Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005616.1 Hibiscus syriacus cultivar Beakdansim tig00013063_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: 56536
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1563 original size:140 final size:139
Alignment explanation
Indices: 1369--1652 Score: 408
Period size: 140 Copynumber: 2.0 Consensus size: 139
1359 GTTTGGGGAC
* * * ** *
1369 CAATTTAGAAATAAGGTTATAGTTATGGATAAATTTAGAATGTTCAAAAGTTTAAGGGTTGATTT
1 CAATTTAGAAAGAAAGTTATAGTTATGGATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATTT
* * * *
1434 AAAATGAGAATCATAGTTT-AGGGATGAAATTGGAATATTCAAAAGTAAATGTTACAGTTTGGGG
66 AAAATGAGAATCATAGTTTCA-AGACGAAATTGAAATATTCAAAAGTAAAGGTTACAGTTTGGGG
*
1498 ACATATTATG
130 ACATATGATG
1508 CAATTTAGAAAGAAAGTTATAGTTTATGGATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATT
1 CAATTTAGAAAGAAAGTTATAG-TTATGGATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATT
* * *
1573 TAAAATGAGAGTCATAGTTTCAAGACGAAATTGAAATATTCAAAAGTGAAGGTTATAGTTTGGGG
65 TAAAATGAGAATCATAGTTTCAAGACGAAATTGAAATATTCAAAAGTAAAGGTTACAGTTTGGGG
1638 ACATATGATG
130 ACATATGATG
*
1648 AAATT
1 CAATT
1653 AATAATTTTC
Statistics
Matches: 128, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
139 20 0.16
140 107 0.84
141 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (139 bp):
CAATTTAGAAAGAAAGTTATAGTTATGGATAAAATTAGAATGTTCAAAAGTTTAAGGACTAATTT
AAAATGAGAATCATAGTTTCAAGACGAAATTGAAATATTCAAAAGTAAAGGTTACAGTTTGGGGA
CATATGATG
Found at i:4279 original size:2 final size:2
Alignment explanation
Indices: 4272--4305 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4262 ATATAACATA
4272 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
4306 GTGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4551 original size:20 final size:20
Alignment explanation
Indices: 4528--4568 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4518 GTTTCGAAAT
4528 TTTC-TCAATAGTTTTAAAAC
1 TTTCATCAA-AGTTTTAAAAC
*
4548 TTTCATCAAAGTTTTGAAAC
1 TTTCATCAAAGTTTTAAAAC
4568 T
1 T
4569 CTCCTTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (20 bp):
TTTCATCAAAGTTTTAAAAC
Found at i:7529 original size:18 final size:18
Alignment explanation
Indices: 7508--7605 Score: 65
Period size: 18 Copynumber: 5.2 Consensus size: 18
7498 TATAATTTAG
7508 ACATAAAATATTGATACA
1 ACATAAAATATTGATACA
* * *
7526 ACATCAAACA-TGATATTTA
1 ACATAAAATATTGATA--CA
*
7545 GACATAAAATATAGATACA
1 -ACATAAAATATTGATACA
* * *
7564 ACATCAAACA-TGATATTTA
1 ACATAAAATATTGATA--CA
7583 GACATAAAATATTGATACA
1 -ACATAAAATATTGATACA
7602 ACAT
1 ACAT
7606 CAAACATGAT
Statistics
Matches: 58, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
17 9 0.16
18 20 0.34
19 4 0.07
20 16 0.28
21 9 0.16
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (18 bp):
ACATAAAATATTGATACA
Found at i:7544 original size:38 final size:38
Alignment explanation
Indices: 7502--7617 Score: 223
Period size: 38 Copynumber: 3.1 Consensus size: 38
7492 ATAAGCTATA
7502 ATTTAGACATAAAATATTGATACAACATCAAACATGAT
1 ATTTAGACATAAAATATTGATACAACATCAAACATGAT
*
7540 ATTTAGACATAAAATATAGATACAACATCAAACATGAT
1 ATTTAGACATAAAATATTGATACAACATCAAACATGAT
7578 ATTTAGACATAAAATATTGATACAACATCAAACATGAT
1 ATTTAGACATAAAATATTGATACAACATCAAACATGAT
7616 AT
1 AT
7618 GAATGCAATG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (38 bp):
ATTTAGACATAAAATATTGATACAACATCAAACATGAT
Found at i:7937 original size:46 final size:46
Alignment explanation
Indices: 7797--7971 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
7787 CATCAGTTTG
* * * * *
7797 TTATTCGGTTATTAGAATTATCATTCGATAATAATGCACCAACAAA
1 TTATTCGGTTATTAGAATTACCATTCGATAAGAATACTCCAACATA
* * * * * *
7843 TTATCCAGTTATT-GAAATTACCATAT-GATAAGGATATTTCAACCTA
1 TTATTCGGTTATTAG-AATTACCAT-TCGATAAGAATACTCCAACATA
* *
7889 TTATTCGGTTATTAGAATTACCATTCGATAAGGATACTCCTACATA
1 TTATTCGGTTATTAGAATTACCATTCGATAAGAATACTCCAACATA
* *
7935 TTATTTGGTTATTAGAATTATCATTCGATAAGAATAC
1 TTATTCGGTTATTAGAATTACCATTCGATAAGAATAC
7972 ATTGGTATGT
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
45 2 0.02
46 101 0.96
47 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (46 bp):
TTATTCGGTTATTAGAATTACCATTCGATAAGAATACTCCAACATA
Found at i:8554 original size:6 final size:6
Alignment explanation
Indices: 8540--8640 Score: 157
Period size: 6 Copynumber: 16.8 Consensus size: 6
8530 TAAAAGCATA
* * *
8540 CATATG CATACG CATACA CATACG CATACG CATACG CATACA CATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* *
8588 CATATG CATACG CATACG CATACG CATACA CATACG CATACG CATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
8636 CATAC
1 CATAC
8641 ACGTACAATA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 86 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.19
Consensus pattern (6 bp):
CATACG
Found at i:10713 original size:23 final size:23
Alignment explanation
Indices: 10687--10730 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
10677 GTGCAATAAT
*
10687 TTTTTATTATTTTAATTTAATCA
1 TTTTAATTATTTTAATTTAATCA
*
10710 TTTTAATTATTTTAGTTTAAT
1 TTTTAATTATTTTAATTTAAT
10731 TGAAATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTAATTATTTTAATTTAATCA
Found at i:18191 original size:38 final size:38
Alignment explanation
Indices: 18138--18752 Score: 710
Period size: 38 Copynumber: 15.8 Consensus size: 38
18128 GAAGCTTCAA
* * *
18138 CTTGACTTCCTCGTGAAGAGAAGTCAATTTTTGCTACT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
**
18176 CTTGACTTCAACGTGAAGAGAAGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * *
18214 TTTGACTTCCTCGTGAAAAAAAGTCAATCTTTCAATGTTGTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
18256 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* *
18294 CTTGACTTTCTCATGAAGAGAAGTCAATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * *
18332 CCTGACTCCCTCGCGAAGAGGAGTCAATCTTTCAATGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
* *
18374 CTTGACTTCCTCGTGAAGAGAATTCGATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * *
18412 TTTGACTTCATCGTGAAGAGAAATCAATCTTTTTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
18450 CTTGACTTTCTCTTGAAGAGAAGTCAATCTTTGTTAACT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTT-ATT
*
18489 CTTGACTTCCTCGTGAAGAGAAGTCAATATTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * ** *
18527 CCTAAC-TCACTTGCAAAGAGGAGTCAATCTTTCAATGTTATT
1 CTTGACTTC-CTCGTGAAGAGAAGTCAATC-TT---TGTTATT
* * * **
18569 ATTGACTTCCTCATGAAGAAAAGTTGATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
18607 CTTGACTTCCTCGTGAAGAGAAGTCGATCTTTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
18645 CTTGACTCCCTCGTGAAAAGAAGTCAATCTTTGTTTTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* *
18683 CTTGACTTACTCGTGAAGAGAAGTCAATCTGTGTTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
18721 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTT
18753 TAGTGTTTTC
Statistics
Matches: 484, Mismatches: 78, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
37 2 0.00
38 350 0.72
39 40 0.08
41 6 0.01
42 84 0.17
43 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (38 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
Found at i:18357 original size:118 final size:113
Alignment explanation
Indices: 18138--18752 Score: 701
Period size: 118 Copynumber: 5.3 Consensus size: 113
18128 GAAGCTTCAA
* * * *
18138 CTTGACTTCCTCGTGAAGAGAAGTCAATTTTTGCTACTCTTGACTTCAACGTGAAGAGAAGTCAA
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTC-TCGTGAAGAGAAGTCAA
* * * *
18203 TCTTTGTTATTTTTGACTTCCTCGTGAAAAAAAGTCAATCTTTCAATGTTGTT
65 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
*
18256 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCATGAAGAGAAGTCAA
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGAC-TTCTCGTGAAGAGAAGTCAA
* * * *
18321 TCTTTGTTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTCAATGTTATT
65 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATT
* * * *
18374 CTTGACTTCCTCGTGAAGAGAATTCGATCTTTGTTATTTTTGACTTCATCGTGAAGAGAAATCAA
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTC-TCGTGAAGAGAAGTCAA
* * * *
18439 TCTTTTTTATTCTTGACTTTCTCTTGAAGAGAAGTCAATCTTTGTTAACT
65 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTT-ATT
* * * * * *
18489 CTTGACTTCCTCGTGAAGAGAAGTCAATATTTGTTATTCCTAAC-TCACTTGCAAAGAGGAGTCA
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCTCGTG--AAGAGAAGTCA
* * * **
18553 ATCTTTCAATGTTATTATTGACTTCCTCATGAAGAAAAGTTGATCTTTGTTATT
64 ATC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * *
18607 CTTGACTTCCTCGTGAAGAGAAGTCGATCTTTGTTATTCTTGACTCCCTCGTGAAAAGAAGTCAA
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACT-TCTCGTGAAGAGAAGTCAA
* * *
18672 TCTTTGTTTTTCTTGACTTACTCGTGAAGAGAAGTCAATCTGTGTTATT
65 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
*
18721 CTTGACTTTCTCGTGAAGAGAAGTCAATCTTT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTT
18753 TAGTGTTTTC
Statistics
Matches: 423, Mismatches: 63, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
113 3 0.01
114 73 0.17
115 52 0.12
116 2 0.00
117 7 0.02
118 244 0.58
119 38 0.09
120 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (113 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCTCGTGAAGAGAAGTCAAT
CTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
Found at i:18772 original size:45 final size:43
Alignment explanation
Indices: 18719--19024 Score: 220
Period size: 45 Copynumber: 6.6 Consensus size: 43
18709 ATCTGTGTTA
* *
18719 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTTTC
1 TTCTTGACTTTCTCGCGAAGAG-AGTCAATCTTTTAGTGTTTCC
* * * *
18763 TTCCTTGACTTTCTCGCAAAGATGAGTCAATCTTTTTGTATTACC
1 TT-CTTGACTTTCTCGCGAAGA-GAGTCAATCTTTTAGTGTTTCC
* *
18808 ATT-TTGGACTTTCTCGTGAAGAGAAATCAATCTCTTAATATTTTAGTGTTTTCC
1 -TTCTT-GACTTTCTCGCGAAGAG-AGTCAA--TC------TTTTAGTG-TTTCC
* * * * * *
18862 TTTTTGACTTTCTCGTGAATATGAGTCAATATTCTAGTGTTGCC
1 TTCTTGACTTTCTCGCGAAGA-GAGTCAATCTTTTAGTGTTTCC
* * *
18906 TTCTTTAACTTTCTCGCGAAGTGGAGTCAATCTTTTATTGTTGT-C
1 TTC-TTGACTTTCTCGCGAAG-AGAGTCAATCTTTTAGTGTT-TCC
* *
18951 TTCATTGACTTTCTCGCGAAGTGGAGTCAATATTTTAGTGTTGTCC
1 TTC-TTGACTTTCTCGCGAAG-AGAGTCAATCTTTTAGTGTT-TCC
18997 TTCTTGACTTTCTCGCGAAGATGAGTCA
1 TTCTTGACTTTCTCGCGAAGA-GAGTCA
19025 TTATTTCAGA
Statistics
Matches: 210, Mismatches: 31, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
44 11 0.05
45 154 0.73
46 7 0.03
47 2 0.01
51 1 0.00
53 28 0.13
54 7 0.03
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (43 bp):
TTCTTGACTTTCTCGCGAAGAGAGTCAATCTTTTAGTGTTTCC
Found at i:19030 original size:45 final size:46
Alignment explanation
Indices: 18844--19030 Score: 224
Period size: 45 Copynumber: 4.2 Consensus size: 46
18834 TCAATCTCTT
* * * *
18844 AATATTTTAGTGTTTTCCTT-TTTGACTTTCTCGTGAA-TATGAGTC
1 AATATTTTAGTGTTGTCCTTCATTGACTTTCTCGCGAAGT-GGAGTC
* * *
18889 AATATTCTAGTGTTG-CCTTCTTTAACTTTCTCGCGAAGTGGAGTC
1 AATATTTTAGTGTTGTCCTTCATTGACTTTCTCGCGAAGTGGAGTC
* *
18934 AATCTTTTATTGTTGT-CTTCATTGACTTTCTCGCGAAGTGGAGTC
1 AATATTTTAGTGTTGTCCTTCATTGACTTTCTCGCGAAGTGGAGTC
18979 AATATTTTAGTGTTGTCCTTC-TTGACTTTCTCGCGAAGAT-GAGTC
1 AATATTTTAGTGTTGTCCTTCATTGACTTTCTCGCGAAG-TGGAGTC
*
19024 ATTATTT
1 AATATTT
19031 CAGATTTGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
44 4 0.03
45 114 0.92
46 6 0.05
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (46 bp):
AATATTTTAGTGTTGTCCTTCATTGACTTTCTCGCGAAGTGGAGTC
Found at i:19454 original size:134 final size:134
Alignment explanation
Indices: 19028--19702 Score: 902
Period size: 134 Copynumber: 5.0 Consensus size: 134
19018 TGAGTCATTA
* * * * *
19028 TTTCAGATTTGGTCTTCCTGAAAAGTAGTGAAGCAAATCAATTCTGATTCAATCTTCCTTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
** * * * ** *
19093 GCAGTGAAGTAAATCAAAATTTTCACGAGTTTGATCTCCCCCAATTAGTAGTGGAGCAGATTCTT
66 GCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTT
*
19158 TTTC
131 CTTC
* * *
19162 TTTCATATTTGGTCTTCCTGAGGAGCAGC-AAAGCAAATCAATTTTGATTCAATCTTCCCTGAAG
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAA-CAAATCAATTCTGATTCAATCTTCCCTGAAG
* * * * * * *
19226 AACAGTGAAGTTGATTGAAATTTTTCTCGAGTCAGATCTCCCCTAAAGAGTAGCGAAGTAGATTC
65 AGCAGTGAAGTGGA-TCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTC
19291 TTCTTC
129 TTCTTC
* **
19297 TTTCAGATTTGGTTTTCCTGAAGAGCAATGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
* * *
19362 GAAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCTTAAAGAGTAGCGGAGCAAATTCTT
66 GCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTT
19427 CTTC
131 CTTC
* * *
19431 TTTCAGATTTGGTCTTCCCGAAGAGCAGCGAAACAAATCGATTCTGATTCAATCTTCCCTAAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
* * * *
19496 GCATTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCTTAAAGAGTAGCAGAGGAGATTCTT
66 GCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTT
19561 CTTC
131 CTTC
* * * * * * *
19565 TTTCAGATTTGGTCTTCCTAAATAGCAGCAAAACAAATCGATTCTGATTCCATCGTCCCTAAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
* * *
19630 GCAGTGAAGTGGATCAAAAGTTTCTCGAGTTTGATCTCCCCTAAAAAGTAGCGGAGCAGATTCTT
66 GCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTT
19695 CTTC
131 CTTC
19699 TTTC
1 TTTC
19703 TACAAGAAAT
Statistics
Matches: 475, Mismatches: 63, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
133 2 0.00
134 361 0.76
135 109 0.23
136 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (134 bp):
TTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
GCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTT
CTTC
Found at i:19518 original size:269 final size:268
Alignment explanation
Indices: 19028--19702 Score: 933
Period size: 269 Copynumber: 2.5 Consensus size: 268
19018 TGAGTCATTA
* * *
19028 TTTCAGATTTGGTCTTCCTGAAAAGTAGTGAAGCAAATCAATTCTGATTCAATCTTCCTTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAAAGCAGTGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
** * * ** *
19093 GCAGTGAAGTAAATCAAAATTTTCACGAGTTTGATCTCCCCCAATTAGTAGTGGAGCAGATTCTT
66 GCAGTGAAGTGGATCAAAATTTTCTCGAGTTTGATCTCCCCTAAAAAGTAGCGGAGCAGATTCTT
* * * * * *
19158 TTTCTTTCATATTTGGTCTTCCTGAGGAGCAGCAAAGCAAATCAATTTTGATTCAATCTTCCCTG
131 CTTCTTTCAGATTTGGTCTTCCCGAAGAGCAGCAAAGCAAATCAATTCTGATTCAATCTTCCCTA
* * * *
19223 AAGAACAGTGAAGTTGATTGAAATTTTTCTCGAGTCAGATCTCCCCTAAAGAGTAGC-GAAGTAG
196 AAGAACAGTGAAGTGGA-TCAAAATTTTCTCGAGTCAGATCTCCCCTAAAGAGTAGCAG-AGGAG
19287 ATTCTTCTTC
259 ATTCTTCTTC
* * *
19297 TTTCAGATTTGGTTTTCCTGAAGAGCAATGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAAAGCAGTGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
* * * * *
19362 GAAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCTTAAAGAGTAGCGGAGCAAATTCTT
66 GCAGTGAAGTGGATCAAAATTTTCTCGAGTTTGATCTCCCCTAAAAAGTAGCGGAGCAGATTCTT
*
19427 CTTCTTTCAGATTTGGTCTTCCCGAAGAGCAGCGAAA-CAAATCGATTCTGATTCAATCTTCCCT
131 CTTCTTTCAGATTTGGTCTTCCCGAAGAGCAGC-AAAGCAAATCAATTCTGATTCAATCTTCCCT
* * * *
19491 AAAGAGCATTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCTTAAAGAGTAGCAGAGGAGA
195 AAAGAACAGTGAAGTGGATCAAAATTTTCTCGAGTCAGATCTCCCCTAAAGAGTAGCAGAGGAGA
19556 TTCTTCTTC
260 TTCTTCTTC
** * * * *
19565 TTTCAGATTTGGTCTTCCT-AAATAGCAGCAAAACAAATCGATTCTGATTCCATCGTCCCTAAAG
1 TTTCAGATTTGGTCTTCCTGAAA-AGCAGTGAAACAAATCAATTCTGATTCAATCTTCCCTGAAG
*
19629 AGCAGTGAAGTGGATCAAAAGTTTCTCGAGTTTGATCTCCCCTAAAAAGTAGCGGAGCAGATTCT
65 AGCAGTGAAGTGGATCAAAATTTTCTCGAGTTTGATCTCCCCTAAAAAGTAGCGGAGCAGATTCT
19694 TCTTCTTTC
130 TCTTCTTTC
19703 TACAAGAAAT
Statistics
Matches: 356, Mismatches: 47, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
267 2 0.01
268 169 0.47
269 182 0.51
270 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (268 bp):
TTTCAGATTTGGTCTTCCTGAAAAGCAGTGAAACAAATCAATTCTGATTCAATCTTCCCTGAAGA
GCAGTGAAGTGGATCAAAATTTTCTCGAGTTTGATCTCCCCTAAAAAGTAGCGGAGCAGATTCTT
CTTCTTTCAGATTTGGTCTTCCCGAAGAGCAGCAAAGCAAATCAATTCTGATTCAATCTTCCCTA
AAGAACAGTGAAGTGGATCAAAATTTTCTCGAGTCAGATCTCCCCTAAAGAGTAGCAGAGGAGAT
TCTTCTTC
Found at i:19751 original size:14 final size:15
Alignment explanation
Indices: 19727--19757 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
19717 ATGATTGTGA
19727 CAAATTTAATTTTGT
1 CAAATTTAATTTTGT
19742 CAAA-TTAATTTTGT
1 CAAATTTAATTTTGT
19756 CA
1 CA
19758 CTATTAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (15 bp):
CAAATTTAATTTTGT
Found at i:25976 original size:23 final size:23
Alignment explanation
Indices: 25950--26018 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
25940 CACCATAGCT
*
25950 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * * *
25973 CGTAGGATTTCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
* * * *
25996 CATAGGATTGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
26019 TATAAAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:27601 original size:21 final size:21
Alignment explanation
Indices: 27577--27624 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
27567 CAAATGCCCA
27577 AGGTATACTATTGAGAAATCT
1 AGGTATACTATTGAGAAATCT
27598 AGGTATACTATTGAGAAATCT
1 AGGTATACTATTGAGAAATCT
27619 AGGTAT
1 AGGTAT
27625 TTGAGTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (21 bp):
AGGTATACTATTGAGAAATCT
Found at i:28000 original size:13 final size:13
Alignment explanation
Indices: 27979--28008 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27969 ATCAAGGCTC
*
27979 ATAATACATAGTT
1 ATAAAACATAGTT
27992 ATAAAACATAGTT
1 ATAAAACATAGTT
28005 ATAA
1 ATAA
28009 CAATGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (13 bp):
ATAAAACATAGTT
Found at i:31808 original size:38 final size:35
Alignment explanation
Indices: 31724--31808 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
31714 TAATTTTGTA
* * *
31724 AAAAATATATATAAATATTATGAATTTAATTTTTT
1 AAAAATATATATAAATATTATCAATTTAATATTAT
* *
31759 AAAGAAAATATATAAATATTTTACAATTTGTAATATTAT
1 AAA-AATATATATAAATATTAT-CAA-TT-TAATATTAT
31798 AAAAATATATA
1 AAAAATATATA
31809 ATAAGGACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.08
36 16 0.40
37 2 0.05
38 9 0.22
39 10 0.25
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (35 bp):
AAAAATATATATAAATATTATCAATTTAATATTAT
Found at i:31969 original size:20 final size:20
Alignment explanation
Indices: 31933--31970 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31923 ATCTTATTTC
**
31933 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
31953 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
31971 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:32454 original size:21 final size:21
Alignment explanation
Indices: 32425--32480 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
32415 ATTCTGACTA
*
32425 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
32446 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
*
32467 TCGCGTAGCGATTT
1 TCGCGTTGCGATTT
32481 TCCTAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:32513 original size:20 final size:20
Alignment explanation
Indices: 32484--32580 Score: 149
Period size: 20 Copynumber: 4.8 Consensus size: 20
32474 GCGATTTTCC
* *
32484 TAAATAGCAATGCGATTACG
1 TAAATCGCAATGCGAATACG
32504 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
* *
32524 TAAATTGCAATGCGATTACG
1 TAAATCGCAATGCGAATACG
*
32544 TAAATCACAATGCGAATACG
1 TAAATCGCAATGCGAATACG
32564 TAAATCGCAATGCGAAT
1 TAAATCGCAATGCGAAT
32581 CTGACTATCG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:32590 original size:20 final size:20
Alignment explanation
Indices: 32567--32618 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
32557 GAATACGTAA
32567 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
32587 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
32607 ATCGCAATGCGA
1 ATCGCAATGCGA
32619 TTTACATAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:32595 original size:40 final size:39
Alignment explanation
Indices: 32484--32600 Score: 148
Period size: 40 Copynumber: 2.9 Consensus size: 39
32474 GCGATTTTCC
*
32484 TAAATAGCAATGCGATTACGTAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGATTACGT-AATCGCAATGCGAATACG
* *
32524 TAAATTGCAATGCGATTACGTAAATCACAATGCGAATACG
1 TAAATCGCAATGCGATTACGT-AATCGCAATGCGAATACG
32564 TAAATCGCAATGCGAATCTGAC-T-ATCGCAATGCGAAT
1 TAAATCGCAATGCG-AT-T-ACGTAATCGCAATGCGAAT
32601 CTGACTATCG
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
40 64 0.91
41 2 0.03
42 2 0.03
43 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (39 bp):
TAAATCGCAATGCGATTACGTAATCGCAATGCGAATACG
Found at i:33191 original size:20 final size:20
Alignment explanation
Indices: 33166--33214 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
33156 CAACGAGTGA
33166 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
33186 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
33206 ATCGCAACG
1 ATCGCAACG
33215 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:33282 original size:20 final size:20
Alignment explanation
Indices: 33235--33311 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
33225 AATGCGGTTT
33235 TCATTTT-GCGTTGCGATAG
1 TCATTTTCGCGTTGCGATAG
** *
33254 TCAAATTCGCATTGCGATAG
1 TCATTTTCGCGTTGCGATAG
* **
33274 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGCGTTGCGATAG
*
33294 TCATTTTCGTGTTGCGAT
1 TCATTTTCGCGTTGCGAT
33312 TTAAAGTTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
19 5 0.10
20 43 0.90
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
TCATTTTCGCGTTGCGATAG
Found at i:33321 original size:20 final size:20
Alignment explanation
Indices: 33278--33321 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
33268 CGATAGTCAT
** *
33278 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
33298 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
33318 TTTC
1 TTTC
33322 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:34975 original size:35 final size:35
Alignment explanation
Indices: 34927--35036 Score: 139
Period size: 35 Copynumber: 3.1 Consensus size: 35
34917 TCTAAACCTT
* *
34927 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
* * *
34962 TAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
* * * *
34997 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
35032 AAATT
1 AAATT
35037 AAGGACTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
Found at i:36215 original size:20 final size:20
Alignment explanation
Indices: 36190--36296 Score: 127
Period size: 20 Copynumber: 5.6 Consensus size: 20
36180 AGAATAGTTT
36190 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
36210 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
36230 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
36246 A--ATCGCAATGCAAAAAATG
1 ACTATCGCAATGC-GAAAATG
*
36265 GCTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
36285 ACTATCGCAATG
1 ACTATCGCAATG
36297 AAAGAATCGC
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.10
16 3 0.04
17 2 0.03
18 4 0.05
19 1 0.01
20 46 0.63
21 10 0.14
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:36280 original size:55 final size:54
Alignment explanation
Indices: 36193--36311 Score: 184
Period size: 55 Copynumber: 2.2 Consensus size: 54
36183 ATAGTTTACT
* *
36193 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGA
* * *
36247 ATCGCAATGCAAAAAATGGCTATCGCAATGCGAAAATGACTATCGCAATGAAAGA
1 ATCGCAATGC-AAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGA
36302 ATCGCAATGC
1 ATCGCAATGC
36312 GAAATGAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
54 10 0.17
55 49 0.83
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (54 bp):
ATCGCAATGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGA
Found at i:36317 original size:21 final size:19
Alignment explanation
Indices: 36268--36332 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
36258 AAAAATGGCT
**
36268 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCG-AAATGAAA
36288 ATCGCAAT--GAAA-G--A
1 ATCGCAATGCGAAATGAAA
36302 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36321 ATCGCATTGCGA
1 ATCGCAATGCGA
36333 TTCTCTCGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 8 0.21
16 5 0.13
17 4 0.11
18 1 0.03
19 12 0.32
20 8 0.21
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:36369 original size:20 final size:20
Alignment explanation
Indices: 36344--36407 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
36334 TCTCTCGTTA
**
36344 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
36364 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
36384 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
36404 CGAT
1 CGAT
36408 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:36933 original size:18 final size:19
Alignment explanation
Indices: 36894--36935 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
36884 CTCACCTGTC
36894 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
36915 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
36933 ATC
1 ATC
36936 ATTCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:38483 original size:33 final size:33
Alignment explanation
Indices: 38426--38554 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
38416 AAAACAGACT
* ** *
38426 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGTGA
*
38460 ATCGTAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
* *
38493 ATCGCAATGCGAAATGAAAATTGCAAAGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
*
38526 ATCGCAATGCGAAAATGAAAATCGTAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
38555 CGAAACTAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
33 61 0.73
34 22 0.27
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
Found at i:38757 original size:33 final size:33
Alignment explanation
Indices: 38720--38824 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
38710 ATGACTATCA
38720 CAACGAGAGAATCGCAATGCGAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAATGAAAATCG
*
38753 CAACGAGGGAATCGCAATGCGAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAATGAAAATCG
*
38786 CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCG-AAATGAAAATCG
38820 CAACG
1 CAACG
38825 CGAAACTAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
33 52 0.75
34 17 0.25
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (33 bp):
CAACGAGAGAATCGCAATGCGAAATGAAAATCG
Found at i:38800 original size:270 final size:270
Alignment explanation
Indices: 38319--39061 Score: 1405
Period size: 270 Copynumber: 2.7 Consensus size: 270
38309 GTAAATGTTA
38319 ATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
1 ATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
38384 TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTATC
66 TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTATC
*
38449 GCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAATGAAAAT
131 GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAATGAAAAT
* * *
38514 TGCAAAGAGTGAATCGCAATGCGAAAATGAAAATCGTAACGCGAAACTAATTTCGCGTTGCGATT
196 CGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTGCGATT
38579 TTCATTTTCG
261 TTCATTTTCG
38589 ATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
1 ATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
*
38654 TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATTGCAACGCGGAAATGACTATC
66 TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTATC
* *
38719 ACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAAT
131 GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAATGAAAAT
38784 CGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTGCGATT
196 CGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTGCGATT
38849 TTCATTTTCG
261 TTCATTTTCG
38859 ATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
1 ATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
*
38924 TTGTTGATTTCAATATGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTATC
66 TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTATC
38989 GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAA
131 GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCG-AAATGAAAA
39054 TCGCAACG
195 TCGCAACG
39062 CGAAACTAAT
Statistics
Matches: 461, Mismatches: 11, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
270 444 0.96
271 17 0.04
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (270 bp):
ATTTGTTTAATTGATGTGTACATAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCGCAACGCGGAAATGACTATC
GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAATGAAAAT
CGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTGCGATT
TTCATTTTCG
Found at i:38820 original size:20 final size:19
Alignment explanation
Indices: 38729--38829 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 19
38719 ACAACGAGAG
38729 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
38748 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
38762 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
38781 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
38795 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
38815 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
38830 CTAATTTCGC
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
14 17 0.27
15 1 0.02
16 7 0.11
17 4 0.06
18 4 0.06
19 20 0.31
20 11 0.17
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:39054 original size:34 final size:33
Alignment explanation
Indices: 38966--39061 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
38956 AAAACAGACT
* **
38966 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
39000 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
39033 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
39062 CGAAACTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:39057 original size:20 final size:19
Alignment explanation
Indices: 38999--39066 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
38989 GCAACGAGAG
38999 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39018 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
39032 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
39052 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
39067 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:39114 original size:33 final size:33
Alignment explanation
Indices: 39070--39151 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
39060 CGCGAAACTA
**
39070 ATTTCGCATTGCGATTCACTCGTTACGATTTTC
1 ATTTCGCATTGCGATTCACTCGTTACGATAGTC
* * *
39103 ATTTCGTATTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCATTGCGATTCACTCGTTACGATAGTC
*
39136 ATTTCCGCGTTGCGAT
1 ATTT-CGCATTGCGAT
39152 AGTCAATTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 32 0.78
34 9 0.22
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCACTCGTTACGATAGTC
Found at i:39148 original size:20 final size:20
Alignment explanation
Indices: 39123--39211 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
39113 GCGATTCTCT
39123 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
39143 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
39163 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
39183 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
39203 CGTTGCGAT
1 CGTTGCGAT
39212 TTCCGTGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:41672 original size:24 final size:24
Alignment explanation
Indices: 41645--41698 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
41635 CTGAAAAATC
*
41645 ATCAAAATCCGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
41669 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
41693 ATCAAA
1 ATCAAA
41699 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:42600 original size:20 final size:20
Alignment explanation
Indices: 42562--42601 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42552 TAGAATCTCG
*
42562 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGAATCGCA
42582 TTGCGATTTAC-GTAATCGCA
1 TTGCGATTTACAG-AATCGCA
42602 ACCTGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGCGATTTACAGAATCGCA
Found at i:43983 original size:44 final size:43
Alignment explanation
Indices: 43865--43995 Score: 124
Period size: 44 Copynumber: 3.0 Consensus size: 43
43855 GCAACATCTT
* *
43865 AGGTCCCTAA-TTTTT-ATTATATTTTTTTATTTTTATAATTG
1 AGGTCCCTAATTTTTTAATTTTATTTTTTTATATTTATAATTG
* ** * ** *
43906 A-GACTTTTAATTTTTTTTAAATTTAAATTTTTATATTTATAGTTG
1 AGGTC-CCTAA--TTTTTTAATTTTATTTTTTTATATTTATAATTG
43951 AGGTCCCTAATTTTTGTAATTTTATTTTTTTATATTTATAATTG
1 AGGTCCCTAATTTTT-TAATTTTATTTTTTTATATTTATAATTG
43995 A
1 A
43996 TGCACTTAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.03
41 4 0.06
43 5 0.07
44 30 0.45
45 24 0.36
46 2 0.03
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.60
Consensus pattern (43 bp):
AGGTCCCTAATTTTTTAATTTTATTTTTTTATATTTATAATTG
Found at i:44006 original size:44 final size:43
Alignment explanation
Indices: 43884--44009 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 43
43874 ATTTTTATTA
* *
43884 TATTTTTTTATTTTTATAATTGAG-ACTTTTAATTTTTTTTAAATT
1 TATTTTTTTATATTTATAATTGAGCAC--TTAA-TTTTTGTAAATT
** * * *
43929 TAAATTTTTATATTTATAGTTGAGGTC-CCTAATTTTTGTAATTT
1 TATTTTTTTATATTTATAATTGA-G-CACTTAATTTTTGTAAATT
43973 TATTTTTTTATATTTATAATTGATGCACTTAATTTTT
1 TATTTTTTTATATTTATAATTGA-GCACTTAATTTTT
44010 TTCAACCTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.02
44 40 0.62
45 22 0.34
46 1 0.02
47 1 0.02
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (43 bp):
TATTTTTTTATATTTATAATTGAGCACTTAATTTTTGTAAATT
Found at i:44034 original size:89 final size:85
Alignment explanation
Indices: 43865--44054 Score: 186
Period size: 89 Copynumber: 2.2 Consensus size: 85
43855 GCAACATCTT
* * *
43865 AGGTCCCTAA-TTTTTATTATATTTTTTTATTTTTATAATTGAGACTTTTAATTTTTTTTAAATT
1 AGGTCCCTAATTTTTTATTATATTTTTTTATATTTATAATTGAGAC-TTTAATTTTTTTCAAACT
* *
43929 TAAATTTTTATATTTATAGTTG
65 CAAATTTTTACATTTATA-TTG
*
43951 AGGTCCCTAATTTTTGTAATTTTATTTTTTTATATTTATAATTGATGCAC-TTAATTTTTTTCAA
1 AGGTCCCTAATTTTT-T-ATTATATTTTTTTATATTTATAATTGA-G-ACTTTAATTTTTTTCAA
* ** * *
44015 CCTCACTTTTTTGCGTTTATATTG
62 ACTCAAATTTTTACATTTATATTG
* * *
44039 ATGACCCTAAGTTTTT
1 AGGTCCCTAATTTTTT
44055 CAATCTCACT
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
86 10 0.12
87 5 0.06
88 16 0.19
89 51 0.60
90 1 0.01
91 2 0.02
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.57
Consensus pattern (85 bp):
AGGTCCCTAATTTTTTATTATATTTTTTTATATTTATAATTGAGACTTTAATTTTTTTCAAACTC
AAATTTTTACATTTATATTG
Found at i:44082 original size:43 final size:42
Alignment explanation
Indices: 43985--44306 Score: 262
Period size: 43 Copynumber: 7.5 Consensus size: 42
43975 TTTTTTTATA
* * * *
43985 TTTATAATTGATGCACTTAATTTTTTTCAACCTCACTTTTTTGCG
1 TTTATAATTGATGC-CCTAA-TTTTTTCAATCTCAC-TTTTTACC
* * *
44030 TTTAT-ATTGATGACCCTAAGTTTTTCAATCTCACTTTGTACT
1 TTTATAATTGATG-CCCTAATTTTTTCAATCTCACTTTTTACC
* * *
44072 TTTATAATTGA-GCTTCTAA-TTTTTCAATCTCACTTTCTATC
1 TTTATAATTGATGC-CCTAATTTTTTCAATCTCACTTTTTACC
* *
44113 TTTATAATTGAGGACTCTAATTTTTT-AATCTCA-TTTTTAACC
1 TTTATAATTGATG-CCCTAATTTTTTCAATCTCACTTTTT-ACC
* * * *
44155 CTTATAATTGAGGCACCTAATTTTTTCAAACTCATTTTTTA-C
1 TTTATAATTGATGC-CCTAATTTTTTCAATCTCACTTTTTACC
* * *
44197 TTATATAATTTAGGCCCCTAATTTTTTCAATCTCAGTTTTTACC
1 TT-TATAATTGATG-CCCTAATTTTTTCAATCTCACTTTTTACC
* * *
44241 TTTAAAATTGATGCCCTTAACTTTTTT-AATATCACTTCTTACC
1 TTTATAATTGATGCCC-TAA-TTTTTTCAATCTCACTTTTTACC
* *
44284 TTTATAATTTAAGCCCATAATTT
1 TTTATAATTGATGCCC-TAATTT
44307 AATCATTTTC
Statistics
Matches: 233, Mismatches: 29, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
41 36 0.15
42 60 0.26
43 105 0.45
44 26 0.11
45 6 0.03
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.48
Consensus pattern (42 bp):
TTTATAATTGATGCCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:44103 original size:41 final size:42
Alignment explanation
Indices: 43933--44306 Score: 246
Period size: 43 Copynumber: 8.7 Consensus size: 42
43923 TAAATTTAAA
* * * *
43933 TTTTTA-TATTTATAGTTGAGGTCCCTAATTTTTGT-AATTTTATT
1 TTTTTACT-TTTATAATTGAGG-CCCTAATTTTT-TCAATCTCA-C
* * *
43977 TTTTTA-TATTTATAATTGATGCACTTAATTTTTTTCAACCTCAC
1 TTTTTACT-TTTATAATTGAGGC-CCTAA-TTTTTTCAATCTCAC
* * * *
44021 TTTTTTGCGTTTAT-ATTGATGACCCTAAGTTTTTCAATCTCAC
1 -TTTTTACTTTTATAATTGA-GGCCCTAATTTTTTCAATCTCAC
* *
44064 TTTGTACTTTTATAATTGA-GCTTCTAA-TTTTTCAATCTCAC
1 TTTTTACTTTTATAATTGAGGC-CCTAATTTTTTCAATCTCAC
* *
44105 TTTCTA-TCTTTATAATTGAGGACTCTAATTTTTT-AATCTCA-
1 TTTTTACT-TTTATAATTGAGG-CCCTAATTTTTTCAATCTCAC
** * *
44146 TTTTTAACCCTTATAATTGAGGCACCTAATTTTTTCAAACTCAT
1 TTTTT-ACTTTTATAATTGAGGC-CCTAATTTTTTCAATCTCAC
* * *
44190 TTTTTACTTATATAATTTAGGCCCCTAATTTTTTCAATCTCAG
1 TTTTTACTTTTATAATTGAGG-CCCTAATTTTTTCAATCTCAC
* * * *
44233 TTTTTACCTTTAAAATTGATGCCCTTAACTTTTTT-AATATCAC
1 TTTTTACTTTTATAATTGAGGCCC-TAA-TTTTTTCAATCTCAC
* * * *
44276 TTCTTACCTTTATAATTTAAGCCCATAATTT
1 TTTTTACTTTTATAATTGAGGCCC-TAATTT
44307 AATCATTTTC
Statistics
Matches: 267, Mismatches: 43, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
40 1 0.00
41 36 0.13
42 56 0.21
43 109 0.41
44 45 0.17
45 20 0.07
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (42 bp):
TTTTTACTTTTATAATTGAGGCCCTAATTTTTTCAATCTCAC
Found at i:44109 original size:21 final size:21
Alignment explanation
Indices: 44045--44110 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
44035 ATTGATGACC
44045 CTAAGTTTTTCAATCTCACTTT
1 CTAA-TTTTTCAATCTCACTTT
* * *
44067 GTACTTTTAT-AAT-TGAGC-TT
1 CTAATTTT-TCAATCTCA-CTTT
44087 CTAATTTTTCAATCTCACTTT
1 CTAATTTTTCAATCTCACTTT
44108 CTA
1 CTA
44111 TCTTTATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 11
0.66 0.12 0.22
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 15 0.45
22 3 0.09
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (21 bp):
CTAATTTTTCAATCTCACTTT
Found at i:44676 original size:47 final size:47
Alignment explanation
Indices: 44623--44718 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
44613 ACAAAATGAC
*
44623 ATGTTCATGCTTCATTTCATGCCCTAAGTGTAACTCTCTAAATTCAA
1 ATGTTCATGCTTCATTTCATGCCCTAAGTGTAACTCTCTAAATCCAA
*
44670 ATGTTCATGCTTCATTTCATGCCTTAAGTGTAACTCTCTAAATCCAA
1 ATGTTCATGCTTCATTTCATGCCCTAAGTGTAACTCTCTAAATCCAA
44717 AT
1 AT
44719 CAGTTATTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (47 bp):
ATGTTCATGCTTCATTTCATGCCCTAAGTGTAACTCTCTAAATCCAA
Found at i:47094 original size:29 final size:29
Alignment explanation
Indices: 47035--47095 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
47025 TTCAATAACT
* * * *
47035 AAAATATAATGAATAAATTGAATAAATTA
1 AAAATACAATAAATAAATAGAATAAAATA
47064 AAAATACAATAAATGAAATAGAA-AAAATA
1 AAAATACAATAAAT-AAATAGAATAAAATA
47093 AAA
1 AAA
47096 TTGAGTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.23
Consensus pattern (29 bp):
AAAATACAATAAATAAATAGAATAAAATA
Found at i:49337 original size:2 final size:2
Alignment explanation
Indices: 49330--49365 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
49320 CAACTTCAAC
49330 CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
49366 ATAATTGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:49721 original size:88 final size:88
Alignment explanation
Indices: 49613--49856 Score: 364
Period size: 88 Copynumber: 2.8 Consensus size: 88
49603 CTAAGTCCAA
*
49613 TATTTACATTAAAACAAAATAAAAATTTAGTGCTATGATTGGATTAATTTAAATTTTAATGATAC
1 TATTTACATTAAAACAAAATAAAAATTTAGTGCTATGATTGGATTAATTTAAATTTTAATGATAA
* * *
49678 AATTATTTGTCCTTTTGGTTTGG
66 AATTATTTGTCATTTAGGTCTGG
* *
49701 TATTTACATTAAAACAAAATAAAAATTTAGTGGTATGATT-GATTTAATTTAAATTTTAATGGTA
1 TATTTACATTAAAACAAAATAAAAATTTAGTGCTATGATTGGA-TTAATTTAAATTTTAATGATA
49765 AAATTATTTGTCATTTAGGTCTGG
65 AAATTATTTGTCATTTAGGTCTGG
** * * *
49789 TATTTACGGTAAAACAAAATAAAAATTTAGTGTTATAATTGAATTAATTTAAATTTTAATGATTA
1 TATTTACATTAAAACAAAATAAAAATTTAGTGCTATGATTGGATTAATTTAAATTTTAATGA-TA
49854 AAA
65 AAA
49857 ATAATTCAGA
Statistics
Matches: 141, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
87 2 0.01
88 133 0.94
89 6 0.04
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.43
Consensus pattern (88 bp):
TATTTACATTAAAACAAAATAAAAATTTAGTGCTATGATTGGATTAATTTAAATTTTAATGATAA
AATTATTTGTCATTTAGGTCTGG
Found at i:51206 original size:15 final size:16
Alignment explanation
Indices: 51179--51208 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
51169 AGTATCATGT
51179 GATGTATAAAATTTAC
1 GATGTATAAAATTTAC
51195 GATGTA-AAAATTTA
1 GATGTATAAAATTTA
51209 TTAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (16 bp):
GATGTATAAAATTTAC
Found at i:53876 original size:31 final size:32
Alignment explanation
Indices: 53771--53892 Score: 129
Period size: 32 Copynumber: 3.8 Consensus size: 32
53761 AACGTGACCC
* ** * * *
53771 TTGGGTAGGCTCTTAGGCCCTGAGATGCTCCA
1 TTGGGTAGGCTCTAAGGCCCCAAGGTACTACA
* * *
53803 TTGGGTAGGTTCTTAGGCCCCAAGGTACTCCA
1 TTGGGTAGGCTCTAAGGCCCCAAGGTACTACA
* *
53835 TTAGGTAGGCTCTAAGGCCCCAAGGTATTAC-
1 TTGGGTAGGCTCTAAGGCCCCAAGGTACTACA
*
53866 TTGGGTAGGCTCTAAGGCCCTAAGGTA
1 TTGGGTAGGCTCTAAGGCCCCAAGGTA
53893 ATCCCTTAGG
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 25 0.32
32 53 0.68
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (32 bp):
TTGGGTAGGCTCTAAGGCCCCAAGGTACTACA
Found at i:55550 original size:24 final size:24
Alignment explanation
Indices: 55500--55575 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 24
55490 GAGTCGAGGG
*
55500 TTCTACGCGGTCC-TTCGGAC-AA
1 TTCTACGCGGTCCTTTGGGACAAA
* *
55522 TTCTATGTGGTCCTTTGGGACAAA
1 TTCTACGCGGTCCTTTGGGACAAA
*
55546 TTCTACGCGGTCCTTTGGGAC-AT
1 TTCTACGCGGTCCTTTGGGACAAA
55569 TTCTACG
1 TTCTACG
55576 TCCTTTAGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 11 0.24
23 14 0.30
24 21 0.46
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (24 bp):
TTCTACGCGGTCCTTTGGGACAAA
Found at i:55580 original size:20 final size:20
Alignment explanation
Indices: 55531--55616 Score: 100
Period size: 20 Copynumber: 4.1 Consensus size: 20
55521 ATTCTATGTG
*
55531 GTCCTTTGGGACAAATTCTACGC
1 GTCCTTTGGGAC-ATTTCTA--C
55554 GGTCCTTTGGGACATTTCTAC
1 -GTCCTTTGGGACATTTCTAC
* *
55575 GTCCTTTAGGACATTTCTAT
1 GTCCTTTGGGACATTTCTAC
*
55595 GTCTTTTGGGACATTTCTAC
1 GTCCTTTGGGACATTTCTAC
55615 GT
1 GT
55617 GGCACTTCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
20 37 0.66
21 1 0.02
23 6 0.11
24 12 0.21
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (20 bp):
GTCCTTTGGGACATTTCTAC
Found at i:55644 original size:24 final size:23
Alignment explanation
Indices: 55609--55660 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
55599 TTTGGGACAT
*
55609 TTCTACGTGGCACTTCGGTGCATA
1 TTCTACGCGGCACTTCGGTGCA-A
55633 TTCTACGCGGCACTTCGGTGCAA
1 TTCTACGCGGCACTTCGGTGCAA
55656 TTCTA
1 TTCTA
55661 TGTGGCTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGCACTTCGGTGCAA
Done.