Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005862.1 Hibiscus syriacus cultivar Beakdansim tig00013780_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: 42751
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:2250 original size:15 final size:15
Alignment explanation
Indices: 2232--2260 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2222 CCAGTTTTTT
2232 TAAAAAAACCGATTA
1 TAAAAAAACCGATTA
2247 TAAAAAAACCGATT
1 TAAAAAAACCGATT
2261 TTAATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (15 bp):
TAAAAAAACCGATTA
Found at i:6620 original size:13 final size:13
Alignment explanation
Indices: 6602--6631 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
6592 GATTGCGAAG
6602 AATTAAAAATTTA
1 AATTAAAAATTTA
6615 AATT-AAAATTTA
1 AATTAAAAATTTA
6627 AATTA
1 AATTA
6632 CTCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAAATTTA
Found at i:6744 original size:19 final size:18
Alignment explanation
Indices: 6698--6757 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
6688 TGTTAGTAAA
6698 AAATAAATAAATAAAAAT
1 AAATAAATAAATAAAAAT
* **
6716 AAAAATAATAAATAAATGTT
1 AAATA-AATAAATAAA-AAT
* *
6736 AAATAAATAAAAAAAAAC
1 AAATAAATAAATAAAAAT
6754 AAAT
1 AAAT
6758 GGAAACGAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 8 0.25
19 19 0.59
20 5 0.16
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATAAATAAATAAAAAT
Found at i:6783 original size:2 final size:2
Alignment explanation
Indices: 6778--6828 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
6768 AAAAGTTCAA
6778 AT AT AT AT AT AT AT AT AT AT AT A- AT A- 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
6818 AT AT AT AT AT A
1 AT AT AT AT AT A
6829 AAAATAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8318 original size:35 final size:35
Alignment explanation
Indices: 8273--8355 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 35
8263 AATTATATGT
8273 TATATGTTTTCAAAAATGACTTCAAAAACTATATA
1 TATATGTTTTCAAAAATGACTTCAAAAACTATATA
**
8308 TATATGTTTTCAAAAATGTTTTCAAAAACTATATA
1 TATATGTTTTCAAAAATGACTTCAAAAACTATATA
8343 TATA--TTTTCAAAA
1 TATATGTTTTCAAAA
8356 TGTTTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 9 0.20
35 37 0.80
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.41
Consensus pattern (35 bp):
TATATGTTTTCAAAAATGACTTCAAAAACTATATA
Found at i:8328 original size:12 final size:12
Alignment explanation
Indices: 8311--8335 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8301 CTATATATAT
8311 ATGTTTTCAAAA
1 ATGTTTTCAAAA
8323 ATGTTTTCAAAA
1 ATGTTTTCAAAA
8335 A
1 A
8336 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:8341 original size:33 final size:33
Alignment explanation
Indices: 8246--8361 Score: 128
Period size: 35 Copynumber: 3.5 Consensus size: 33
8236 AAACTTATAG
* * *
8246 TTTCAAAAATGTTTTGAAATTA-TATGTTATATGT
1 TTTCAAAAATGTTTTCAAA-AACTAT-ATATATGT
**
8280 TTTCAAAAATGACTTCAAAAACTATATATATATGT
1 TTTCAAAAATGTTTTCAAAAAC--TATATATATGT
*
8315 TTTCAAAAATGTTTTCAAAAACTATATATATAT
1 TTTCAAAAATGTTTTCAAAAACTATATATATGT
8348 TTTC-AAAATGTTTT
1 TTTCAAAAATGTTTT
8362 TTTTTAAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
32 10 0.14
33 15 0.21
34 16 0.23
35 27 0.38
36 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (33 bp):
TTTCAAAAATGTTTTCAAAAACTATATATATGT
Found at i:8414 original size:2 final size:2
Alignment explanation
Indices: 8407--8432 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8397 GATTTCAAAC
8407 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
8433 ATAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9322 original size:248 final size:245
Alignment explanation
Indices: 8976--9726 Score: 816
Period size: 248 Copynumber: 3.0 Consensus size: 245
8966 TTATTGACAA
* * * * * *
8976 ATAGTCCTTCTTGACTTAAGTTGTGCTACAAATGATATG-CCTTGGAGCTGAGCGTAGTCAAACT
1 ATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACT
* * * * *
9040 CGAAGGTTTTTAGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTT
65 CGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
* *
9105 GAGCGTAGTCGAACTCAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAA
130 GAGCGTAGTCGAACTCAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAA
*
9170 ATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
194 ATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTTGGCAG
* * * *
9223 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACT
** * * *
9288 CGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTACCTTGGAGCT
65 CGAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
* ** * * *
9353 GAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA
130 GAGCGTAGTCGAACTC-AAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAA
* * * * *
9418 ATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC-T--TTGGCAG
194 ATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTGGTTGGCAG
* * * *
9468 ATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTC
* * * * * * * *
9533 GAAGGTCTTTTGGTCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGA
66 GAAGGTC-TTTGG-C--AGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGG
** * * * * * * *
9598 AGCTGAATGTAATCGAACTTAAGGGTC--T-TTGGCAGATAGCTCTTCTCGACTTAAGCTATACT
126 AGCTGAGCGTAGTCGAACTCAA-GGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCT
* *
9660 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGGCAG
190 GCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTTGGCAG
9716 ATAGCCCTTCT
1 ATAGCCCTTCT
9727 GGCCTTGAGC
Statistics
Matches: 412, Mismatches: 77, Indels: 29
0.80 0.15 0.06
Matches are distributed among these distances:
244 23 0.06
245 77 0.19
246 37 0.09
247 36 0.09
248 182 0.44
249 57 0.14
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (245 bp):
ATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTG
AGCGTAGTCGAACTCAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
GATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTTGGCAG
Found at i:9349 original size:165 final size:165
Alignment explanation
Indices: 8976--9726 Score: 883
Period size: 165 Copynumber: 4.6 Consensus size: 165
8966 TTATTGACAA
* * * * * * * *
8976 ATAGTCCTTCTTGACTTAAGTTGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * *
9041 GAAGG--TTT--TTAGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGG
66 GAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGA
* * *
9101 AGTTGAGCGTAGTCGAACTCAA-GGTCTTTTGTTGGCAG
131 AGCTGAGTGTAATCGAACTCAAGGGTC---T-TTGGCAG
* * * * * * **
9139 ACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * *
9204 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
66 GAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGA
**
9269 AGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
131 AGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
* * *
9304 ATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * *
9369 AAAGGTCTTT-GCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGA
66 GAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGA
*
9433 AGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAG
131 AGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
*
9468 ATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACT
* * * * * *
9532 CGAAGGTCTTTTGGTCA-TAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTT
65 CGAAGGTC-TTTGGTTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTT
* *
9596 GAAGCTGAATGTAATCGAACTTAAGGGTCTTTGGCAG
129 GAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
*
9633 ATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
** *
9698 GAAGGTC-TTGGTGGGCAGATAGCCCTTCT
66 GAAGGTCTTTGGTTAGCAGATAACCCTTCT
9727 GGCCTTGAGC
Statistics
Matches: 523, Mismatches: 54, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
163 68 0.13
164 154 0.29
165 231 0.44
166 3 0.01
167 42 0.08
168 21 0.04
169 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (165 bp):
ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGA
AGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAG
Found at i:9734 original size:329 final size:327
Alignment explanation
Indices: 8976--9748 Score: 926
Period size: 329 Copynumber: 2.3 Consensus size: 327
8966 TTATTGACAA
* * * * * * * *
8976 ATAGTCCTTCTTGACTTAAGTTGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * * *
9041 GAAGGT-TTTTAGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTT
66 GAAGGTCTTGTAGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGAAGCT
* * * *
9105 GAGCGTAGTCGAACTCAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAA
131 GAGCGTAATCGAACTCAAGGTC--TTGTTGGCAGACAACCCTTCTAGACTTAAGCTATACTGCAA
** *
9170 ATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
194 ATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTCACAGATAACCCTTCTA
* * **
9235 GACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
259 GACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAATGTAATCGAACTCAAGGGTCTTTG
9300 GCAG
324 GCAG
* * *
9304 ATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * *
9369 AAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAA
66 GAAGGTC-TTG-TAGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATG-CCTTGAA
* * * * * *
9434 GCTGAGTGTAATCGAACTTAAGGGTC-T-TTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGC
128 GCTGAGCGTAATCGAACTCAA-GGTCTTGTTGGCAGACAACCCTTCTAGACTTAAGCTATACTGC
** *
9497 AAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TCATAGATAACCCT
192 AAATGACATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTCACAGATAACCCT
* * * * * *
9560 TCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAATGTAATCGAACTTAAGGGTC
255 TCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAATGTAATCGAACTCAAGGGTC
9625 TTTGGCAG
320 TTTGGCAG
*
9633 ATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
9698 GAAGGTCTTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
66 GAAGGTCTT-GT-AGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAAT
9749 AGTTTTTTAA
Statistics
Matches: 376, Mismatches: 60, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
328 65 0.17
329 239 0.64
330 10 0.03
331 35 0.09
332 23 0.06
333 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (327 bp):
ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTGTAGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGAAGCT
GAGCGTAATCGAACTCAAGGTCTTGTTGGCAGACAACCCTTCTAGACTTAAGCTATACTGCAAAT
GACATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTCACAGATAACCCTTCTAGA
CTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAATGTAATCGAACTCAAGGGTCTTTGGC
AG
Found at i:14792 original size:13 final size:13
Alignment explanation
Indices: 14774--14803 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14764 GATTGCGAAG
14774 AATTAAAAATTTA
1 AATTAAAAATTTA
14787 AATT-AAAATTTA
1 AATTAAAAATTTA
14799 AATTA
1 AATTA
14804 CTCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAAATTTA
Found at i:14879 original size:4 final size:4
Alignment explanation
Indices: 14866--14922 Score: 50
Period size: 4 Copynumber: 15.0 Consensus size: 4
14856 AAAATGTTAG
* **
14866 TAAA -AAA TAAA TAAA T-AA -AAA TAAA AATAA TAAA TAAA T-GT TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAAA TAAA
14911 TAAA TAAA TAAA
1 TAAA TAAA TAAA
14923 ACAATGGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
3 8 0.19
4 31 0.74
5 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:14916 original size:19 final size:18
Alignment explanation
Indices: 14870--14923 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
14860 TGTTAGTAAA
14870 AAATAAATAAATAAAAAT
1 AAATAAATAAATAAAAAT
* **
14888 AAAAATAATAAATAAATGTT
1 AAATA-AATAAATAAA-AAT
14908 AAATAAATAAATAAAA
1 AAATAAATAAATAAAA
14924 CAATGGAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.14
19 20 0.69
20 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATAAATAAATAAAAAT
Found at i:14920 original size:23 final size:22
Alignment explanation
Indices: 14857--14922 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
14847 ACAAAGTCAA
*
14857 AAATGTT-AGTAAAAAATAAAT
1 AAATGTTAAATAAAAAATAAAT
**
14878 AAAT-AAAAATAAAAATAATAAAT
1 AAATGTTAAAT-AAAA-AATAAAT
14901 AAATGTTAAATAAATAAATAAA
1 AAATGTTAAATAAA-AAATAAA
14923 ACAATGGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
21 6 0.17
22 4 0.11
23 20 0.57
24 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (22 bp):
AAATGTTAAATAAAAAATAAAT
Found at i:14951 original size:2 final size:2
Alignment explanation
Indices: 14946--14980 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14936 AAAAATTTCA
14946 AT AT AT AT 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 AT AT AT AT A
14981 AATAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16345 original size:35 final size:36
Alignment explanation
Indices: 16306--16388 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 36
16296 ATAATAATAA
*
16306 AAAATATTTTTCAAAAACCTATATAATATA-TTTTC
1 AAAATATTTTTCAAAAACATATATAATATATTTTTC
** * *
16341 AAAATA-TTTT-AAAATTATATATTATATATTTTTT
1 AAAATATTTTTCAAAAACATATATAATATATTTTTC
16375 AAAA-ATTTTTCAAA
1 AAAATATTTTTCAAA
16389 CTTATAGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 15 0.38
34 16 0.40
35 9 0.22
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTTTCAAAAACATATATAATATATTTTTC
Found at i:16434 original size:34 final size:34
Alignment explanation
Indices: 16396--16511 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 34
16386 AAACTTATAG
* * **
16396 TTTCAAAAATGTTTTGAAATTATATGTTATATGT
1 TTTCAAAAATGTTTTAAAACTATATAATATATGT
**
16430 TTTCAAAAATGACTTCAAAAACTATATAATATATGT
1 TTTCAAAAATG--TTTTAAAACTATATAATATATGT
16466 TTTCAAAAATGTTTTCAAAAACTATAT-AT-TA--T
1 TTTCAAAAATGTTTT--AAAACTATATAATATATGT
16498 TTTC-AAAATGTTTT
1 TTTCAAAAATGTTTT
16512 TTTTTAAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
31 10 0.14
32 5 0.07
34 15 0.21
35 2 0.03
36 38 0.54
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (34 bp):
TTTCAAAAATGTTTTAAAACTATATAATATATGT
Found at i:16447 original size:60 final size:59
Alignment explanation
Indices: 16332--16448 Score: 137
Period size: 60 Copynumber: 2.0 Consensus size: 59
16322 ACCTATATAA
* * * **
16332 TATATTTTCAAAATATTTTAAAATTATATATTATATATTTTTTAAAAATTTTTCAAACT
1 TATAGTTTCAAAATATTTTAAAATTATATATTATATAGTTTTCAAAAATACTTCAAACT
* * *
16391 TATAGTTTCAAAAATGTTTTGAAATTATATGTTATAT-GTTTTCAAAAATGACTTCAAA
1 TATAGTTTC-AAAATATTTTAAAATTATATATTATATAGTTTTCAAAAAT-ACTTCAAA
16449 AACTATATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 18 0.38
60 30 0.62
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (59 bp):
TATAGTTTCAAAATATTTTAAAATTATATATTATATAGTTTTCAAAAATACTTCAAACT
Found at i:16463 original size:36 final size:36
Alignment explanation
Indices: 16423--16493 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
16413 AATTATATGT
16423 TATATGTTTTCAAAAATGACTTCAAAAACTATATAA
1 TATATGTTTTCAAAAATGACTTCAAAAACTATATAA
**
16459 TATATGTTTTCAAAAATGTTTTCAAAAACTATATA
1 TATATGTTTTCAAAAATGACTTCAAAAACTATATA
16494 TTATTTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (36 bp):
TATATGTTTTCAAAAATGACTTCAAAAACTATATAA
Found at i:16479 original size:12 final size:12
Alignment explanation
Indices: 16462--16486 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16452 TATATAATAT
16462 ATGTTTTCAAAA
1 ATGTTTTCAAAA
16474 ATGTTTTCAAAA
1 ATGTTTTCAAAA
16486 A
1 A
16487 CTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:16567 original size:2 final size:2
Alignment explanation
Indices: 16556--16602 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
16546 GATTTCAAAC
16556 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16597 TA TA TA
1 TA TA TA
16603 ATAATAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22841 original size:26 final size:25
Alignment explanation
Indices: 22805--22867 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
22795 TTTATTATTC
* *
22805 TTTTAATTTTATTCTTTACTGATTAT
1 TTTTATTTTTATTATTT-CTGATTAT
*
22831 TTTTATTTTTATTATTTCTGTTTAT
1 TTTTATTTTTATTATTTCTGATTAT
22856 TTTT-TTTATTAT
1 TTTTATTT-TTAT
22868 ATATATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.09
25 15 0.45
26 15 0.45
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (25 bp):
TTTTATTTTTATTATTTCTGATTAT
Found at i:26980 original size:105 final size:104
Alignment explanation
Indices: 26644--28213 Score: 2239
Period size: 105 Copynumber: 15.1 Consensus size: 104
26634 ACTTCTCAAT
* * * * ** * * *
26644 GAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCTTGACGAAGGGGCGGCTGATTGTCAA
1 GAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
26708 CAAACACTT-CCAATTTCAGAGCCAATTTCAACTTCACATC
65 CAAA-ATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
* *
26748 GAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* *
26813 AAATTTTCCCGATTTCAGAGCCAATTTCAACTTCACAGC
66 AAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
26852 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
**
26917 AATAATTTCATAATTTCAGAGCCAATTTCAACTTCACAGC
66 AA-AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
* *
26957 GAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAAT
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-
* *
27022 AAAAAATTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
65 CAAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
27062 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* *
27127 AAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
66 AAA-ATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
27167 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA-GGACCGCTGCTTGTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
**
27231 AATAATTTCATAATTTCAGAGCCAATTTCAACTTCACAGC
66 AA-AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
* *
27271 GAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAAT
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-
* *
27336 AAAAAAATTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
64 ACAAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
27377 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
*
27442 AAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGC
66 AAA-ATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
27482 GAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-
* *
27547 AAAAAAATTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
64 ACAAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
27588 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTTTCAA-
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* * *
27651 TAAA-----CAACTTC----CCAATTTCAACTTCACAAC
66 AAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
27681 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAAT
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-
* * *
27746 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACATC
65 CAA-AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
* *
27787 GAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* *
27852 AAATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
66 AAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
* *
27891 GAAGGATATTGGAATCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* * *
27956 AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAAC
66 AA-AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
** *
27996 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTCTTCTCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
** *
28061 AAAATTT--C-A-TTCAGAATCAATTTCAACTTCACAAC
66 AAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
* * * *
28096 GAAGGATGTTGGACTCGAGACAA--CAAGTTCAACTTCACAACGAAGGGACGGCTGGTT-TCAAC
1 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
** *
28158 AACCAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GAC
66 AA--AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-C
*
28199 GGAGGATATTGGACT
1 GAAGGATATTGGACT
28214 TGGAACAATG
Statistics
Matches: 1334, Mismatches: 99, Indels: 67
0.89 0.07 0.04
Matches are distributed among these distances:
93 68 0.05
94 11 0.01
96 1 0.00
97 15 0.01
98 30 0.02
99 5 0.00
100 44 0.03
101 2 0.00
102 10 0.01
103 37 0.03
104 349 0.26
105 495 0.37
106 260 0.19
107 7 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (104 bp):
GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
AAAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
Found at i:27635 original size:43 final size:43
Alignment explanation
Indices: 27574--27728 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
27564 CAGAGCCAAT
27574 TTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCAGACAACGCAAG
*** ** * * * *
27617 TTCAACTTCACGACGAAGGGACGCTGGTTTTCAATAAACAACTTCCCAAT
1 TTCAACTTCACGACGAA-GGATATTGG-ACTC--CAGACAA---CGCAAG
*
27667 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
27710 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
27729 GACCACTGGT
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
43 37 0.44
44 7 0.08
45 2 0.02
46 5 0.06
47 5 0.06
48 2 0.02
49 6 0.07
50 20 0.24
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:29989 original size:26 final size:25
Alignment explanation
Indices: 29953--30007 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
29943 TTTATTATTC
*
29953 TTTTAATTTTATTCTTTACTGATTAT
1 TTTTAATTTTATTATTT-CTGATTAT
* *
29979 TTTTATTTTTATTATTTCTGTTTAT
1 TTTTAATTTTATTATTTCTGATTAT
30004 TTTT
1 TTTT
30008 TTATTATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTTAATTTTATTATTTCTGATTAT
Found at i:30773 original size:24 final size:26
Alignment explanation
Indices: 30729--30787 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
30719 TTTTCTTTTC
30729 ATTTTCTTTACTATTATTATTTTT-T
1 ATTTTCTTTACTATTATTATTTTTAT
30754 -TTTTCTTT-CTGATT-TATATTTTTAT
1 ATTTTCTTTACT-ATTAT-TATTTTTAT
30779 ATTTTCTTT
1 ATTTTCTTT
30788 TTCTTTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 3 0.10
24 18 0.60
25 1 0.03
26 8 0.27
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (26 bp):
ATTTTCTTTACTATTATTATTTTTAT
Found at i:34811 original size:106 final size:106
Alignment explanation
Indices: 34677--35468 Score: 1299
Period size: 106 Copynumber: 7.6 Consensus size: 106
34667 AAAAGTTGTC
*
34677 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
34742 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
34783 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
34848 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
34889 TGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCT
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
34954 AGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
34995 TGTCAGTAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
35060 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
35101 TGTCAAT----AA-----CAA-TTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
35152 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
35193 TGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCT
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
35258 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
35299 TGTCAGTAAACAACTTCTCAATTTCAGAGCCAATTTCAATTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
35364 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * ** * * *
35405 TGTCAATAAATAA-TTTTCCAGTCCCAGAACCAATTTCAACTTCACATCGGAGGATATTGGACTC
1 TGTCAATAAACAACTTCT-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
35469 GGAACAATAC
Statistics
Matches: 644, Mismatches: 27, Indels: 30
0.92 0.04 0.04
Matches are distributed among these distances:
92 84 0.13
96 5 0.01
97 3 0.00
101 3 0.00
102 5 0.01
105 3 0.00
106 541 0.84
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:35090 original size:43 final size:43
Alignment explanation
Indices: 35029--35182 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 43
35019 CAGAGCCAAT
35029 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
35072 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACAATTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTCCA-GACAA--CGCAAG
35121 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
35164 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
35183 GACCGCTGGT
Statistics
Matches: 84, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
43 38 0.45
44 3 0.04
45 7 0.08
46 6 0.07
47 7 0.08
48 3 0.04
49 20 0.24
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:35361 original size:304 final size:307
Alignment explanation
Indices: 34684--35413 Score: 1313
Period size: 304 Copynumber: 2.4 Consensus size: 307
34674 GTCTGTCAAC
34684 AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
34749 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCC
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT----AA----TCAATTTC--A-CC
34814 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
120 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
34879 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGAT
185 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGAT
*
34944 ATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAGT
250 ATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGT
35002 AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
35067 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA-CAA-TTC-CCAATTTCAACTT
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAATCAATTTCACCAATTTCAACTT
35129 CACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
131 CACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
35194 GTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCTA
196 GTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCTA
35259 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGT
261 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGT
*
35306 AAACAACTTCTCAATTTCAGAGCCAATTTCAATTTCACAACGAAGGATATTGGACTCCAGACAAC
1 AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
*
35371 ACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
35414 ATAATTTTCC
Statistics
Matches: 409, Mismatches: 3, Indels: 14
0.96 0.01 0.03
Matches are distributed among these distances:
304 295 0.72
308 3 0.01
309 3 0.01
314 2 0.00
318 106 0.26
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (307 bp):
AAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAATCAATTTCACCAATTTCAACTT
CACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
GTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCTA
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGT
Found at i:35466 original size:410 final size:410
Alignment explanation
Indices: 34706--35468 Score: 1348
Period size: 410 Copynumber: 1.9 Consensus size: 410
34696 AATTTCAGAG
34706 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
34771 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGG
34836 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* *
34901 ACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAG
196 ACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
* * ** *
34966 TTCAACTTCACGACGAATGGACCGCTGGTTGTCAGTAAACAACTTCTCAATTTCAGAGCCAATTT
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATCCCAGAACCAATTT
35031 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
326 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
35096 CTGGTTGTCAATAACAATTC
391 CTGGTTGTCAATAACAATTC
35116 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
35181 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGG
* *
35246 ATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGTAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* *
35311 ACTTCTCAATTTCAGAGCCAATTTCAATTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
196 ACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
* * *
35376 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAA-TTTTCCAGTCCCAGAACCAATT
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT-CAATCCCAGAACCAATT
* *
35440 TCAACTTCACATCGGAGGATATTGGACTC
325 TCAACTTCACAACGAAGGATATTGGACTC
35469 GGAACAATAC
Statistics
Matches: 334, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
409 3 0.01
410 331 0.99
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (410 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
ACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATCCCAGAACCAATTT
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAATAACAATTC
Found at i:35972 original size:14 final size:14
Alignment explanation
Indices: 35955--35997 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
35945 GTCCCTTTTA
35955 TTTTTATAATATAC
1 TTTTTATAATATAC
*
35969 TTTTGATTAATATTA-
1 TTTTTA-TAATA-TAC
35984 TTTTTATAATATAC
1 TTTTTATAATATAC
35998 ATTATTGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 10 0.42
16 2 0.08
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTTTATAATATAC
Found at i:39752 original size:21 final size:21
Alignment explanation
Indices: 39726--39769 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
39716 TAATATTTAA
*
39726 ATTAGTTTGTTAATTTAAATT
1 ATTAGTGTGTTAATTTAAATT
* *
39747 ATTAGTGTGTTAGTTTAAGTT
1 ATTAGTGTGTTAATTTAAATT
39768 AT
1 AT
39770 ATTATATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTGTGTTAATTTAAATT
Done.