Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020221.1 Corchorus olitorius cultivar O-4 contig20254, 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: 53706
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:78 original size:16 final size:15
Alignment explanation
Indices: 49--81 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
39 GACAGAAAGT
49 AATTAAACAGAAAAC
1 AATTAAACAGAAAAC
64 AATTAAACTAGAAAAC
1 AATTAAAC-AGAAAAC
80 AA
1 AA
82 AGCAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (15 bp):
AATTAAACAGAAAAC
Found at i:3330 original size:18 final size:18
Alignment explanation
Indices: 3304--3345 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3294 CTTGAGATTC
3304 AATGATTTCAAGTGATTGG
1 AATG-TTTCAAGTGATTGG
*
3323 AATGTTTCAAGTGCTTGG
1 AATGTTTCAAGTGATTGG
3341 AATGT
1 AATGT
3346 AAGAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.38
Consensus pattern (18 bp):
AATGTTTCAAGTGATTGG
Found at i:8586 original size:39 final size:41
Alignment explanation
Indices: 8544--8624 Score: 101
Period size: 45 Copynumber: 1.9 Consensus size: 41
8534 CTAAATTCTA
*
8544 CTCC-TCTAGGTAATTCATCAAAATAAAGCTAATATTCAACTC
1 CTCCTTCTAGATAATTCATCAAAATAAAGCTAATATTCAA--C
*
8586 CTCCATTTCTAGATAATTCATCAAAATAAAGCAAATATT
1 CTCC--TTCTAGATAATTCATCAAAATAAAGCTAATATT
8625 AATTGTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
42 4 0.12
45 30 0.88
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (41 bp):
CTCCTTCTAGATAATTCATCAAAATAAAGCTAATATTCAAC
Found at i:9950 original size:22 final size:22
Alignment explanation
Indices: 9925--9966 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9915 AATTTTGTTA
* *
9925 ACCTCCCTAAGGAATTTTGAAG
1 ACCTCACTAAGAAATTTTGAAG
*
9947 ACCTCACTATGAAATTTTGA
1 ACCTCACTAAGAAATTTTGA
9967 TAACTTCCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (22 bp):
ACCTCACTAAGAAATTTTGAAG
Found at i:10112 original size:22 final size:22
Alignment explanation
Indices: 9937--10337 Score: 123
Period size: 22 Copynumber: 18.5 Consensus size: 22
9927 CTCCCTAAGG
* *
9937 AATTTTGA-AGACCTCACTATGA
1 AATTTTGATA-ACCACATTATGA
** ***
9959 AATTTTGATAACTTCCGAATGA
1 AATTTTGATAACCACATTATGA
*
9981 AATTTTGATAACCAACACTATGA
1 AATTTTGATAACC-ACATTATGA
* * *
10004 GATGTTGATAACCTCCA-TATG-
1 AATTTTGATAACC-ACATTATGA
* **
10025 -ATATTGATAACCAGGTTATGA
1 AATTTTGATAACCACATTATGA
* * * *
10046 AAATTTAAAAACCTTCA-TATG-
1 AATTTTGATAACC-ACATTATGA
* * * *
10067 AATTGTTAATAATCACACTCTGA
1 AATT-TTGATAACCACATTATGA
*
10090 AATTTTGATAATCACATTATGA
1 AATTTTGATAACCACATTATGA
* * ** *
10112 AATTGTGATAACCTCGCTATAA
1 AATTTTGATAACCACATTATGA
* * *
10134 AATTTTGATAAACCTCCTTATAA
1 AATTTTGAT-AACCACATTATGA
* *
10157 AATTTTGATACCCATCCTTATGA
1 AATTTTGATAACCA-CATTATGA
* *
10180 AATCTTGAT-A--AC--TA-CA
1 AATTTTGATAACCACATTATGA
* **
10196 AATTTTGATAACCTCCCTATGA
1 AATTTTGATAACCACATTATGA
** * * *
10218 TTTTTTGATACCCTCGTTATGA
1 AATTTTGATAACCACATTATGA
* * * **
10240 AATTTTGTTAATCTCCCTATGA
1 AATTTTGATAACCACATTATGA
*
10262 AATTTTGAT--CTACATACTATGA
1 AATTTTGATAACCACAT--TATGA
* *
10284 AATTTTGATAGCC-CTCTTATGA
1 AATTTTGATAACCAC-ATTATGA
*
10306 AATTTTGATAACCTTCA-TATGA
1 AATTTTGATAACC-ACATTATGA
10328 AATTTTGATA
1 AATTTTGATA
10338 TCCTCCCTAA
Statistics
Matches: 283, Mismatches: 72, Indels: 48
0.70 0.18 0.12
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
19 2 0.01
20 17 0.06
21 7 0.02
22 183 0.65
23 59 0.21
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCACATTATGA
Found at i:10155 original size:23 final size:22
Alignment explanation
Indices: 10089--10383 Score: 137
Period size: 22 Copynumber: 13.7 Consensus size: 22
10079 TCACACTCTG
* * * *
10089 AAATTTTGATAATCACATTATG
1 AAATTTTGATAACCTCCTTATA
*
10111 AAATTGTGATAACCTCGC-TATA
1 AAATTTTGATAACCTC-CTTATA
10133 AAATTTTGATAAACCTCCTTATA
1 AAATTTTGAT-AACCTCCTTATA
* *
10156 AAATTTTGATACCCATCCTTATG
1 AAATTTTGATAACC-TCCTTATA
* *
10179 AAATCTTGATAA----C-TA-C
1 AAATTTTGATAACCTCCTTATA
* *
10195 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCTTATA
** * * *
10217 ATTTTTTGATACCCTCGTTATG
1 AAATTTTGATAACCTCCTTATA
* * * *
10239 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCTTATA
* * * *
10261 AAATTTTGATCTACATAC-TATG
1 AAATTTTGAT-AACCTCCTTATA
* *
10283 AAATTTTGATAGCC-CTCTTATG
1 AAATTTTGATAACCTC-CTTATA
* * *
10305 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCTTATA
* *
10327 AAATTTTGATATCCTCC--CTA
1 AAATTTTGATAACCTCCTTATA
* *
10347 AAATTTTGATTA-CTCCATAATA
1 AAATTTTGATAACCTCC-TTATA
* *
10369 AAAGTTTAATAACCT
1 AAATTTTGATAACCT
10384 TCCTAATTTG
Statistics
Matches: 208, Mismatches: 47, Indels: 35
0.72 0.16 0.12
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
19 4 0.02
20 12 0.06
21 4 0.02
22 132 0.63
23 42 0.20
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATA
Found at i:10776 original size:4 final size:4
Alignment explanation
Indices: 10767--10991 Score: 82
Period size: 4 Copynumber: 58.5 Consensus size: 4
10757 AAAATTATTA
* *
10767 AAAT AAAT AAAT AAA- AAAGT -AAT AGAT AAAT ATAT AAAT AGAA- AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
* * * * * * *
10814 AAGT AAAA AAAT -CAT AGAT GAAT AAA- AGAAT AAAT ATAT -AAT AGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* ** * * **
10860 AAAT AGAT AGGT AAAA AAAT -AAT -AAT AAAT AAAT AGAT -AAT AGCT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * **
10905 AAAT TAAT AAAT AAA- AAGAT AAAT -AGT AAAT AAAT AGAT -AAT AGTT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
10951 CAAT TAAT AAAT AAA- AAGAT AAAT -AGT AAAT AAAT AGAT AA
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AA
10992 TAGTTCATTT
Statistics
Matches: 157, Mismatches: 46, Indels: 36
0.66 0.19 0.15
Matches are distributed among these distances:
3 29 0.18
4 121 0.77
5 7 0.04
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:10863 original size:15 final size:15
Alignment explanation
Indices: 10842--10993 Score: 89
Period size: 15 Copynumber: 10.0 Consensus size: 15
10832 TGAATAAAAG
*
10842 AATAAATATATAATA
1 AATAAATAGATAATA
* *
10857 GATAAATAGATAGGTA
1 AATAAATAGATA-ATA
*
10873 AAAAAATA-ATAATA
1 AATAAATAGATAATA
10887 AATAAATAGATAATA
1 AATAAATAGATAATA
**
10902 GCTAAATTA-ATAAATA
1 AATAAA-TAGAT-AATA
* *
10918 AA-AAGATAAATAGTA
1 AATAA-ATAGATAATA
10933 AATAAATAGATAATA
1 AATAAATAGATAATA
** *
10948 GTTCAATTA-ATAAATA
1 AAT-AAATAGAT-AATA
* *
10964 AA-AAGATAAATAGTA
1 AATAA-ATAGATAATA
10979 AATAAATAGATAATA
1 AATAAATAGATAATA
10994 GTTCATTTTA
Statistics
Matches: 102, Mismatches: 23, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
14 11 0.11
15 60 0.59
16 31 0.30
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (15 bp):
AATAAATAGATAATA
Found at i:10924 original size:27 final size:27
Alignment explanation
Indices: 10882--10991 Score: 96
Period size: 27 Copynumber: 4.4 Consensus size: 27
10872 AAAAAAATAA
*
10882 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
10909 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
10933 -AATAAAT----AGAT-AATAGTTCAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
10955 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
10982 AAATAGATAA
1 TAATAAATAA
10992 TAGTTCATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
18 5 0.07
19 5 0.07
21 1 0.01
23 14 0.21
25 1 0.01
27 32 0.47
28 10 0.15
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:10934 original size:19 final size:19
Alignment explanation
Indices: 10912--10995 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 19
10902 GCTAAATTAA
10912 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
10931 TAAATAAATAGATAATAGTTCAATTAA
1 TAAATAAA-A-A-GATA----AA-TAG
10958 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
*
10977 TAAATAAATAGAT-AATAG
1 TAAATAAAAAGATAAATAG
10995 T
1 T
10996 TCATTTTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
18 6 0.12
19 22 0.42
20 3 0.06
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 3 0.06
27 10 0.19
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:10947 original size:46 final size:46
Alignment explanation
Indices: 10842--10994 Score: 211
Period size: 46 Copynumber: 3.3 Consensus size: 46
10832 TGAATAAAAG
* ** * *
10842 AATAAATATATAATAGATAAA-TAGATAGGTAAAAAAAT-AATAATA
1 AATAAATAGATAATAGATAAATTA-ATAAATAAAAAGATAAATAGTA
*
10887 AATAAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGTA
1 AATAAATAGATAATAGATAAATTAATAAATAAAAAGATAAATAGTA
* *
10933 AATAAATAGATAATAGTTCAATTAATAAATAAAAAGATAAATAGTA
1 AATAAATAGATAATAGATAAATTAATAAATAAAAAGATAAATAGTA
10979 AATAAATAGATAATAG
1 AATAAATAGATAATAG
10995 TTCATTTTAA
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
45 30 0.31
46 68 0.69
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (46 bp):
AATAAATAGATAATAGATAAATTAATAAATAAAAAGATAAATAGTA
Found at i:10995 original size:46 final size:46
Alignment explanation
Indices: 10871--10998 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
10861 AATAGATAGG
* * * *
10871 TAAAAAAAT-AATAATAAATAAATAGATAATAGCTAAATTAATAAA
1 TAAAAAGATAAATAGTAAATAAATAGATAATAGTTCAATTAATAAA
10916 TAAAAAGATAAATAGTAAATAAATAGATAATAGTTCAATTAATAAA
1 TAAAAAGATAAATAGTAAATAAATAGATAATAGTTCAATTAATAAA
10962 TAAAAAGATAAATAGTAAATAAATAGATAATAGTTCA
1 TAAAAAGATAAATAGTAAATAAATAGATAATAGTTCA
10999 TTTTAAAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 8 0.10
46 70 0.90
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.27
Consensus pattern (46 bp):
TAAAAAGATAAATAGTAAATAAATAGATAATAGTTCAATTAATAAA
Found at i:12936 original size:27 final size:27
Alignment explanation
Indices: 12894--13003 Score: 87
Period size: 27 Copynumber: 4.4 Consensus size: 27
12884 AGGTAAAAAA
*
12894 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
*
12921 TAATATATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
12945 -AATAAAT----AGAT-AATAGTTCAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
12967 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
12994 AAATAGATAA
1 TAATAAATAA
13004 TAGTTCAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
18 5 0.08
19 5 0.08
21 1 0.02
23 13 0.20
25 1 0.02
27 31 0.47
28 10 0.15
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:12949 original size:19 final size:19
Alignment explanation
Indices: 12927--13007 Score: 56
Period size: 19 Copynumber: 3.9 Consensus size: 19
12917 AAATTAATAT
12927 ATAAAAAGATAAATAGTAA
1 ATAAAAAGATAAATAGTAA
* *
12946 ATAAATAGATAATAGTTCAATTAATA
1 ATAAAAAGATAA-A--T--AGT-A-A
12972 AATAAAAAGATAAATAGTAA
1 -ATAAAAAGATAAATAGTAA
*
12992 ATAAATAGAT-AATAGT
1 ATAAAAAGATAAATAGT
13008 TCAATTTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
18 6 0.12
19 20 0.41
20 2 0.04
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 2 0.04
27 11 0.22
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (19 bp):
ATAAAAAGATAAATAGTAA
Found at i:13007 original size:46 final size:46
Alignment explanation
Indices: 12891--13013 Score: 210
Period size: 46 Copynumber: 2.7 Consensus size: 46
12881 GATAGGTAAA
* * * *
12891 AAATAATAAATAAATAGATAATAGCTAAATTAATATATAAAAAGAT
1 AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
12937 AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
1 AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
12983 AAATAGTAAATAAATAGATAATAGTTCAATT
1 AAATAGTAAATAAATAGATAATAGTTCAATT
13014 TAAAAAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (46 bp):
AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
Found at i:13420 original size:21 final size:21
Alignment explanation
Indices: 13391--13437 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
13381 AAACTAAACT
*
13391 CTAATTATGAAACTAAAAAGA
1 CTAACTATGAAACTAAAAAGA
*
13412 CTAACTATGAAACTAAAAGGA
1 CTAACTATGAAACTAAAAAGA
13433 CTAAC
1 CTAAC
13438 GTACAGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (21 bp):
CTAACTATGAAACTAAAAAGA
Found at i:14186 original size:22 final size:22
Alignment explanation
Indices: 14160--14565 Score: 219
Period size: 22 Copynumber: 18.3 Consensus size: 22
14150 CATTACATTT
* *
14160 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
14182 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
14204 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
***
14226 TGAAATTTTGATATTTTCAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
14248 TGTAATTTTGATAACCTCACTT
1 TGAAATTTTGATAACCTCTCTA
* ** *
14270 TGAAATTTTGAAAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
14292 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
*
14314 T-AAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
14335 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * **
14359 TGAAATTTCGATAATCAGTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
14381 TGAGA-TTTGATAAGCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
14401 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
14421 TGAAATTAAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
*
14449 TGAAATTTTGATAACCAT-ACTA
1 TGAAATTTTGATAACC-TCTCTA
** * * *
14471 AAAAATTTTAATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
14493 TGAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCTCTA
*
14515 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
14537 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
14559 TGAAATT
1 TGAAATT
14566 CTTATAAGCT
Statistics
Matches: 298, Mismatches: 60, Indels: 52
0.73 0.15 0.13
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 49 0.16
22 194 0.65
23 4 0.01
24 6 0.02
25 12 0.04
26 4 0.01
27 2 0.01
28 10 0.03
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:14249 original size:66 final size:65
Alignment explanation
Indices: 14160--14830 Score: 174
Period size: 66 Copynumber: 10.0 Consensus size: 65
14150 CATTACATTT
* * *** ** *
14160 TGAAAATTTGATAA-CCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTC
1 TGAAATTTTGATAATCTTC-TTATGAAATTTTGATAACCTCTCTAT-AAATTTTGAAAACAACAC
14224 TA
64 TA
* * * *
14226 TGAAATTTTGAT-ATTTTCATTATGTAATTTTGATAACCTCACTTTGAAATTTTGAAAACAACAC
1 TGAAATTTTGATAATCTTC-TTATGAAATTTTGATAACCTCTCTAT-AAATTTTGAAAACAACAC
14290 TA
64 TA
* * * *
14292 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAATCT-TCCTATAAATTTTGATAATCCGATC
1 TGAAATTTTGATAATCTTCTTATGAAATTTTGATAACCTCT-CTATAAATTTTGA-AA-AC-AAC
*
14355 TCTA
62 ACTA
* * * * ** *
14359 TGAAATTTCGATAATCAGTC-TATGAGA-TTTGATAAGCT-TCTATCAAATTTTG-GTAC-TC-C
1 TGAAATTTTGATAATC-TTCTTATGAAATTTTGATAACCTCTCTAT-AAATTTTGAAAACAACAC
14418 TTA
64 -TA
* * * * *
14421 TGAAATTAAGACTTTTATAACCTTCATATGAAATTTTGATAACCATACT-AAAAAATTTT-AATA
1 TGAAA-T-----TTTGATAATCTTCTTATGAAATTTTGATAACC-T-CTCTATAAATTTTGAA-A
*
14484 ACCACACTA
57 ACAACACTA
* * * * ** *
14493 TGAAATTTTGATAACCTCCCTATGAAATATT-AGTAACCTC-CTTATGAAATTTTGTTAACCACA
1 TGAAATTTTGATAATCTTCTTATGAAATTTTGA-TAACCTCTC-TAT-AAATTTTGAAAACAACA
14556 CTA
63 CTA
* * * * *
14559 TGAAATTCTT-ATAAGCTATGACATTTTGATAATCTCTTTGATAACCTTTCTATAAAATTGTGAT
1 TGAAATT-TTGATAATCT-T--C-TTATGA-AA--T-TTTGATAACCTCTCTAT-AAATTTTGAA
* *
14623 AGCCACACTA
56 AACAACACTA
* * * ** * * * * * *
14633 TGAAA-TTTAATTAACCTTCCTAAAAAATTGTAATAATCTGATCTTATGAAATTTTGGTAATC-A
1 TGAAATTTTGA-TAATCTTCTTATGAAATTTTGATAACCT-CTC-TAT-AAATTTT-GAAAACAA
14696 CACTA
61 CACTA
* * ** * * ** *
14701 TGATATTTTGATAACCTTCCCATGAAATTTTGATAACTTC-CACATGAAATTTTGGTAACCACAC
1 TGAAATTTTGATAATCTTCTTATGAAATTTTGATAACCTCTC-TAT-AAATTTTGAAAACAACAC
14765 TA
64 TA
* * * * * * * * *
14767 TGGAATTTTGATAACCTCCTCATGAAATTATAATAATCATCT-TATGAAATTTTGATAACCACAC
1 TGAAATTTTGATAATCTTCTTATGAAATTTTGATAA-CCTCTCTAT-AAATTTTGAAAACAACAC
14831 AAAGACAAGA
Statistics
Matches: 458, Mismatches: 97, Indels: 100
0.70 0.15 0.15
Matches are distributed among these distances:
61 1 0.00
62 9 0.02
63 1 0.00
64 11 0.02
65 25 0.05
66 201 0.44
67 57 0.12
68 57 0.12
69 19 0.04
70 14 0.03
71 7 0.02
72 11 0.02
73 5 0.01
74 38 0.08
75 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (65 bp):
TGAAATTTTGATAATCTTCTTATGAAATTTTGATAACCTCTCTATAAATTTTGAAAACAACACTA
Found at i:14320 original size:21 final size:21
Alignment explanation
Indices: 14289--14349 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
14279 GAAAACAACA
14289 CTATGAAATTTTGATAATCTTC
1 CTAT-AAATTTTGATAATCTTC
14311 CTATAAATTTTGATAATCTTC
1 CTATAAATTTTGATAATCTTC
14332 CTATAAATTTTGATAATC
1 CTATAAATTTTGATAATC
14350 CGATCTCTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
21 35 0.90
22 4 0.10
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (21 bp):
CTATAAATTTTGATAATCTTC
Found at i:14725 original size:22 final size:23
Alignment explanation
Indices: 14700--14826 Score: 104
Period size: 22 Copynumber: 5.7 Consensus size: 23
14690 TAATCACACT
*
14700 ATGATATTTTGATAACCTTCC-C
1 ATGAAATTTTGATAACCTTCCAC
14722 ATGAAATTTTGATAA-CTTCCAC
1 ATGAAATTTTGATAACCTTCCAC
* *
14744 ATGAAATTTTGGTAACC--ACAC
1 ATGAAATTTTGATAACCTTCCAC
* *
14765 TATGGAATTTTGATAACC-TCCTC
1 -ATGAAATTTTGATAACCTTCCAC
* * * * **
14788 ATGAAATTATAATAATCAT-CTT
1 ATGAAATTTTGATAACCTTCCAC
14810 ATGAAATTTTGATAACC
1 ATGAAATTTTGATAACC
14827 ACACAAAGAC
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
21 8 0.09
22 73 0.86
23 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (23 bp):
ATGAAATTTTGATAACCTTCCAC
Found at i:14753 original size:44 final size:42
Alignment explanation
Indices: 14677--14825 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 42
14667 AATCTGATCT
* *
14677 TATGAAATTTTGGTAA-TCACACTATGATATTTTGATAACCTTCC
1 TATGAAATTTTGATAACTC-CAC-ATGAAATTTTGATAACC-TCC
* * *
14721 CATGAAATTTTGATAACTTCCACATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAAC-TCCACATGAAATTTTGATAACCTC-C
* * * * * *
14765 TATGGAATTTTGATAACCTCCTCATGAAATTATAATAATCATCT
1 TATGAAATTTTGATAA-CTCCACATGAAATTTTGATAA-CCTCC
14809 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
14826 CACACAAAGA
Statistics
Matches: 85, Mismatches: 15, Indels: 11
0.77 0.14 0.10
Matches are distributed among these distances:
43 2 0.02
44 75 0.88
45 6 0.07
46 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (42 bp):
TATGAAATTTTGATAACTCCACATGAAATTTTGATAACCTCC
Found at i:19053 original size:16 final size:16
Alignment explanation
Indices: 19028--19101 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
19018 CGGGTTGATC
19028 GGGTTCGGGTCATTTT
1 GGGTTCGGGTCATTTT
*
19044 GGGTTTGGGTCATTTT
1 GGGTTCGGGTCATTTT
* *
19060 CGGGTTCGGATC-GTTT
1 -GGGTTCGGGTCATTTT
* * *
19076 GGATTCGGGTAATTTC
1 GGGTTCGGGTCATTTT
*
19092 GGGTTTGGGT
1 GGGTTCGGGT
19102 ACCCAAAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
15 8 0.18
16 28 0.62
17 9 0.20
ACGTcount: A:0.08, C:0.11, G:0.39, T:0.42
Consensus pattern (16 bp):
GGGTTCGGGTCATTTT
Found at i:19150 original size:17 final size:17
Alignment explanation
Indices: 19110--19150 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
19100 GTACCCAAAA
19110 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
19127 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
19143 TTTCGGGT
1 TTTCGGGT
19151 TGGGCGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:26457 original size:46 final size:46
Alignment explanation
Indices: 26407--26518 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
26397 TGGTAAGTGT
*
26407 TTTATGAAGTTTTTGAATTAGGAATTTACAATTCATAACTAAGTAC
1 TTTATGAAGTTTTTGAATTAGGAATTTACAATACATAACTAAGTAC
*
26453 TTTATGAAGTTTTTGAATTAGGAATTTACAATACATAACTAAGTGC
1 TTTATGAAGTTTTTGAATTAGGAATTTACAATACATAACTAAGTAC
*
26499 TTTATGAATGGTTTTGAATT
1 TTTATGAA-GTTTTTGAATT
26519 TATGCAGAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
46 52 0.84
47 10 0.16
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (46 bp):
TTTATGAAGTTTTTGAATTAGGAATTTACAATACATAACTAAGTAC
Found at i:26841 original size:14 final size:14
Alignment explanation
Indices: 26822--26848 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26812 CTGCAGAAAA
26822 TTATAGGCTCACTG
1 TTATAGGCTCACTG
26836 TTATAGGCTCACT
1 TTATAGGCTCACT
26849 TTTGCTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:28039 original size:31 final size:31
Alignment explanation
Indices: 27996--28060 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
27986 GTATATTGGA
* *
27996 TATGTATAATATGTAGTATGAGACCTATTCT
1 TATGCATAATATGTAGTATGAGACCTATTAT
28027 TATGCATAATATGTAGTATGAGACCTATTAT
1 TATGCATAATATGTAGTATGAGACCTATTAT
28058 TAT
1 TAT
28061 TAATTAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (31 bp):
TATGCATAATATGTAGTATGAGACCTATTAT
Found at i:29127 original size:11 final size:11
Alignment explanation
Indices: 29113--29150 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29103 ATTAATAACA
29113 AATTTATAATT
1 AATTTATAATT
29124 AATTTATAATT
1 AATTTATAATT
29135 -ATTTGATAATT
1 AATTT-ATAATT
*
29146 TATTT
1 AATTT
29151 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:32756 original size:48 final size:48
Alignment explanation
Indices: 32700--32797 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
32690 TAACATGCAA
* * *
32700 TTATTTCCTTTGACTTATAAGGTTAGAGGAGTCAATCGGGCAAGTTGG
1 TTATTTCCTTTGACTTATAAGATTAGAGGAATCAATCAGGCAAGTTGG
*
32748 TTATTTCCTTTGACTTATAAGATTAGAGGAATCAATTAGGCAAGTTGG
1 TTATTTCCTTTGACTTATAAGATTAGAGGAATCAATCAGGCAAGTTGG
32796 TT
1 TT
32798 TAGCAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (48 bp):
TTATTTCCTTTGACTTATAAGATTAGAGGAATCAATCAGGCAAGTTGG
Found at i:33212 original size:45 final size:45
Alignment explanation
Indices: 33163--33253 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
33153 TAACAACTAA
33163 TATGTATAAGTTGTTAAAAACAAACCCACAACACAACTATGAAAC
1 TATGTATAAGTTGTTAAAAACAAACCCACAACACAACTATGAAAC
33208 TATGTATAAGTTGTTAAAAACAAACCCACAACACAACTATGAAAC
1 TATGTATAAGTTGTTAAAAACAAACCCACAACACAACTATGAAAC
33253 T
1 T
33254 GTCCAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (45 bp):
TATGTATAAGTTGTTAAAAACAAACCCACAACACAACTATGAAAC
Found at i:35209 original size:23 final size:22
Alignment explanation
Indices: 35179--35235 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 22
35169 CCTCAGTATG
*
35179 AAATTTTGATAAACATTCATATA
1 AAATTTTGATAAACATCCA-ATA
*
35202 AAATTTTGATAAACCTCCAATA
1 AAATTTTGATAAACATCCAATA
35224 AAATTTTGATAA
1 AAATTTTGATAA
35236 CCTCTTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAAACATCCAATA
Found at i:35331 original size:22 final size:21
Alignment explanation
Indices: 35175--36082 Score: 163
Period size: 22 Copynumber: 41.7 Consensus size: 21
35165 ATGACCTCAG
* *
35175 TATGAAATTTTGATAAACATTCA
1 TATGAAATTTTGAT-AAC-TCCC
*
35198 TATAAAATTTTGATAAAC-CTCC
1 TATGAAATTTTGAT-AACTC-CC
* * **
35220 AATAAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAA-CTCCC
35242 TATGAAATTTTGATAA-T--C
1 TATGAAATTTTGATAACTCCC
*
35260 -AT-AAATTTTGACAACCTCCC
1 TATGAAATTTTGATAA-CTCCC
* ***
35280 TATG-ATTTTTCGATAACTTTAT
1 TATGAAATTTT-GATAAC-TCCC
* *
35302 TATAAAATTTTGTTAACATCCC
1 TATGAAATTTTGATAAC-TCCC
*
35324 TATGAAATTTAGATAAC-CCC
1 TATGAAATTTTGATAACTCCC
* * **
35344 TATAAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACT-CCC
*
35366 TATGAAATTTTGATATCCTCCC
1 TATGAAATTTTGATA-ACTCCC
*
35388 TATGAAATTTTGATAATCCCCC
1 TATGAAATTTTGATAA-CTCCC
* * *
35410 TTTGAAATTTTGATAATCTTCA
1 TATGAAATTTTGATAA-CTCCC
* *
35432 TACGAAATTTTGGTAAC-CACAC
1 TATGAAATTTTGATAACTC-C-C
* *
35454 AAATGCAATTTTGATAACCTCCC
1 -TATGAAATTTTGATAA-CTCCC
* ** * *
35477 TTTGAAA---T-ACCACACTC
1 TATGAAATTTTGATAACTCCC
**
35494 TA--AAATTTTGATAA-TAACAT
1 TATGAAATTTTGATAACT--CCC
*
35514 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAA-CTCCC
* * *
35536 AATGAAATGTTGCTAAC-CGCTC
1 TATGAAATTTTGATAACTC-C-C
*
35558 TATGAAATTTTGATAA-TCATAC
1 TATGAAATTTTGATAACTC--CC
* *
35580 TATGAAA-TTT-AAAATCTCCA
1 TATGAAATTTTGATAA-CTCCC
* *
35600 TATGAAATTTTAATAAC-CACAA
1 TATGAAATTTTGATAACTC-C-C
* *
35622 TATGAAAATTTTTCATAACTTCAC
1 TATG-AAA-TTTTGATAAC-TCCC
** * **
35646 TGGGAAAATTTGATAACGTCGG
1 TATGAAATTTTGATAAC-TCCC
* * **
35668 TTTAAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAA-CTCCC
* *
35690 TATGAAATTTCGATAAC-CACAT
1 TATGAAATTTTGATAACTC-C-C
* **
35712 TATG-AATTTTTATAACATTTC
1 TATGAAATTTTGATAAC-TCCC
* *
35733 TATGAAATTTTGGTAATCTGATCTC
1 TATGAAATTTTGATAA-C---TCCC
* * *
35758 TATGAATTTTTTATAACT-AC
1 TATGAAATTTTGATAACTCCC
* * **
35778 TCTGAGATTTTGATTGCTTCCC
1 TATGAAATTTTGATAAC-TCCC
* *
35800 GATGAAATTTTGAT---T-AC
1 TATGAAATTTTGATAACTCCC
* * * *
35817 TATAAAATTTTGATAATTTTCA
1 TATGAAATTTTGATAA-CTCCC
* **
35839 TATGAAATTTAGATTTTTCTAACATTAC
1 TATGAAATTTTGA------TAAC-TCCC
* *
35867 TATGAAATTTTGGTAAC-CAGAC
1 TATGAAATTTTGATAACTC--CC
* *
35889 TATGAAATCTTTAATAACCTCCT
1 TATGAAAT-TTTGATAA-CTCCC
*
35912 TA-AAATATTTTGATAAC-CACAC
1 TATGAA-ATTTTGATAACTC-C-C
* **
35934 TATGAAATTCTGATAACCTTGC
1 TATGAAATTTTGATAA-CTCCC
*
35956 TATGGAATTTTGATAACCTCCC
1 TATGAAATTTTGATAA-CTCCC
35978 TATGAAATTTTGATAAC-CACAC
1 TATGAAATTTTGATAACTC-C-C
*
36000 TATGAAATTTTGATAACTTTCC
1 TATGAAATTTTGATAAC-TCCC
* * *
36022 TATTAAATTTTAATAACCTAATCCA
1 TATGAAATTTTGATAA-C---TCCC
*
36047 TATGAAATGTTGATAAC-CACAC
1 TATGAAATTTTGATAACTC-C-C
36069 TATGAAATTTTGAT
1 TATGAAATTTTGAT
36083 TACCTCATTG
Statistics
Matches: 633, Mismatches: 164, Indels: 177
0.65 0.17 0.18
Matches are distributed among these distances:
15 3 0.00
16 11 0.02
17 19 0.03
18 5 0.01
19 3 0.00
20 48 0.08
21 45 0.07
22 370 0.58
23 61 0.10
24 17 0.03
25 34 0.05
26 1 0.00
28 16 0.03
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACTCCC
Found at i:35966 original size:44 final size:44
Alignment explanation
Indices: 35858--36111 Score: 199
Period size: 44 Copynumber: 5.7 Consensus size: 44
35848 TAGATTTTTC
* * * *
35858 TAACATTACTATGAAATTTTGGTAACCAGACTATGAAATCTTTAA
1 TAACCTTACTATGAAATTTTGATAACCACACTATGAAAT-TTTGA
* * *
35903 TAACC-TCCT-TAAAATATTTTGATAACCACACTATGAAATTCTGA
1 TAACCTTACTAT-GAA-ATTTTGATAACCACACTATGAAATTTTGA
* * * *
35947 TAACCTTGCTATGGAATTTTGATAACCTCCCTATGAAATTTTGA
1 TAACCTTACTATGAAATTTTGATAACCACACTATGAAATTTTGA
** ** * *
35991 TAACCACACTATGAAATTTTGATAACTTTC-CTATTAAATTTTAA
1 TAACCTTACTATGAAATTTTGATAAC-CACACTATGAAATTTTGA
* *
36035 TAACCTAATCCATATGAAATGTTGATAACCACACTATGAAATTTTGA
1 TAACCT--TAC-TATGAAATTTTGATAACCACACTATGAAATTTTGA
* * * * * *
36082 TTACCTCATTGTAAAATTTTGATAATCACA
1 TAACCTTACTATGAAATTTTGATAACCACA
36112 GGATTATATT
Statistics
Matches: 164, Mismatches: 36, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
43 1 0.01
44 95 0.58
45 32 0.20
46 3 0.02
47 33 0.20
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (44 bp):
TAACCTTACTATGAAATTTTGATAACCACACTATGAAATTTTGA
Found at i:35995 original size:66 final size:66
Alignment explanation
Indices: 35865--36087 Score: 261
Period size: 66 Copynumber: 3.3 Consensus size: 66
35855 TTCTAACATT
* * * *
35865 ACTATGAAATTTTGGTAACC-AGACTATGAAATCTTTAATAACCTCCTTA-AAATATTTTGATAA
1 ACTATGAAATTTTGATAACCTTG-CTATGAAAT-TTTAATAACCTCCATATGAA-ATTTTGATAA
35928 CCAC
63 CCAC
* * * *
35932 ACTATGAAATTCTGATAACCTTGCTATGGAATTTTGATAACCTCCCTATGAAATTTTGATAACCA
1 ACTATGAAATTTTGATAACCTTGCTATGAAATTTTAATAACCTCCATATGAAATTTTGATAACCA
35997 C
66 C
* * * *
35998 ACTATGAAATTTTGATAACTTTCCTATTAAATTTTAATAACCTAATCCATATGAAATGTTGATAA
1 ACTATGAAATTTTGATAACCTTGCTATGAAATTTTAATAACC---TCCATATGAAATTTTGATAA
36063 CCAC
63 CCAC
*
36067 ACTATGAAATTTTGATTACCT
1 ACTATGAAATTTTGATAACCT
36088 CATTGTAAAA
Statistics
Matches: 134, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
66 64 0.48
67 28 0.21
68 1 0.01
69 41 0.31
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (66 bp):
ACTATGAAATTTTGATAACCTTGCTATGAAATTTTAATAACCTCCATATGAAATTTTGATAACCA
C
Found at i:36099 original size:69 final size:64
Alignment explanation
Indices: 35921--36106 Score: 194
Period size: 69 Copynumber: 2.8 Consensus size: 64
35911 TTAAAATATT
* ** *
35921 TTGATAACCACACTATGAAATTCTGATAACCTTGC-TATGGAATTTTGATAACCTCCCTATGAAA
1 TTGATAACCACACTATGAAATTTTGATAACC-T-CAT-TTAAATTTTGATAACCTCCATATGAAA
*
35985 TT
63 TG
* * *
35987 TTGATAACCACACTATGAAATTTTGATAACTTTCCTATTAAATTTTAATAACCTAATCCATATGA
1 TTGATAACCACACTATGAAATTTTGATAAC-CTCAT-TTAAATTTTGATAACC---TCCATATGA
36052 AATG
61 AATG
*
36056 TTGATAACCACACTATGAAATTTTGATTACCTCATTGTAAAATTTTGATAA
1 TTGATAACCACACTATGAAATTTTGATAACCTCATT-T-AAATTTTGATAA
36107 TCACAGGATT
Statistics
Matches: 102, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
65 1 0.01
66 45 0.44
67 1 0.01
68 4 0.04
69 51 0.50
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (64 bp):
TTGATAACCACACTATGAAATTTTGATAACCTCATTTAAATTTTGATAACCTCCATATGAAATG
Found at i:36742 original size:22 final size:22
Alignment explanation
Indices: 36717--36759 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
36707 TAATTTCTCA
36717 GTGAGATTATCAAACTTTCATG
1 GTGAGATTATCAAACTTTCATG
*
36739 GTGAGATTATCAAGCTTTCAT
1 GTGAGATTATCAAACTTTCAT
36760 AGGAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (22 bp):
GTGAGATTATCAAACTTTCATG
Found at i:36769 original size:22 final size:22
Alignment explanation
Indices: 36722--36769 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
36712 TCTCAGTGAG
* *
36722 ATTATCAAACTTTCATGGTGAG
1 ATTATCAAACTTTCATGGTAAA
*
36744 ATTATCAAGCTTTCATAGG-AAA
1 ATTATCAAACTTTCAT-GGTAAA
36766 ATTA
1 ATTA
36770 ATGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
ATTATCAAACTTTCATGGTAAA
Found at i:36890 original size:23 final size:22
Alignment explanation
Indices: 36833--36913 Score: 108
Period size: 22 Copynumber: 3.6 Consensus size: 22
36823 TTGTTTGGTA
* *
36833 ATCAAAATTTTATAATGAGATT
1 ATCAAAATTTCATAAGGAGATT
* *
36855 ATCATAATTTCATAAGGAAATT
1 ATCAAAATTTCATAAGGAGATT
*
36877 ATCAAAAATTTCATAAGGAGGTT
1 ATC-AAAATTTCATAAGGAGATT
36900 ATCAAAATTTCATA
1 ATCAAAATTTCATA
36914 GTCCGGTTAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 32 0.63
23 19 0.37
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGATT
Found at i:36942 original size:21 final size:22
Alignment explanation
Indices: 36833--37001 Score: 106
Period size: 22 Copynumber: 7.7 Consensus size: 22
36823 TTGTTTGGTA
* ** *
36833 ATCAAAATTTTATAATGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * **
36855 ATCATAATTTCATAAGGAAATT
1 ATCAAAATTTCATAGGGAGGTT
*
36877 ATCAAAAATTTCATAAGGAGGTT
1 ATC-AAAATTTCATAGGGAGGTT
***
36900 ATCAAAATTTCATAGTCCGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
36922 A-CCAAATTTTATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * ** *
36943 ATAAAAAATCCATACCGCGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
36965 ACCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
36987 ATCAAAGTTTCATAG
1 ATCAAAATTTCATAG
37002 AATGATTATC
Statistics
Matches: 110, Mismatches: 35, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
21 16 0.15
22 75 0.68
23 19 0.17
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:36943 original size:43 final size:45
Alignment explanation
Indices: 36881--37001 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 45
36871 GAAATTATCA
*
36881 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGTC-CGGTTACC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGCCGCGGTTACC
* * * * *
36925 -AAATTTTATAGGGAGGTTATAAAAAATCCATA-CCGCGGTTACC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGCCGCGGTTACC
* * *
36968 AAAATTTCATATGAAGGTTATCAAAGTTTCATAG
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAG
37002 AATGATTATC
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
42 1 0.02
43 35 0.57
44 25 0.41
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (45 bp):
AAAATTTCATAAGGAGGTTATCAAAATTTCATAGCCGCGGTTACC
Found at i:37010 original size:22 final size:22
Alignment explanation
Indices: 36967--37017 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
36957 CCGCGGTTAC
*
36967 CAAAATTTCATATGAAGGTTAT
1 CAAAATTTCATATGAAGATTAT
*
36989 CAAAGTTTCATA-GAATGATTAT
1 CAAAATTTCATATGAA-GATTAT
37011 CAAAATT
1 CAAAATT
37018 ACATTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATATGAAGATTAT
Found at i:37190 original size:22 final size:21
Alignment explanation
Indices: 37090--37190 Score: 78
Period size: 22 Copynumber: 4.6 Consensus size: 21
37080 AAGATTATGA
* * *
37090 TTATCAAAATTTTACAGTGTGG
1 TTATC-AAATTTCACAGAGAGG
* *
37112 TTATCAAATTTTCATATAGAGG
1 TTATCAAA-TTTCACAGAGAGG
*
37134 TTATCGAAATTTCATA-ATGAGG
1 TTATC-AAATTTCACAGA-GAGG
*
37156 TTATCAAATTTTCACAGAGTGG
1 TTATCAAA-TTTCACAGAGAGG
37178 TTATCAATATTTC
1 TTATCAA-ATTTC
37191 TACGTTGGAG
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.11
22 54 0.82
23 5 0.08
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (21 bp):
TTATCAAATTTCACAGAGAGG
Found at i:40593 original size:31 final size:31
Alignment explanation
Indices: 40558--40725 Score: 148
Period size: 31 Copynumber: 5.5 Consensus size: 31
40548 AAAGGCTAAT
* *
40558 TGCTCAAATAAGAGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
* * **
40589 TGCTCAAATAAGGGCCTGATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
** *
40618 TGGACAAATAAGGGCCTAACGTTTGCTAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
** * * **
40649 TGCTCAAATAAATGCCTGATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
*
40678 TGACT-AAATAAGGGCCTAATGTTTGCCAAAA
1 TG-CTCAAATAAGGGCCTAATGTTTGCTAAAA
40709 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
40726 GGCATCGGAA
Statistics
Matches: 102, Mismatches: 29, Indels: 12
0.71 0.20 0.08
Matches are distributed among these distances:
29 41 0.40
30 4 0.04
31 57 0.56
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
Found at i:40635 original size:60 final size:59
Alignment explanation
Indices: 40562--40726 Score: 267
Period size: 60 Copynumber: 2.8 Consensus size: 59
40552 GCTAATTGCT
*
40562 CAAATAAGAGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGA
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTT-GA
* * **
40622 CAAATAAGGGCCTAACGTTTGCTAAAATGCTCAAATAAATGCCTGATCTTTTAATTTGA
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGA
40681 CTAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTG
1 C-AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTG
40727 GCATCGGAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 3 0.03
60 92 0.97
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (59 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGA
Found at i:40802 original size:31 final size:31
Alignment explanation
Indices: 40764--40867 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 31
40754 AACTGACGCC
40764 AGGCCCTTATTTGAACATTTTCGATAACGTT
1 AGGCCCTTATTTGAACATTTTCGATAACGTT
** ** * **
40795 AGGCCCTTATTTGGCCAAATT--AAAATATT
1 AGGCCCTTATTTGAACATTTTCGATAACGTT
* *
40824 GGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAACATTTTCGATAACGTT
40855 AGGCCCTTATTTG
1 AGGCCCTTATTTG
40868 GCCAAATTAA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
29 21 0.38
31 34 0.62
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (31 bp):
AGGCCCTTATTTGAACATTTTCGATAACGTT
Found at i:40858 original size:60 final size:60
Alignment explanation
Indices: 40765--40927 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
40755 ACTGACGCCA
* * *
40765 GGCCCTTATTTGAACATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAATATTG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
40825 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * *
40885 GGTCCTTATTTGAGCATTTTGGCA-AACGTTAGGTCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
40928 AGCAATTAGG
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 95 0.99
61 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:44202 original size:8 final size:7
Alignment explanation
Indices: 44171--44201 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
44161 CCTGTCTTTC
44171 AAAAATA
1 AAAAATA
44178 AAAAATA
1 AAAAATA
44185 AAAAATA
1 AAAAATA
44192 AATAAATA
1 AA-AAATA
44200 AA
1 AA
44202 TTACTTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:51644 original size:41 final size:41
Alignment explanation
Indices: 51585--51663 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
51575 CTTACGTTTC
* * *
51585 TTTTAAATTTCCTGAATTCCTAGTCATAACCTTAGTTTTTT
1 TTTTAAATTTCCTAAATTCCTAATCATAACCATAGTTTTTT
* *
51626 TTTTTAATTTCCTAAATTCCTAATCATAATCATAGTTT
1 TTTTAAATTTCCTAAATTCCTAATCATAACCATAGTTT
51664 ATTCTCTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (41 bp):
TTTTAAATTTCCTAAATTCCTAATCATAACCATAGTTTTTT
Done.