Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003880.1 Hibiscus syriacus cultivar Beakdansim tig00008359_pilon, 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: 61447
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:296 original size:85 final size:85
Alignment explanation
Indices: 2--627 Score: 669
Period size: 85 Copynumber: 7.4 Consensus size: 85
1 A
* * * *
2 ACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATACCATTGAGCTAAATGTAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
67 GAACTCGAAGGTTTTTATTG
66 GAACTCGAAGGTTTTTATTG
* * * * *
87 ACAAATAACCCTT-TTGCCTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTGAATGTAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
* *
151 AAACTCGAAGG--TTTGTTG
66 GAACTCGAAGGTTTTTATTG
* *
169 ACAGATAGCCCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
234 GAACTCGAAGGTTTTTATTG
66 GAACTCGAAGGTTTTTATTG
* * * * * * * *
254 AAAAATAAACCTTCTCACCTTGAGTTATGATGTAAATTTGATATGTCCTTGAGTTGAATGTAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
* * *
319 AAACTAGAAGG--TTTGTTG
66 GAACTCGAAGGTTTTTATTG
* * * *
337 ACAGATATCCCTTCTCGCCTTGAGCTATTCTGTAAATTTGATATTCCCTTGAGCTGAATATAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
* **
402 GAACGCGAAGGTTTTGGTTG
66 GAACTCGAAGGTTTTTATTG
* * * * * * *
422 ACATATAACTCTTCTCACCTTGAGCTAT-CATGTATATTTAATATGCCCTTTAGCTTAATGTAAT
1 ACAGATAACCCTTCTCGCCTTGAGCTATGC-TGTAAATTTGATATGCCCTTGAGCTGAATGTAAT
* ** *
486 C-AAGCTCAAACATTTTTTACTG
65 CGAA-CTCGAA-GGTTTTTATTG
* ** * * * * *
508 GCAGA-AGTCTTTCTCGCCTTGAGTTATGCTGCAAATTTGATATGTCCTTGAGCTGAA-ATAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
*
571 GAACTCGAAGGTTTTTACTGG
66 GAACTCGAAGGTTTTTA-TTG
* *
592 A-AGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAAT
1 ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
628 AGTTTCTTTA
Statistics
Matches: 439, Mismatches: 90, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
82 17 0.04
83 132 0.30
84 94 0.21
85 186 0.42
86 10 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (85 bp):
ACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
GAACTCGAAGGTTTTTATTG
Found at i:356 original size:168 final size:168
Alignment explanation
Indices: 2--587 Score: 743
Period size: 168 Copynumber: 3.5 Consensus size: 168
1 A
* * * *
2 ACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATACCATTGAGCTAAATGTAATC
1 ACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATATAATC
* ** * *
67 GAACTCGAAGGTTTTTATTGACAAATAACCCTT-TTGCCTTGAGTTATGCTATAAATTTGATATG
66 GAACTCGAAGGTTTTTATTGACAAATAAACCTTCTCACCTTGAGTTATGATGTAAATTTGATATG
* *
131 TCCTTGAGCTGAATGTAATCAAACTCGAAGGTTTGTTG
131 TCCTTGAGTTGAATGTAATCAAACTAGAAGGTTTGTTG
* *
169 ACAGATAGCCCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGCCCTTGAGCTGAATGTAATC
1 ACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATATAATC
*
234 GAACTCGAAGGTTTTTATTGAAAAATAAACCTTCTCACCTTGAGTTATGATGTAAATTTGATATG
66 GAACTCGAAGGTTTTTATTGACAAATAAACCTTCTCACCTTGAGTTATGATGTAAATTTGATATG
299 TCCTTGAGTTGAATGTAATCAAACTAGAAGGTTTGTTG
131 TCCTTGAGTTGAATGTAATCAAACTAGAAGGTTTGTTG
* * *
337 ACAGATATCCCTTCTCGCCTTGAGCTATTCTGTAAATTTGATATTCCCTTGAGCTGAATATAATC
1 ACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATATAATC
* ** * * * * *
402 GAACGCGAAGGTTTTGGTTGACATAT-AACTCTTCTCACCTTGAGCTATCATGTATATTTAATAT
66 GAACTCGAAGGTTTTTATTGACAAATAAAC-CTTCTCACCTTGAGTTATGATGTAAATTTGATAT
* * * ** *
466 GCCCTTTAGCTT-AATGTAATCAAGCTCA-AACATTTTTTACTG
130 GTCCTTGAG-TTGAATGTAATCAAACT-AGAA-GGTTTGT--TG
* * * * * *
508 GCAGA-AGTCTTTCTCGCCTTGAGTTATGCTGCAAATTTGATATGTCCTTGAGCTGAA-ATAATC
1 ACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATATAATC
571 GAACTCGAAGGTTTTTA
66 GAACTCGAAGGTTTTTA
588 CTGGAAGATA
Statistics
Matches: 368, Mismatches: 44, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
167 95 0.26
168 196 0.53
169 27 0.07
170 44 0.12
171 6 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (168 bp):
ACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATATAATC
GAACTCGAAGGTTTTTATTGACAAATAAACCTTCTCACCTTGAGTTATGATGTAAATTTGATATG
TCCTTGAGTTGAATGTAATCAAACTAGAAGGTTTGTTG
Found at i:2236 original size:97 final size:98
Alignment explanation
Indices: 2064--2262 Score: 312
Period size: 97 Copynumber: 2.0 Consensus size: 98
2054 GGATAGCTCA
* *
2064 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGATGTTTAACTAATT
1 ATATTATAATCACCTTTATCAAGCTAGCTGAATCTTATCCATAAAGCCGGGATGTTTAACCAATT
*
2129 ACTTAGAGGGACA-CTCAAGCTTTATTGTATAG
66 ACTTAAAGGGACAGCTCAAGCTTTATTGTATAG
* *
2161 ATATTATAATCACCTTTATCAAGCTAGCTGAATCTTATCCAT-AAGTCGGGGTGTTTAACCAATT
1 ATATTATAATCACCTTTATCAAGCTAGCTGAATCTTATCCATAAAGCCGGGATGTTTAACCAATT
* *
2225 GCTCTAAAGGGACAGCTCAAGCTTTATTGTATAT
66 ACT-TAAAGGGACAGCTCAAGCTTTATTGTATAG
2259 ATAT
1 ATAT
2263 ATTATAATAT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
96 21 0.23
97 50 0.54
98 22 0.24
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (98 bp):
ATATTATAATCACCTTTATCAAGCTAGCTGAATCTTATCCATAAAGCCGGGATGTTTAACCAATT
ACTTAAAGGGACAGCTCAAGCTTTATTGTATAG
Found at i:5182 original size:834 final size:834
Alignment explanation
Indices: 3575--5246 Score: 3283
Period size: 834 Copynumber: 2.0 Consensus size: 834
3565 TTTCTTCCTT
*
3575 GGTTCTCTCGAATCTTGTCTAGAATATGGTACAACTGTAATTAGTTTTGATTTGAAGATTGTAAC
1 GGTTCTCTCGAATCTTGTCTAGAATATGGTACAACTGCAATTAGTTTTGATTTGAAGATTGTAAC
*
3640 ACCTTTGCTAGCGTTTAAAATGCTAATGATCTCTCTTTCTTTATTCTTCAAGGGAGGTTTTCTAC
66 ACCTTTGCTAGCGTTTAAAATGCTAATGATCTCTCCTTCTTTATTCTTCAAGGGAGGTTTTCTAC
3705 TCGACCTGCCTCCTTGTTTAATGGTCATTTCTATCATCTTTGTTTTGACTTCCTCGTCAAATTTC
131 TCGACCTGCCTCCTTGTTTAATGGTCATTTCTATCATCTTTGTTTTGACTTCCTCGTCAAATTTC
3770 GGAATGCGGTAACCATCTGAATTATTTTGAAGGTTAGTTACAAAGGCATGTGCTTTCGTGGCCGA
196 GGAATGCGGTAACCATCTGAATTATTTTGAAGGTTAGTTACAAAGGCATGTGCTTTCGTGGCCGA
3835 TGAAACCCCTTGAAGTCCTGGTAAGATTCCAAGTGAAATTACCAACTGTGGAGTAGGCGGTACAT
261 TGAAACCCCTTGAAGTCCTGGTAAGATTCCAAGTGAAATTACCAACTGTGGAGTAGGCGGTACAT
3900 CCACCCCCTCAGATGCCCCTTCCCCAAGAGCATTCATTGATTCAGGCCGGACAACCTTGAAATAA
326 CCACCCCCTCAGATGCCCCTTCCCCAAGAGCATTCATTGATTCAGGCCGGACAACCTTGAAATAA
*
3965 TATTGTCAACCAACATGTCTTGGTTTCTAGTGATGGAATCCTAGGTATTTTTTGATTTTGACTTA
391 TATTGTCAACCAACATGTCTTGGTTTCTAGTGATGGAATCCTAGGTATATTTTGATTTTGACTTA
4030 TTTTTTCTTCCAGTTTCTTCTGTAAGCTTAGTATGTTCGCTTCAAGTTGAGCAATCTTAGCTTCC
456 TTTTTTCTTCCAGTTTCTTCTGTAAGCTTAGTATGTTCGCTTCAAGTTGAGCAATCTTAGCTTCC
4095 ATTTTCGAGTGTTATGTGGATGAGGTGTGTCCAACGCTTGAGGTGGAATGTCCAGTGTTTGTTTA
521 ATTTTCGAGTGTTATGTGGATGAGGTGTGTCCAACGCTTGAGGTGGAATGTCCAGTGTTTGTTTA
4160 TTTTTTATGAGACATCTCTTGTTAGTTAATGTGAATGTAATGAAGAAAAAAAATGCAAAATATGT
586 TTTTTTATGAGACATCTCTTGTTAGTTAATGTGAATGTAATGAAGAAAAAAAATGCAAAATATGT
4225 CTAAATGCATGATGCATGAAATGTTTGAGGCATTAATCCAAAAATGTGTCTATTATTATAAATAA
651 CTAAATGCATGATGCATGAAATGTTTGAGGCATTAATCCAAAAATGTGTCTATTATTATAAATAA
4290 TCCTTATTGGGGACAAAAGTGTTATTTCTTAAGAGACAAAAAACATTTTAAAGGTATATTCTTCT
716 TCCTTATTGGGGACAAAAGTGTTATTTCTTAAGAGACAAAAAACATTTTAAAGGTATATTCTTCT
4355 AGA-CCCGAACAACTTCTGACAGGTTGATTCGTCTTTTGCCTTCTTTTGACACC
781 AGACCCCGAACAACTTCTGACAGGTTGATTCGTCTTTTGCCTTCTTTTGACACC
4408 GGTTCTCTCGAATCTTGTCTAGAATATGGTACAACTGCAATTAGTTTTGATTTGAAGATTGTAAC
1 GGTTCTCTCGAATCTTGTCTAGAATATGGTACAACTGCAATTAGTTTTGATTTGAAGATTGTAAC
4473 ACCTTTGCTAGCGTTTAAAATGCTAATGATCTCTCCTTCTTTATTCTTCAAGGGAGGTTTTCTAC
66 ACCTTTGCTAGCGTTTAAAATGCTAATGATCTCTCCTTCTTTATTCTTCAAGGGAGGTTTTCTAC
4538 TCGACCTGCCTCCTTGTTTAATGGTCATTTCTATCATCTTTGTTTTGACTTCCTCGTCAAATTTC
131 TCGACCTGCCTCCTTGTTTAATGGTCATTTCTATCATCTTTGTTTTGACTTCCTCGTCAAATTTC
4603 GGAATGCGGTAACCATCTGAATTATTTTGAAGGTTAGTTACAAAGGCATGTGCTTTCGTGGCCGA
196 GGAATGCGGTAACCATCTGAATTATTTTGAAGGTTAGTTACAAAGGCATGTGCTTTCGTGGCCGA
4668 TGAAACCCCTTGAAGTCCTGGTAAGATTCCAAGTGAAATTACCAACTGTGGAGTAGGCGGTACAT
261 TGAAACCCCTTGAAGTCCTGGTAAGATTCCAAGTGAAATTACCAACTGTGGAGTAGGCGGTACAT
4733 CCACCCCCTCAGATGCCCCTTCCCCAAGAGCATTCATTTGATTCAGGCCGGACAACCTTGAAATA
326 CCACCCCCTCAGATGCCCCTTCCCCAAGAGCATTCA-TTGATTCAGGCCGGACAACCTTGAAATA
4798 ATATTGTCAACCAACATGTCTTGGTTTCTAGTGATGGAATCCTAGGTATATTTTGATTTTGACTT
390 ATATTGTCAACCAACATGTCTTGGTTTCTAGTGATGGAATCCTAGGTATATTTTGATTTTGACTT
*
4863 ATTTTTTCTTCCAGTTTCTTCTGTAAGCTTAGTATGTTCGCTTCAAGTTGAGCAATCTTAGCTTT
455 ATTTTTTCTTCCAGTTTCTTCTGTAAGCTTAGTATGTTCGCTTCAAGTTGAGCAATCTTAGCTTC
4928 CATTTTCGAGTGTTATGTGGATGAGGTGTGTCCAACGCTTGAGGTGGAATGTCCAGTGTTTGTTT
520 CATTTTCGAGTGTTATGTGGATGAGGTGTGTCCAACGCTTGAGGTGGAATGTCCAGTGTTTGTTT
4993 ATTTTTTATGAGACATCTCTTGTTAGTTAATGTGAATGTAATGAAGAAAAAAAATGCAAAATATG
585 ATTTTTTATGAGACATCTCTTGTTAGTTAATGTGAATGTAATGAAGAAAAAAAATGCAAAATATG
*
5058 TCTAAATGCATGATGCATGAAATGTTTGAGGCATTGATCCAAAAATGTGTCTATTATTATAAATA
650 TCTAAATGCATGATGCATGAAATGTTTGAGGCATTAATCCAAAAATGTGTCTATTATTATAAATA
5123 ATCCTTATTGGGGACAAAAGTGTTATTTCTTAAGAGACAAAAAACATTTTAAAGGTATATTCTTC
715 ATCCTTATTGGGGACAAAAGTGTTATTTCTTAAGAGACAAAAAACATTTTAAAGGTATATTCTTC
5188 TAGACCCCGAACAACTTCTGACAGGTTGATTCGTCTTTTGCCTTCTTTTGACACC
780 TAGACCCCGAACAACTTCTGACAGGTTGATTCGTCTTTTGCCTTCTTTTGACACC
5243 GGTT
1 GGTT
5247 GAATACCCTG
Statistics
Matches: 832, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
833 359 0.43
834 419 0.50
835 54 0.06
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (834 bp):
GGTTCTCTCGAATCTTGTCTAGAATATGGTACAACTGCAATTAGTTTTGATTTGAAGATTGTAAC
ACCTTTGCTAGCGTTTAAAATGCTAATGATCTCTCCTTCTTTATTCTTCAAGGGAGGTTTTCTAC
TCGACCTGCCTCCTTGTTTAATGGTCATTTCTATCATCTTTGTTTTGACTTCCTCGTCAAATTTC
GGAATGCGGTAACCATCTGAATTATTTTGAAGGTTAGTTACAAAGGCATGTGCTTTCGTGGCCGA
TGAAACCCCTTGAAGTCCTGGTAAGATTCCAAGTGAAATTACCAACTGTGGAGTAGGCGGTACAT
CCACCCCCTCAGATGCCCCTTCCCCAAGAGCATTCATTGATTCAGGCCGGACAACCTTGAAATAA
TATTGTCAACCAACATGTCTTGGTTTCTAGTGATGGAATCCTAGGTATATTTTGATTTTGACTTA
TTTTTTCTTCCAGTTTCTTCTGTAAGCTTAGTATGTTCGCTTCAAGTTGAGCAATCTTAGCTTCC
ATTTTCGAGTGTTATGTGGATGAGGTGTGTCCAACGCTTGAGGTGGAATGTCCAGTGTTTGTTTA
TTTTTTATGAGACATCTCTTGTTAGTTAATGTGAATGTAATGAAGAAAAAAAATGCAAAATATGT
CTAAATGCATGATGCATGAAATGTTTGAGGCATTAATCCAAAAATGTGTCTATTATTATAAATAA
TCCTTATTGGGGACAAAAGTGTTATTTCTTAAGAGACAAAAAACATTTTAAAGGTATATTCTTCT
AGACCCCGAACAACTTCTGACAGGTTGATTCGTCTTTTGCCTTCTTTTGACACC
Found at i:8194 original size:18 final size:19
Alignment explanation
Indices: 8173--8214 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
8163 GAAAAGGGAA
8173 AAATAAAAAAACAT-TAAT
1 AAATAAAAAAACATATAAT
* *
8191 AAAT-AATAAATATATAAT
1 AAATAAAAAAACATATAAT
8209 AAATAA
1 AAATAA
8215 TAAATAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.35
18 12 0.60
19 1 0.05
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAAAAAACATATAAT
Found at i:8215 original size:18 final size:18
Alignment explanation
Indices: 8187--8257 Score: 81
Period size: 18 Copynumber: 3.8 Consensus size: 18
8177 AAAAAAACAT
8187 TAATAAATAATAAATATA
1 TAATAAATAATAAATATA
8205 TAATAAATAATAAATAGTA
1 TAATAAATAATAAATA-TA
8224 TTAATATAAT-ATAATATATA
1 -TAATA-AATAATAA-ATATA
* *
8244 AAATAAAAAATAAA
1 TAATAAATAATAAA
8258 AAAATCATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 19 0.41
19 10 0.22
20 11 0.24
21 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (18 bp):
TAATAAATAATAAATATA
Found at i:8360 original size:35 final size:35
Alignment explanation
Indices: 8285--8400 Score: 112
Period size: 35 Copynumber: 3.3 Consensus size: 35
8275 TATATATTAT
* * * * *
8285 ATATTATCAAAAACATTGTTTTTAAAACCATACAAT
1 ATATTTTCAAAAA-ATTATTTTTAAAACTATAAAAC
*
8321 ATATTTTCAAAAAATTATTTTTGAAACTATAAAAC
1 ATATTTTCAAAAAATTATTTTTAAAACTATAAAAC
* * *
8356 ATATTTTC--AAAATCATTTTCAAAACTATATATAC
1 ATATTTTCAAAAAATTATTTTTAAAACTATA-AAAC
8390 ATA-TTTCAAAA
1 ATATTTTCAAAA
8401 TATATATTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
33 22 0.33
34 6 0.09
35 27 0.40
36 12 0.18
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (35 bp):
ATATTTTCAAAAAATTATTTTTAAAACTATAAAAC
Found at i:8374 original size:33 final size:33
Alignment explanation
Indices: 8303--8401 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 33
8293 AAAAACATTG
* * * *
8303 TTTTTAAAACCATACAATATATTTTCAAAAAATTA
1 TTTTTAAAACTATAAAACATATTTTC--AAAATCA
*
8338 TTTTTGAAACTATAAAACATATTTTCAAAATCA
1 TTTTTAAAACTATAAAACATATTTTCAAAATCA
* *
8371 TTTTCAAAACTATATATACATA-TTTCAAAAT
1 TTTTTAAAACTATA-AAACATATTTTCAAAAT
8402 ATATATTATA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
33 27 0.49
34 6 0.11
35 22 0.40
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (33 bp):
TTTTTAAAACTATAAAACATATTTTCAAAATCA
Found at i:8405 original size:2 final size:2
Alignment explanation
Indices: 8400--8518 Score: 203
Period size: 2 Copynumber: 62.0 Consensus size: 2
8390 ATATTTCAAA
8400 AT AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8440 AT AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8519 TCATAATTTT
Statistics
Matches: 112, Mismatches: 0, Indels: 10
0.92 0.00 0.08
Matches are distributed among these distances:
1 5 0.04
2 107 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8618 original size:37 final size:36
Alignment explanation
Indices: 8500--8618 Score: 143
Period size: 36 Copynumber: 3.3 Consensus size: 36
8490 TATATATATA
* * * *
8500 TATATATATATATATATATTCATAATTTTTAAAAAC
1 TATATATATATATATGTTTTCAAAAGTTTTAAAAAC
*
8536 TATATAT-TATATATGTTTTCAAATGTTTTTAAAAAC
1 TATATATATATATATGTTTTCAAAAG-TTTTAAAAAC
* *
8572 TATAT-TATATACATGTTTTCAAAAAGTTTTCAAAAC
1 TATATATATATATATGTTTTC-AAAAGTTTTAAAAAC
8608 TATATATATAT
1 TATATATATAT
8619 GTTTTCAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
35 14 0.20
36 48 0.68
37 9 0.13
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATATATATATATGTTTTCAAAAGTTTTAAAAAC
Found at i:8625 original size:22 final size:24
Alignment explanation
Indices: 8597--8642 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
8587 TTTTCAAAAA
8597 GTTTTC-AAAACTATA-TATATAT
1 GTTTTCAAAAACTATATTATATAT
8619 GTTTTCAAAAACTATATTATATAT
1 GTTTTCAAAAACTATATTATATAT
8643 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.27
23 9 0.41
24 7 0.32
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
GTTTTCAAAAACTATATTATATAT
Found at i:8678 original size:36 final size:35
Alignment explanation
Indices: 8502--8757 Score: 131
Period size: 36 Copynumber: 7.3 Consensus size: 35
8492 TATATATATA
* * *
8502 TATATATATATATATATTCATAAT-TTTTAAAAAC
1 TATATATATATATATTTTAAAAATATTTTAAAAAC
** *
8536 TATATAT-TATATATGTTTTCAAATGTTTTTAAAAAC
1 TATATATATATATAT-TTTAAAAAT-ATTTTAAAAAC
* * * *
8572 TATATTATATACATGTTTTCAAAAA-GTTTTCAAAAC
1 TATA-TATATATATATTTT-AAAAATATTTTAAAAAC
* * *
8608 TATATATATATGT-TTTCAAAAACTATATT----A-
1 TATATATATATATATTTTAAAAA-TATTTTAAAAAC
*
8638 TATATATATATATATTTTAAAAATATTTTCCAAAAC
1 TATATATATATATATTTTAAAAATATTTT-AAAAAC
* * *
8674 TATATATATAT-T-TTTTCAAAATTCGTTTTCTAAAAAT
1 TATATATATATATATTTT-AAAAAT--ATTT-TAAAAAC
* *
8711 TATATAT-TATATTTTTTCAAAAAATATTTTCAAAAAT
1 TATATATATATATATTTT--AAAAATATTTT-AAAAAC
8748 TATACTATAT
1 TATA-TATAT
8758 TGATATATAT
Statistics
Matches: 172, Mismatches: 25, Indels: 45
0.71 0.10 0.19
Matches are distributed among these distances:
30 17 0.10
31 9 0.05
33 12 0.07
34 19 0.11
35 17 0.10
36 42 0.24
37 34 0.20
38 16 0.09
39 6 0.03
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.47
Consensus pattern (35 bp):
TATATATATATATATTTTAAAAATATTTTAAAAAC
Found at i:8678 original size:38 final size:38
Alignment explanation
Indices: 8636--8767 Score: 103
Period size: 38 Copynumber: 3.4 Consensus size: 38
8626 AAAACTATAT
* *
8636 TATATATATATATATATTTTAAAAATATTTTCCAAAAC
1 TATATATATATATATATTTTAAAAATATTTTCAAAAAA
* * * *
8674 TATATATATAT-T-T-TTTCAAAATTCGTTTTCTAAAAA
1 TATATATATATATATATTTTAAAAAT-ATTTTCAAAAAA
* *
8710 T-TATATAT-TATATTTTTTCAAAAAATATTTTCAAAAAT
1 TATATATATATATATATTTT--AAAAATATTTTCAAAAAA
8748 TATACTATATTGATATATAT
1 TATA-TATA-T-ATATATAT
8768 ATATATATAT
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
34 1 0.01
35 16 0.22
36 12 0.17
37 4 0.06
38 21 0.29
39 7 0.10
40 4 0.06
41 1 0.01
43 6 0.08
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (38 bp):
TATATATATATATATATTTTAAAAATATTTTCAAAAAA
Found at i:8684 original size:66 final size:64
Alignment explanation
Indices: 8572--8694 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 64
8562 TTTTAAAAAC
* *
8572 TATATTATATACATGTTTTCAAAAAGTTTTCAAAACTATATATATATGTTTTCAAAAACTATAT
1 TATATTATATACATATTTTCAAAAAATTTTCAAAACTATATATATATGTTTTCAAAAACTATAT
* *
8636 TATATATATATATATATTTT-AAAAATATTTTCCAAAACTATATATATATTTTTTCAAAA
1 TATAT-TATATACATATTTTCAAAAA-ATTTT-CAAAACTATATATATATGTTTTCAAAA
8695 TTCGTTTTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
64 10 0.19
65 16 0.31
66 26 0.50
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (64 bp):
TATATTATATACATATTTTCAAAAAATTTTCAAAACTATATATATATGTTTTCAAAAACTATAT
Found at i:8734 original size:138 final size:138
Alignment explanation
Indices: 8494--8745 Score: 320
Period size: 136 Copynumber: 1.8 Consensus size: 138
8484 TATATATATA
* *
8494 TATATATATATATATATATATATATTCATAATTTTTAAAAACTATATATTATATATGTTTTCAAA
1 TATATATATATATATATATATATATTAAAAATTTTTAAAAACTATATATTATATATGTTTTCAAA
*
8559 TGTTTTTAAAAACTATATTATATACATGTTTTCAAAAA-GTTTTCAAAACTATATATATATGTTT
66 TGTTTTTAAAAACTATATTATATACATGTTTTCAAAAATATTTTCAAAACTATATATATATGTTT
8623 TCAAAAAC
131 TCAAAAAC
* *
8631 TATAT-TATATATATATATATATTTTAAAAATATTTTCCAAAACTATATA-TATAT-T-TTTTCA
1 TATATATATATATATATATATATATTAAAAAT-TTTT-AAAAACTATATATTATATATGTTTTC-
* * *
8692 AAATTCGTTTTCTAAAAATTATA-TAT-TATATTTTTTCAAAAAATATTTTCAAAA
63 AAA-T-GTTTT-TAAAAACTATATTATATACATGTTTTC-AAAAATATTTTCAAAA
8746 ATTATACTAT
Statistics
Matches: 99, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
135 5 0.05
136 27 0.27
137 24 0.24
138 24 0.24
139 19 0.19
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.47
Consensus pattern (138 bp):
TATATATATATATATATATATATATTAAAAATTTTTAAAAACTATATATTATATATGTTTTCAAA
TGTTTTTAAAAACTATATTATATACATGTTTTCAAAAATATTTTCAAAACTATATATATATGTTT
TCAAAAAC
Found at i:8798 original size:9 final size:9
Alignment explanation
Indices: 8778--8830 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
8768 ATATATATAT
8778 ATAAATATAA
1 ATAAA-ATAA
8788 ATAAAATAA
1 ATAAAATAA
8797 ATAAAATAA
1 ATAAAATAA
8806 A-AAAA-AA
1 ATAAAATAA
*
8813 A-AAAAAAA
1 ATAAAATAA
*
8821 AGAAAA-AA
1 ATAAAATAA
8829 AT
1 AT
8831 CGGATGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
7 7 0.17
8 10 0.25
9 18 0.45
10 5 0.12
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (9 bp):
ATAAAATAA
Found at i:9039 original size:50 final size:50
Alignment explanation
Indices: 8957--9052 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
8947 GCTTCAGTCT
* *** * *
8957 GAGCTGGCGCCACGTCAAGAAAGGTGTGGATCGTCATCTGCGCCTTATCC
1 GAGCTGACGCCACGTCAAGAAAGGTACAGATCGCCATCCGCGCCTTATCC
9007 GAGCTGACGCCACGTCAAGAAAGGTACAGATCGCCATCCGCGCCTT
1 GAGCTGACGCCACGTCAAGAAAGGTACAGATCGCCATCCGCGCCTT
9053 CGCGAGTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (50 bp):
GAGCTGACGCCACGTCAAGAAAGGTACAGATCGCCATCCGCGCCTTATCC
Found at i:18162 original size:56 final size:56
Alignment explanation
Indices: 18086--18198 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
18076 AACTATGAAG
* *
18086 AAGAAAAACCCCACAGCCACACAATTTTCTCTTCATGCAAAAATGAATCAAATCAA
1 AAGAAAAACCCCACACCCACACAAATTTCTCTTCATGCAAAAATGAATCAAATCAA
* * *
18142 AAGAAGAACCCCATACCCACAGAAATTTCTCTTCATGCAAAAATGAATCAAATCAA
1 AAGAAAAACCCCACACCCACACAAATTTCTCTTCATGCAAAAATGAATCAAATCAA
18198 A
1 A
18199 CAACCCAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.19
Consensus pattern (56 bp):
AAGAAAAACCCCACACCCACACAAATTTCTCTTCATGCAAAAATGAATCAAATCAA
Found at i:20062 original size:60 final size:60
Alignment explanation
Indices: 19989--20176 Score: 247
Period size: 60 Copynumber: 3.1 Consensus size: 60
19979 GAGTATATAG
*
19989 ATGAT-ATCCGATTATATGGAGTTGTTTTGTTGAGTTTTTTAATCATTAAAATTTATAAA
1 ATGATCATTCGATTATATGGAGTTGTTTTGTTGAGTTTTTTAATCATTAAAATTTATAAA
* *
20048 ATGATCATTCGATTATATGGAGTTGTTTTGTTAAGTTTTTTAATCATTAAAATTTATAGA
1 ATGATCATTCGATTATATGGAGTTGTTTTGTTGAGTTTTTTAATCATTAAAATTTATAAA
* * ** * * *
20108 ATGATCATTCGATTATCA-GGTGTTGTTTTATTGAGTCATTTGA-CTAATAAAAGTTATAAA
1 ATGATCATTCGATTAT-ATGGAGTTGTTTTGTTGAGTTTTTTAATC-ATTAAAATTTATAAA
20168 ATGATCATT
1 ATGATCATT
20177 GACTATTCTT
Statistics
Matches: 114, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
59 6 0.05
60 107 0.94
61 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (60 bp):
ATGATCATTCGATTATATGGAGTTGTTTTGTTGAGTTTTTTAATCATTAAAATTTATAAA
Found at i:20820 original size:15 final size:15
Alignment explanation
Indices: 20797--20827 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20787 ACAATGCAAC
20797 ATTCCCAATAATCTT
1 ATTCCCAATAATCTT
*
20812 ATTCTCAATAATCTT
1 ATTCCCAATAATCTT
20827 A
1 A
20828 CATTCCGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTCCCAATAATCTT
Found at i:21620 original size:60 final size:60
Alignment explanation
Indices: 21527--21641 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
21517 TTGTCTAAAT
* *
21527 TTATTGATTAATGAGTCTATGAGTATAATATTAAAGTTTAATAATATTTTCAATCGATAA
1 TTATTGATCAATGAGTCTATGAGCATAATATTAAAGTTTAATAATATTTTCAATCGATAA
21587 TTATTGATCAATGAGTCTATGAGCATAATATTAAAGTTTAATAATATTTTCAATC
1 TTATTGATCAATGAGTCTATGAGCATAATATTAAAGTTTAATAATATTTTCAATC
21642 TTCAAACTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (60 bp):
TTATTGATCAATGAGTCTATGAGCATAATATTAAAGTTTAATAATATTTTCAATCGATAA
Found at i:23411 original size:2 final size:2
Alignment explanation
Indices: 23406--23435 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23396 AAAAAAATGA
23406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23436 TAAGTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25719 original size:55 final size:55
Alignment explanation
Indices: 25658--25765 Score: 162
Period size: 55 Copynumber: 2.0 Consensus size: 55
25648 CTTTTTACAA
* ** *
25658 CATAAAGGTATTTTTTTTATTTTACCCCATAAGGATATTTTTGTAATTTTACCCC
1 CATAAAGCTATTTTCGTAATTTTACCCCATAAGGATATTTTTGTAATTTTACCCC
* *
25713 CATAAAGCTATTTTCGTAATTTTACCCTATAAGGGTATTTTTGTAATTTTACC
1 CATAAAGCTATTTTCGTAATTTTACCCCATAAGGATATTTTTGTAATTTTACC
25766 TAAGTATTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (55 bp):
CATAAAGCTATTTTCGTAATTTTACCCCATAAGGATATTTTTGTAATTTTACCCC
Found at i:25765 original size:27 final size:27
Alignment explanation
Indices: 25658--25765 Score: 137
Period size: 27 Copynumber: 4.0 Consensus size: 27
25648 CTTTTTACAA
* *
25658 CATAAAGGTATTTTTTTTATTTTACCC
1 CATAAAGGTATTTTTGTAATTTTACCC
25685 CAT-AAGGATATTTTTGTAATTTTACCCC
1 CATAAAGG-TATTTTTGTAATTTTA-CCC
* *
25713 CATAAAGCTATTTTCGTAATTTTACCC
1 CATAAAGGTATTTTTGTAATTTTACCC
* *
25740 TATAAGGGTATTTTTGTAATTTTACC
1 CATAAAGGTATTTTTGTAATTTTACC
25766 TAAGTATTGT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.06
27 42 0.60
28 21 0.30
29 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (27 bp):
CATAAAGGTATTTTTGTAATTTTACCC
Found at i:26653 original size:17 final size:17
Alignment explanation
Indices: 26631--26665 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
26621 AACTTAGGTT
26631 AGCTCATTACAGAGAGG
1 AGCTCATTACAGAGAGG
26648 AGCTCATTACAGAGAGG
1 AGCTCATTACAGAGAGG
26665 A
1 A
26666 ACTCGACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (17 bp):
AGCTCATTACAGAGAGG
Found at i:26966 original size:31 final size:30
Alignment explanation
Indices: 26926--26993 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
26916 TAAAACGATT
26926 AAAA-TCATAAAA-CAATT-TATAATTAAAATA
1 AAAATTCATAAAATC-ATTATAT-ATTAAAA-A
*
26956 AAAATTCATAAAATCATTATATATTAAAAG
1 AAAATTCATAAAATCATTATATATTAAAAA
26986 AAAATTCA
1 AAAATTCA
26994 ACAATATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 12 0.35
31 18 0.53
32 4 0.12
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.31
Consensus pattern (30 bp):
AAAATTCATAAAATCATTATATATTAAAAA
Found at i:26976 original size:30 final size:31
Alignment explanation
Indices: 26926--26993 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
26916 TAAAACGATT
26926 AAAA-TCATAAAACAATTTATA-ATTAAAATA
1 AAAATTCATAAAACAATTTATATATTAAAA-A
*
26956 AAAATTCATAAAATC-A-TTATATATTAAAAG
1 AAAATTCATAAAA-CAATTTATATATTAAAAA
26986 AAAATTCA
1 AAAATTCA
26994 ACAATATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 17 0.50
31 16 0.47
32 1 0.03
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.31
Consensus pattern (31 bp):
AAAATTCATAAAACAATTTATATATTAAAAA
Found at i:27798 original size:35 final size:35
Alignment explanation
Indices: 27746--27813 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
27736 CCTTAGATCC
*
27746 ATAAGGAATTACAAGTTTGATCGATCTGAACCTAT
1 ATAAGGAATTACAAGTTTGATCGAGCTGAACCTAT
27781 ATAAGGAATTATC-AGTTTGATCGAGCTGAACCT
1 ATAAGGAATTA-CAAGTTTGATCGAGCTGAACCT
27814 GTAAAGACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (35 bp):
ATAAGGAATTACAAGTTTGATCGAGCTGAACCTAT
Found at i:30625 original size:27 final size:27
Alignment explanation
Indices: 30534--30636 Score: 102
Period size: 27 Copynumber: 3.8 Consensus size: 27
30524 CCTTTTACAA
* **
30534 CATAAGGTTATTTTTGTAATTTTACCT
1 CATAAGGATATTTTCATAATTTTACCT
* **
30561 CATAAAGATATTTTTGTAATTTTACCT
1 CATAAGGATATTTTCATAATTTTACCT
*
30588 CATAAGGGTATTTTCATAATTTTACCT
1 CATAAGGATATTTTCATAATTTTACCT
*
30615 AACATAA-G-TATTGTCATAATTT
1 --CATAAGGATATTTTCATAATTT
30637 CTCATCCAAG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
27 61 0.91
28 1 0.01
29 5 0.07
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (27 bp):
CATAAGGATATTTTCATAATTTTACCT
Found at i:30635 original size:54 final size:54
Alignment explanation
Indices: 30534--30636 Score: 120
Period size: 54 Copynumber: 1.9 Consensus size: 54
30524 CCTTTTACAA
* ** * **
30534 CATAAGGTTATTTTTGTAATTTTACCTCATAAAGATATTTTTGTAATTTTACCT
1 CATAAGGGTATTTTCATAATTTTACCTCATAAAGATATTGTCATAATTTTACCT
30588 CATAAGGGTATTTTCATAATTTTACCTAACAT-AAG-TATTGTCATAATTT
1 CATAAGGGTATTTTCATAATTTTACCT--CATAAAGATATTGTCATAATTT
30637 CTCATCCAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
54 35 0.85
55 3 0.07
56 3 0.07
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (54 bp):
CATAAGGGTATTTTCATAATTTTACCTCATAAAGATATTGTCATAATTTTACCT
Found at i:31181 original size:19 final size:19
Alignment explanation
Indices: 31157--31193 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
31147 AATGATCAAC
31157 TCTGGTCAAAGTCAACGGG
1 TCTGGTCAAAGTCAACGGG
31176 TCTGGTCAAAGTCAACGG
1 TCTGGTCAAAGTCAACGG
31194 ATATGGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (19 bp):
TCTGGTCAAAGTCAACGGG
Found at i:31200 original size:19 final size:19
Alignment explanation
Indices: 31159--31201 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
31149 TGATCAACTC
* *
31159 TGGTCAAAGTCAACGGGTC
1 TGGTCAAAGTCAACGGATA
31178 TGGTCAAAGTCAACGGATA
1 TGGTCAAAGTCAACGGATA
31197 TGGTC
1 TGGTC
31202 GGATTGACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (19 bp):
TGGTCAAAGTCAACGGATA
Found at i:37552 original size:20 final size:20
Alignment explanation
Indices: 37524--37569 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
37514 AGAAAAAAGT
*
37524 AAAAGTTAAGAATGAAAGAG
1 AAAAATTAAGAATGAAAGAG
37544 AAAAATTAAGAATGAAAGAG
1 AAAAATTAAGAATGAAAGAG
37564 AAAAAT
1 AAAAAT
37570 AAAAAGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAAATTAAGAATGAAAGAG
Found at i:59833 original size:15 final size:17
Alignment explanation
Indices: 59802--59838 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
59792 CTACTCTACT
59802 TTATTCACAATATTTAA
1 TTATTCACAATATTTAA
59819 TTATTCAC-A-ATTTAA
1 TTATTCACAATATTTAA
59834 TTATT
1 TTATT
59839 AGTATGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 1 0.05
17 8 0.40
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTCACAATATTTAA
Found at i:59982 original size:22 final size:22
Alignment explanation
Indices: 59942--60013 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
59932 AAAGTACAAT
*
59942 AAAAATATAAAAG-ATAGAATAA
1 AAAAATA-AAAAGAAAAGAATAA
59964 AAAAATAAAAAGAAAAGAA-AA
1 AAAAATAAAAAGAAAAGAATAA
* *
59985 TAACAAA-AGAAAGTAAAAAAATAA
1 -AA-AAATAAAAAG-AAAAGAATAA
60009 AAAAA
1 AAAAA
60014 AAACCAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
21 7 0.17
22 22 0.52
23 11 0.26
24 2 0.05
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.11
Consensus pattern (22 bp):
AAAAATAAAAAGAAAAGAATAA
Found at i:60022 original size:18 final size:18
Alignment explanation
Indices: 59959--60041 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 18
59949 TAAAAGATAG
59959 AATAA-AAAAATAAAAAGA
1 AATAACAAAAATAAAAA-A
*
59977 AA-AGA-AAATAACAAAAGAA
1 AATA-ACAAA-AATAAAA-AA
*
59996 AGTAA-AAAAATAAAAAA
1 AATAACAAAAATAAAAAA
60013 AA-AACCAAAAATAAAAAA
1 AATAA-CAAAAATAAAAAA
60031 AATAACAAAAA
1 AATAACAAAAA
60042 AATAATATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.04
17 4 0.07
18 32 0.59
19 14 0.26
20 2 0.04
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.08
Consensus pattern (18 bp):
AATAACAAAAATAAAAAA
Done.