAGT
45585 GAGATAGAGT
Statistics
Matches: 272, Mismatches: 57, Indels: 46
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.01
21 40 0.15
22 201 0.74
23 7 0.03
24 2 0.01
25 1 0.00
26 1 0.00
27 18 0.07
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGTAG
Found at i:45786 original size:61 final size:59
Alignment explanation
Indices: 45691--45806 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 59
45681 GGTTGTCGAA
* * * * *
45691 ATTTTAGAGGGAGATTTACAAAATTTCATAGTGTGGTTATCAAGATTTTATAATGTGGT
1 ATTTCAGAGGGAGAGTTACAAAATTTCATAGTGTGGTAATCAAAATTTCATAATGTGGT
* * *
45750 ATTTCAGAGGGAGAGGTTATCAAATTTTCATTGTGTGGTAATTAAAATTTCATAATG
1 ATTTCAGAGGGAGA-GTTA-CAAAATTTCATAGTGTGGTAATCAAAATTTCATAATG
45807 AGTTTATCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 13 0.28
60 3 0.06
61 31 0.66
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.40
Consensus pattern (59 bp):
ATTTCAGAGGGAGAGTTACAAAATTTCATAGTGTGGTAATCAAAATTTCATAATGTGGT
Found at i:45838 original size:21 final size:21
Alignment explanation
Indices: 45793--45890 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
45783 TGTGGTAATT
* *
45793 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAGTGAG-TTAAC
45815 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAGTGAG-TTAAC
* * **
45836 AAAATTTGATAGTGTGGTTCTC
1 AAAATTTCATAGTG-AGTTAAC
* *
45858 AAAATTTTATAGGGAGTTAAC
1 AAAATTTCATAGTGAGTTAAC
45879 AAAATTTCATAG
1 AAAATTTCATAG
45891 GTAAGTTATC
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
21 33 0.53
22 28 0.45
23 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (21 bp):
AAAATTTCATAGTGAGTTAAC
Found at i:45907 original size:43 final size:44
Alignment explanation
Indices: 45793--45910 Score: 127
Period size: 43 Copynumber: 2.7 Consensus size: 44
45783 TGTGGTAATT
* *
45793 AAAATTTCATAATG-AGTTTATCAAAA-TTTATAGTGAGATTAAC
1 AAAATTTCATAGTGTAG-TTATCAAAATTTTATAGGGAGATTAAC
* * *
45836 AAAATTTGATAGTGTGGTTCTCAAAATTTTATAGGGAG-TTAAC
1 AAAATTTCATAGTGTAGTTATCAAAATTTTATAGGGAGATTAAC
**
45879 AAAATTTCATAG-GTAAGTTATCGTAATTTTAT
1 AAAATTTCATAGTGT-AGTTATCAAAATTTTAT
45911 GGTGCAGTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
42 2 0.03
43 49 0.79
44 11 0.18
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (44 bp):
AAAATTTCATAGTGTAGTTATCAAAATTTTATAGGGAGATTAAC
Found at i:45997 original size:22 final size:22
Alignment explanation
Indices: 45963--46016 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
45953 AAAATTTCGT
*
45963 AGGAGGTTAAAAAATATTTTATA
1 AGGAGGTTAAAAAA-AATTTATA
45986 AGGAGGTTAAAAAAAATTTATA
1 AGGAGGTTAAAAAAAATTTATA
* *
46008 GGGATGTTA
1 AGGAGGTTA
46017 TCAAAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.31
Consensus pattern (22 bp):
AGGAGGTTAAAAAAAATTTATA
Found at i:46022 original size:22 final size:23
Alignment explanation
Indices: 45998--46292 Score: 189
Period size: 22 Copynumber: 13.4 Consensus size: 23
45988 GAGGTTAAAA
*
45998 AAAATTT-ATAGGGAT-GTTATC
1 AAAATTTCATAGAGATGGTTATC
*
46019 AAAATTTCATA-AAATGGTTATC
1 AAAATTTCATAGAGATGGTTATC
*
46041 AAAATTTCAT-GAGATGGTTTTC
1 AAAATTTCATAGAGATGGTTATC
46063 AAAATTTCAT---GA-GGTTATC
1 AAAATTTCATAGAGATGGTTATC
* *
46082 AAAATTTTATAG-GCA-GGTTTATA
1 AAAATTTCATAGAG-ATGG-TTATC
* *
46105 AAAATTTCAAAGGGAT-GTTATC
1 AAAATTTCATAGAGATGGTTATC
*
46127 AGAATTTCATA-AGATGGTTATC
1 AAAATTTCATAGAGATGGTTATC
46149 AAAATTTCAT-GAGATGGTTATC
1 AAAATTTCATAGAGATGGTTATC
* *
46171 AAAATTTCATA-ATG-TGATTACC
1 AAAATTTCATAGA-GATGGTTATC
* * * **
46193 AATATTTTATCG-GAAAGTTATC
1 AAAATTTCATAGAGATGGTTATC
* *
46215 AAAATTTCATA-ATG-TGCACTTACC
1 AAAATTTCATAGA-GATG--GTTATC
* * * *
46239 AACATTTCATTGGGA-GATTATC
1 AAAATTTCATAGAGATGGTTATC
*
46261 AAAATTTCATAG-GGTGGTTATC
1 AAAATTTCATAGAGATGGTTATC
*
46283 AAATTTTCAT
1 AAAATTTCAT
46293 TAGGTGGTTA
Statistics
Matches: 212, Mismatches: 40, Indels: 43
0.72 0.14 0.15
Matches are distributed among these distances:
19 15 0.07
20 2 0.01
21 15 0.07
22 146 0.69
23 18 0.08
24 16 0.08
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (23 bp):
AAAATTTCATAGAGATGGTTATC
Found at i:46123 original size:108 final size:108
Alignment explanation
Indices: 45948--46180 Score: 335
Period size: 108 Copynumber: 2.1 Consensus size: 108
45938 GGGGGTTATC
* *
45948 TTATCAAAATTTCGTAGGAGGTTAAAAAATATTTTATAAGGAGGTTAAAAAAAATTTATAGGGAT
1 TTATCAAAATTTC--ATGAGGTTAAAAAATATTTTATAAGGAGGTTAAAAAAAATTTAAAGGGAT
46013 GTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATGAGATGG
64 GTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATGAGATGG
* ** * *
46058 TTTTCAAAATTTCATGAGGTTATCAAA-ATTTTAT-AGGCAGGTTTATAAAAATTTCAAAGGGAT
1 TTATCAAAATTTCATGAGGTTAAAAAATATTTTATAAGG-AGGTTAAAAAAAATTT-AAAGGGAT
* *
46121 GTTATCAGAATTTCATAAGATGGTTATCAAAATTTCATGAGATGG
64 GTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATGAGATGG
46166 TTATCAAAATTTCAT
1 TTATCAAAATTTCAT
46181 AATGTGATTA
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
106 3 0.03
107 21 0.19
108 75 0.68
110 12 0.11
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (108 bp):
TTATCAAAATTTCATGAGGTTAAAAAATATTTTATAAGGAGGTTAAAAAAAATTTAAAGGGATGT
TATCAAAATTTCATAAAATGGTTATCAAAATTTCATGAGATGG
Found at i:46443 original size:20 final size:20
Alignment explanation
Indices: 46395--46445 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
46385 TTATAGTGTA
*
46395 ATTATTAAAATTTTATATGG
1 ATTATCAAAATTTTATATGG
*
46415 AGGTTATCAAAATTTTATATTG
1 A--TTATCAAAATTTTATATGG
46437 ATTATCAAA
1 ATTATCAAA
46446 TTTCATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.33
22 18 0.67
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (20 bp):
ATTATCAAAATTTTATATGG
Done.