Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 23
Found at i:3137910 original size:2 final size:2
Alignment explanation
Indices: 3137903--3137938 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3137893 AGTCATTAAT
3137903 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
3137939 GGATAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3140611 original size:12 final size:12
Alignment explanation
Indices: 3140596--3140622 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3140586 AGGAGGAAAG
3140596 AGAGAATGAACA
1 AGAGAATGAACA
3140608 AGAGAATGAACA
1 AGAGAATGAACA
3140620 AGA
1 AGA
3140623 AAAGGACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.26, T:0.07
Consensus pattern (12 bp):
AGAGAATGAACA
Found at i:3142530 original size:18 final size:19
Alignment explanation
Indices: 3142492--3142532 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3142482 CCAAAGTTTA
* *
3142492 TATGTGAATTATAATTTTG
1 TATGTGAATGATAATTATG
3142511 TATGTGAATGA-AATTATG
1 TATGTGAATGATAATTATG
3142529 TATG
1 TATG
3142533 AGATAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (19 bp):
TATGTGAATGATAATTATG
Found at i:3145362 original size:200 final size:199
Alignment explanation
Indices: 3145103--3145507 Score: 600
Period size: 199 Copynumber: 2.0 Consensus size: 199
3145093 ATCCTTCTTG
* * * **
3145103 TATATGTATCGCTACTTTTTGTCCAATATGCTTCCCAAATGAGATGCACGCAGAAAGTATCGATA
1 TATAAGTATCGATACTTTTTGTCCAACATGCTTCCCAAACAAGATGCACGCAGAAAGTATCGATA
3145168 CACGTATGAAAAGTATCGATTCTTAAAACTTCGAAAGCAATTAATTTAAAGTAATAGGTAAATTT
66 CACGTATG-AAAGTATCGATTCTTAAAACTTCGAAAG-AATTAATTTAAAGTAATAGGTAAATTT
*
3145233 ACAATGTTAGCGGT-AAAAAGATA-CTGGTGTAATGACAAAATATGTTAACATAAAGTATC-AAA
129 ACAATGTTAGCGGTAAAAAAGATATC-GGTGTAATGACAAAATACGTTAACATAAAGTATCGAAA
3145295 GCATTTTA
193 -CATTTTA
* *
3145303 TATAAGTATCGATACTTTTTGTCCAGCATGCTTCCCAAACAAGATGCACGCAGAAAGTATTGATA
1 TATAAGTATCGATACTTTTTGTCCAACATGCTTCCCAAACAAGATGCACGCAGAAAGTATCGATA
* * ** *
3145368 CACGTATGAAAGTATCGATTCTTAGAACTTTGAAAGTGTTAATTTAATGTAATAGGTAAATTTAC
66 CACGTATGAAAGTATCGATTCTTAAAACTTCGAAAGAATTAATTTAAAGTAATAGGTAAATTTAC
* * * *
3145433 AATGTTAGTGGTAAAAAAGATATCGGTTTAATGACAAAATACGTTAACATAAAGTATCGATACTT
131 AATGTTAGCGGTAAAAAAGATATCGGTGTAATGACAAAATACGTTAACATAAAGTATCGAAACAT
3145498 TTTA
196 TTTA
3145502 TATAAG
1 TATAAG
3145508 GACTCGATCA
Statistics
Matches: 185, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
198 37 0.20
199 79 0.43
200 69 0.37
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (199 bp):
TATAAGTATCGATACTTTTTGTCCAACATGCTTCCCAAACAAGATGCACGCAGAAAGTATCGATA
CACGTATGAAAGTATCGATTCTTAAAACTTCGAAAGAATTAATTTAAAGTAATAGGTAAATTTAC
AATGTTAGCGGTAAAAAAGATATCGGTGTAATGACAAAATACGTTAACATAAAGTATCGAAACAT
TTTA
Found at i:3145503 original size:199 final size:199
Alignment explanation
Indices: 3145014--3145507 Score: 629
Period size: 200 Copynumber: 2.5 Consensus size: 199
3145004 CATTTATAAC
* * * * * * *
3145014 TTTAAAATAATAGGTAAATTTACAATGTAAGAGGCAAAAATATACCAGTTTAAT-A-ACAATGCG
1 TTTAAAGTAATAGGTAAATTTACAATGTTAGAGGTAAAAAGATA-CGGTTTAATGACAAAATACG
* * * * * * * * *
3145077 TAAACATAAAGTTTTGATCCTTCTTGTATATGTATCGCTACTTTTTGTCCAATATGCTTCCCAAA
65 TTAACATAAAGTATCGATACTTTTTATATAAGTATCGATACTTTTTGTCCAACATGCTTCCCAAA
**
3145142 TGAGATGCACGCAGAAAGTATCGATACACGTATGAAAAGTATCGATTCTTAAAACTTCGAAAGCA
130 CAAGATGCACGCAGAAAGTATCGATACACGTATGAAAAGTATCGATTCTTAAAACTTCGAAAGCA
3145207 ATTAA
195 ATTAA
* * *
3145212 TTTAAAGTAATAGGTAAATTTACAATGTTAGCGGTAAAAAGATACTGGTGTAATGACAAAATATG
1 TTTAAAGTAATAGGTAAATTTACAATGTTAGAGGTAAAAAGATAC-GGTTTAATGACAAAATACG
* * *
3145277 TTAACATAAAGTATC-AAAGCATTTTATATAAGTATCGATACTTTTTGTCCAGCATGCTTCCCAA
65 TTAACATAAAGTATCGATA-CTTTTTATATAAGTATCGATACTTTTTGTCCAACATGCTTCCCAA
* * *
3145341 ACAAGATGCACGCAGAAAGTATTGATACACGTATG-AAAGTATCGATTCTTAGAACTTTGAAAG-
129 ACAAGATGCACGCAGAAAGTATCGATACACGTATGAAAAGTATCGATTCTTAAAACTTCGAAAGC
**
3145404 TGTTAA
194 AATTAA
* *
3145410 TTTAATGTAATAGGTAAATTTACAATGTTAGTGGTAAAAAAGATATCGGTTTAATGACAAAATAC
1 TTTAAAGTAATAGGTAAATTTACAATGTTAGAGGT-AAAAAGATA-CGGTTTAATGACAAAATAC
3145475 GTTAACATAAAGTATCGATACTTTTTATATAAG
64 GTTAACATAAAGTATCGATACTTTTTATATAAG
3145508 GACTCGATCA
Statistics
Matches: 254, Mismatches: 35, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
197 1 0.00
198 82 0.32
199 81 0.32
200 90 0.35
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (199 bp):
TTTAAAGTAATAGGTAAATTTACAATGTTAGAGGTAAAAAGATACGGTTTAATGACAAAATACGT
TAACATAAAGTATCGATACTTTTTATATAAGTATCGATACTTTTTGTCCAACATGCTTCCCAAAC
AAGATGCACGCAGAAAGTATCGATACACGTATGAAAAGTATCGATTCTTAAAACTTCGAAAGCAA
TTAA
Found at i:3146810 original size:16 final size:15
Alignment explanation
Indices: 3146789--3146818 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3146779 ATGCCTAAAC
3146789 TAAAATTTGATAATGA
1 TAAAATTTG-TAATGA
3146805 TAAAATTTGTAATG
1 TAAAATTTGTAATG
3146819 CTTGTGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
TAAAATTTGTAATGA
Found at i:3149678 original size:21 final size:21
Alignment explanation
Indices: 3149654--3149722 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
3149644 GAATCGATAC
3149654 CCCCTTGAAGGGGAACCGATT
1 CCCCTTGAAGGGGAACCGATT
3149675 CCCCCTTTGAAGGGGAACCGATT
1 -CCCC-TTGAAGGGGAACCGATT
* * * *
3149698 CCCCCTGTAGGGGAATCGATA
1 CCCCTTGAAGGGGAACCGATT
3149719 CCCC
1 CCCC
3149723 CCTAGGGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 17 0.40
22 8 0.19
23 17 0.40
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (21 bp):
CCCCTTGAAGGGGAACCGATT
Found at i:3149724 original size:23 final size:22
Alignment explanation
Indices: 3149642--3149723 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
3149632 ATAGGGCAGA
*
3149642 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
3149664 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
3149687 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
*
3149708 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
3149724 CTAGGGTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.33
22 14 0.26
23 22 0.41
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:3153710 original size:18 final size:18
Alignment explanation
Indices: 3153687--3153731 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3153677 CCAGTCGCAT
3153687 TTCTTCTCAACAAAAACC
1 TTCTTCTCAACAAAAACC
* **
3153705 TTCTTCTCAACCAAAATT
1 TTCTTCTCAACAAAAACC
3153723 TTCTTCTCA
1 TTCTTCTCA
3153732 TGTAAGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (18 bp):
TTCTTCTCAACAAAAACC
Found at i:3155925 original size:15 final size:15
Alignment explanation
Indices: 3155905--3155934 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3155895 TAGACTATTG
3155905 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
3155920 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
3155935 GTATGTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:3156265 original size:6 final size:6
Alignment explanation
Indices: 3156254--3156330 Score: 66
Period size: 6 Copynumber: 12.7 Consensus size: 6
3156244 TTTATGCAGT
* * * *
3156254 TTTCAA TTTCAA TTTGAGA -TTGAA TTTCATT TTTCAA TTTCAA TTTTAA
1 TTTCAA TTTCAA TTTCA-A TTTCAA TTTCA-A TTTCAA TTTCAA TTTCAA
* * *
3156303 TTTGAG TTTGAA TTTCAA TTTCAA TTTC
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTC
3156331 GGCTCCACTA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
5 1 0.02
6 52 0.88
7 6 0.10
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (6 bp):
TTTCAA
Found at i:3156295 original size:37 final size:36
Alignment explanation
Indices: 3156254--3156330 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 36
3156244 TTTATGCAGT
*
3156254 TTTCAATTTCAATTTGAGATTGAATTTCATTTTTCAA
1 TTTCAATTTCAATTTGAGATTGAATTTCA-ATTTCAA
* *
3156291 TTTCAATTTTAATTTGAGTTTGAATTTCAATTTCAA
1 TTTCAATTTCAATTTGAGATTGAATTTCAATTTCAA
3156327 TTTC
1 TTTC
3156331 GGCTCCACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 10 0.27
37 27 0.73
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (36 bp):
TTTCAATTTCAATTTGAGATTGAATTTCAATTTCAA
Found at i:3157704 original size:19 final size:19
Alignment explanation
Indices: 3157657--3157703 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
3157647 ATTTCTAAAC
3157657 CGATTAAAATTTGACAAAA
1 CGATTAAAATTTGACAAAA
*
3157676 CGGTTAAAATTTGACAAAA
1 CGATTAAAATTTGACAAAA
3157695 TCGATTAAA
1 -CGATTAAA
3157704 TATAACAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.28
Consensus pattern (19 bp):
CGATTAAAATTTGACAAAA
Found at i:3159383 original size:108 final size:107
Alignment explanation
Indices: 3159227--3159841 Score: 413
Period size: 108 Copynumber: 5.5 Consensus size: 107
3159217 AAATTTTTCC
** * * * * *** * *
3159227 AGTAATTAACCGGTTATGTTATCATCAGAGTTCTAAGGCTTTATCAGCTTAACAGTTGGTAACAT
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAA-AATTGCTAACAT
3159292 TTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTA
65 TTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTA
* * *
3159335 AGTAATTAACCTATTTTATTATCGT-GAGATTTTTAAGGCCCCATCAGCTTTAATAATATGCTAC
1 AGTAATTAACCTATTTTGTTATCGTCG-GATTTCTAAGGCCCCATCAGC-TTAA-AAT-TGCTAA
* ** * * ***
3159399 CTATTACGTTACATAAGCGCTACCTAATATGTT-ATTATGCTTGATAA-TGTTTCA
62 C-A-T---TT---TAGGCATTACCTAATATGTTGATAATAC-TGATAACAAATT-A
* * * * * *
3159453 AGTAATTAACC-AGTTATGTTATCATCGGATTTCTAAGGCTCCGTCAGCTTAAACTTTGGTAACA
1 AGTAATTAACCTA-TTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAA-ATTGCTAACA
* *
3159517 TTTTAGGCATTACCTAATATGTTGATAATACTAATGACAAATTA
64 TTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTA
* * *
3159561 AGTAATTAACCTATTTTGTTATCGTGGGATTTCTAAGGCCCCATCAACTTTAATAATATGCTACC
1 AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGC-TTAA-AAT-TGCTAAC
* * ***
3159626 TATTACGTTACATAAGCGCA--ACCTAATATGTT-ATTATGATTGATAA-TGTTTCA
63 -A-T---TT---T-AG-GCATTACCTAATATGTTGATAAT-ACTGATAACAAATT-A
* * * *
3159679 AGTAATTAACC-AGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGATAACA
1 AGTAATTAACCTA-TTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAA-ATTGCTAACA
* *
3159743 TTTTAGGCATTACCTAATATGTTGATAATACTAATGACAAATTA
64 TTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTA
* **
3159787 AGTAATTAACATATTTTGTTAT-GATCGGATTTCTAAGGCCCTGTCAGCTTTAAAA
1 AGTAATTAACCTATTTTGTTATCG-TCGGATTTCTAAGGCCCCATCAGC-TTAAAA
3159842 AGGCACTACC
Statistics
Matches: 386, Mismatches: 78, Indels: 86
0.70 0.14 0.16
Matches are distributed among these distances:
106 3 0.01
107 3 0.01
108 156 0.40
109 31 0.08
110 11 0.03
111 6 0.02
112 2 0.01
114 2 0.01
115 6 0.02
116 12 0.03
117 25 0.06
118 123 0.32
119 3 0.01
120 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (107 bp):
AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAAATTGCTAACATT
TTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTA
Found at i:3159399 original size:226 final size:226
Alignment explanation
Indices: 3158999--3159926 Score: 1398
Period size: 226 Copynumber: 4.1 Consensus size: 226
3158989 GATAACAAAA
* * * *
3158999 CAAGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATTAGCTTACACTTTGTTAAC
1 CAAGTAATTAACCGGTTATGTTATCATCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAAC
* * * *
3159064 ATTTTAGGCGTTACCTAATATATTGACAATACTGATAACAAATTAAGTAATTAACCTATTTTGTT
66 ATTTTAGGCATTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTT
* * * * *
3159129 ATCGTAAGATTTCTAGGGCCCCATCAGCTTTAATAATGTGCTACCTATTACGTTACAAAAACGCA
131 ATCGTGAGATTTCTAAGGCCCCATCAGCTTTAATAATATGCTACCTATTACGTTACATAAGCGCA
* *
3159194 ACCTAATATGTTATTATGCTTGAAAATTTTT
196 ACCTAATATGTTATTATGCTTGATAATGTTT
* * * ** *
3159225 CCAGTAATTAACCGGTTATGTTATCATCAGAGTTCTAAGGCTTTATCAGCTT-AACAGTTGGTAA
1 CAAGTAATTAACCGGTTATGTTATCATCGGATTTCTAAGGCTCCATCAGCTTAAAC-TTTGGTAA
* *
3159289 CATTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTAT
65 CATTTTAGGCATTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGT
*
3159354 TATCGTGAGATTTTTAAGGCCCCATCAGCTTTAATAATATGCTACCTATTACGTTACATAAGCGC
130 TATCGTGAGATTTCTAAGGCCCCATCAGCTTTAATAATATGCTACCTATTACGTTACATAAGCGC
*
3159419 TACCTAATATGTTATTATGCTTGATAATGTTT
195 AACCTAATATGTTATTATGCTTGATAATGTTT
* *
3159451 CAAGTAATTAACCAGTTATGTTATCATCGGATTTCTAAGGCTCCGTCAGCTTAAACTTTGGTAAC
1 CAAGTAATTAACCGGTTATGTTATCATCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAAC
*
3159516 ATTTTAGGCATTACCTAATATGTTGATAATACTAATGACAAATTAAGTAATTAACCTATTTTGTT
66 ATTTTAGGCATTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTT
* *
3159581 ATCGTGGGATTTCTAAGGCCCCATCAACTTTAATAATATGCTACCTATTACGTTACATAAGCGCA
131 ATCGTGAGATTTCTAAGGCCCCATCAGCTTTAATAATATGCTACCTATTACGTTACATAAGCGCA
*
3159646 ACCTAATATGTTATTATGATTGATAATGTTT
196 ACCTAATATGTTATTATGCTTGATAATGTTT
* * *
3159677 CAAGTAATTAACCAGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGATAAC
1 CAAGTAATTAACCGGTTATGTTATCATCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAAC
* *
3159742 ATTTTAGGCATTACCTAATATGTTGATAATACTAATGACAAATTAAGTAATTAACATATTTTGTT
66 ATTTTAGGCATTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTT
** *
3159807 AT-GATCG-GATTTCTAAGGCCCTGTCAGCTTTAA-AA-AGGCACTACCTATTACGTTACATAAG
131 ATCG-T-GAGATTTCTAAGGCCCCATCAGCTTTAATAATATG--CTACCTATTACGTTACATAAG
* *
3159868 CGCTACCTAATATGTTATTATGTTTGATAATGTTT
192 CGCAACCTAATATGTTATTATGCTTGATAATGTTT
*
3159903 CCAGTAATTAACCGGTTATGTTAT
1 CAAGTAATTAACCGGTTATGTTAT
3159927 TGTCAATATT
Statistics
Matches: 645, Mismatches: 51, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
224 2 0.00
225 5 0.01
226 634 0.98
227 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (226 bp):
CAAGTAATTAACCGGTTATGTTATCATCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAAC
ATTTTAGGCATTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTT
ATCGTGAGATTTCTAAGGCCCCATCAGCTTTAATAATATGCTACCTATTACGTTACATAAGCGCA
ACCTAATATGTTATTATGCTTGATAATGTTT
Found at i:3165559 original size:3 final size:3
Alignment explanation
Indices: 3165551--3165595 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
3165541 CAAGAAATAG
3165551 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3165596 TTATTACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3172439 original size:44 final size:44
Alignment explanation
Indices: 3172376--3172480 Score: 149
Period size: 44 Copynumber: 2.4 Consensus size: 44
3172366 TTTTGTGCAC
* *
3172376 TATGCATCGATATAC-ATAAAAGTGTACCGATGCATCCCTTGAA
1 TATGCATCGATACACTATAAAAGTGTACCAATGCATCCCTTGAA
* * *
3172419 TATGAATCGATACACTATAAAGGTGTACCAATGCATTCCTTGAA
1 TATGCATCGATACACTATAAAAGTGTACCAATGCATCCCTTGAA
*
3172463 TGTGCATCGATACACTAT
1 TATGCATCGATACACTAT
3172481 GTAGTGCATC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 13 0.24
44 41 0.76
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (44 bp):
TATGCATCGATACACTATAAAAGTGTACCAATGCATCCCTTGAA
Found at i:3172967 original size:13 final size:13
Alignment explanation
Indices: 3172949--3172986 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3172939 TCCATATTAA
3172949 TTTTCAAACATTG
1 TTTTCAAACATTG
**
3172962 TTTTCAAACATAA
1 TTTTCAAACATTG
3172975 TTTTCAAA-ATTG
1 TTTTCAAACATTG
3172987 CCCATTAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 2 0.10
13 19 0.90
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:3174701 original size:13 final size:13
Alignment explanation
Indices: 3174679--3174712 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3174669 AAGGGGAGTA
*
3174679 ATTTTCAAAATTG
1 ATTTTCAAAAATG
3174692 A-TTTCAAAAATG
1 ATTTTCAAAAATG
3174704 ATTTTCAAA
1 ATTTTCAAA
3174713 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:3175189 original size:65 final size:64
Alignment explanation
Indices: 3175056--3175203 Score: 163
Period size: 65 Copynumber: 2.3 Consensus size: 64
3175046 CCCTATTTCG
* * * * *
3175056 AATGCATTTTGTGTACCGATGCACAACAATGCATCGATTCACTCTTGAATTTATTGAAACATCC
1 AATGTATTTTGTGTACCGATGCACAACAATGCATCGATGCACTCCTGAATTTATTAAAACATCA
* * * **
3175120 AATGTATTTTGTGTACTGATGCACAAACCATTCATCGATGCACTCCTGGCTATT-TTAAAACATC
1 AATGTATTTTGTGTACCGATGCAC-AACAATGCATCGATGCACTCCTGAAT-TTATTAAAACATC
3175184 A
64 A
* *
3175185 AATGTAATTAGTGTACCGA
1 AATGTATTTTGTGTACCGA
3175204 CACCCCAAGT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
64 22 0.32
65 45 0.65
66 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (64 bp):
AATGTATTTTGTGTACCGATGCACAACAATGCATCGATGCACTCCTGAATTTATTAAAACATCA
Found at i:3177713 original size:18 final size:17
Alignment explanation
Indices: 3177690--3177746 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 17
3177680 TATATTTTCC
3177690 AACAATTAGTATCTTTTT
1 AACAATT-GTATCTTTTT
3177708 AACAATTGATATCATTTTGTT
1 AACAATTG-TATC--TTT-TT
*
3177729 AGCAATTGGTATCTTTTT
1 AACAATT-GTATCTTTTT
3177747 CATTAAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
17 1 0.03
18 13 0.39
19 3 0.09
20 3 0.09
21 12 0.36
22 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
AACAATTGTATCTTTTT
Found at i:3177998 original size:20 final size:20
Alignment explanation
Indices: 3177973--3178021 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3177963 TGAACAGTAA
**
3177973 TGAACAGTACCGATATTGTG
1 TGAACAGTACAAATATTGTG
*
3177993 TGAACAATACAAATATTGTG
1 TGAACAGTACAAATATTGTG
3178013 TGAACAGTA
1 TGAACAGTA
3178022 ATGAACAGTA
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:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (20 bp):
TGAACAGTACAAATATTGTG
Found at i:3178479 original size:34 final size:33
Alignment explanation
Indices: 3178440--3178510 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
3178430 TTTTGTAAAG
*
3178440 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTTAGCCCGTG-AAAAACTA
* *
3178474 GGGAAATGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAATGTTCTAGCTTAGCCCGTGAAAAACTA
3178507 GGGA
1 GGGA
3178511 GTTGTAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (33 bp):
GGGAAATGTTCTAGCTTAGCCCGTGAAAAACTA
Found at i:3184727 original size:117 final size:117
Alignment explanation
Indices: 3184511--3184731 Score: 352
Period size: 117 Copynumber: 1.9 Consensus size: 117
3184501 GAACACTATT
* * * *
3184511 TCCATCCAATCACTCCGATCACTAGAATTTGTATGTTCTCCAGAACCATACACCCACCTGCACAC
1 TCCATCCAATCACTCCGATCACTAAAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACAC
**
3184576 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCGGTAATAACTGA
66 CAGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGCGGTAATAACTGA
*
3184628 TCCATCCAATCACTCTGATCACTAAAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACAC
1 TCCATCCAATCACTCCGATCACTAAAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACAC
* * *
3184693 CAGTAAGGTCTTACCCTGAGCTCACAGCAAAGGAGCCTG
66 CAGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTG
3184732 AAATACTTCT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 94 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (117 bp):
TCCATCCAATCACTCCGATCACTAAAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACAC
CAGTAAGGACTTACCCTGAGCACAAAGCAAAGGAGCCTGCGGTAATAACTGA
Found at i:3185727 original size:28 final size:29
Alignment explanation
Indices: 3185647--3185767 Score: 199
Period size: 29 Copynumber: 4.2 Consensus size: 29
3185637 ACACAATTAT
*
3185647 CACCCTTTTAAGAAATATTTACGAAATTAA
1 CACCCTTTTAA-AAATATTTACGAAACTAA
*
3185677 CACCCTTTTAAAAACATTTACGAAACTAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
3185706 CACCCTTTTAAAAATA-TTACGAAACTAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
*
3185734 CACCCTTTTAAAAATATTTACTAAACTAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
3185763 CACCC
1 CACCC
3185768 GAGTCAACGG
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
28 28 0.33
29 47 0.55
30 11 0.13
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.30
Consensus pattern (29 bp):
CACCCTTTTAAAAATATTTACGAAACTAA
Found at i:3185738 original size:57 final size:59
Alignment explanation
Indices: 3185647--3185767 Score: 201
Period size: 57 Copynumber: 2.1 Consensus size: 59
3185637 ACACAATTAT
*
3185647 CACCCTTTTAAGAAATATTTACGAAATTAACACCCTTTTAAAAACATTTACGAAACTAA
1 CACCCTTTTAAGAAATATTTACGAAACTAACACCCTTTTAAAAACATTTACGAAACTAA
* *
3185706 CACCCTTTTAA-AAATA-TTACGAAACTAACACCCTTTTAAAAATATTTACTAAACTAA
1 CACCCTTTTAAGAAATATTTACGAAACTAACACCCTTTTAAAAACATTTACGAAACTAA
3185763 CACCC
1 CACCC
3185768 GAGTCAACGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 43 0.73
58 5 0.08
59 11 0.19
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.30
Consensus pattern (59 bp):
CACCCTTTTAAGAAATATTTACGAAACTAACACCCTTTTAAAAACATTTACGAAACTAA
Found at i:3190870 original size:10 final size:10
Alignment explanation
Indices: 3190841--3190909 Score: 81
Period size: 10 Copynumber: 7.1 Consensus size: 10
3190831 GCTGATGGAA
3190841 AACCGGTTTG
1 AACCGGTTTG
*
3190851 -ACCAGTTTTG
1 AACC-GGTTTG
3190861 AACCGGTTTG
1 AACCGGTTTG
*
3190871 -ACCGGTCTG
1 AACCGGTTTG
3190880 AACCGGTTTG
1 AACCGGTTTG
*
3190890 -ACCGGTGTG
1 AACCGGTTTG
3190899 AACCGGTTTG
1 AACCGGTTTG
3190909 A
1 A
3190910 CCGATCTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
9 19 0.39
10 27 0.55
11 3 0.06
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:3190883 original size:19 final size:19
Alignment explanation
Indices: 3190841--3190930 Score: 117
Period size: 19 Copynumber: 4.7 Consensus size: 19
3190831 GCTGATGGAA
* *
3190841 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
3190861 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
3190880 AACCGGTTTGACCGGTGTG
1 AACCGGTTTGACCGGTCTG
* *
3190899 AACCGGTTTGACCGATCTA
1 AACCGGTTTGACCGGTCTG
*
3190918 AACCGGGTTGACC
1 AACCGGTTTGACC
3190931 CGACCCGACT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 50 0.79
20 13 0.21
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3190909 original size:38 final size:39
Alignment explanation
Indices: 3190840--3190930 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 39
3190830 AGCTGATGGA
* * *
3190840 AAACCGGTTTGACCAGTTTTGAACCGGTTTGACCGGTCT
1 AAACCGGTTTGACCAGGTGTGAACCGGTTTGACCGATCT
*
3190879 GAACCGGTTTGACC-GGTGTGAACCGGTTTGACCGATCT
1 AAACCGGTTTGACCAGGTGTGAACCGGTTTGACCGATCT
*
3190917 AAACCGGGTTGACC
1 AAACCGGTTTGACC
3190931 CGACCCGACT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 33 0.72
39 13 0.28
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (39 bp):
AAACCGGTTTGACCAGGTGTGAACCGGTTTGACCGATCT
Found at i:3190978 original size:17 final size:17
Alignment explanation
Indices: 3190924--3190981 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
3190914 TCTAAACCGG
3190924 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
3190941 GTTAACCCGACCCGACT
1 GTTGACCCGACCCGACT
* *
3190958 GTTGACCCGATCCGACC
1 GTTGACCCGACCCGACT
3190975 GTTGACC
1 GTTGACC
3190982 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.40, G:0.22, T:0.19
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:3190983 original size:7 final size:7
Alignment explanation
Indices: 3190971--3191001 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3190961 GACCCGATCC
3190971 GACCGTT
1 GACCGTT
3190978 GACCGTT
1 GACCGTT
3190985 GACCGTT
1 GACCGTT
3190992 GACCGTT
1 GACCGTT
3190999 GAC
1 GAC
3191002 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:3198194 original size:10 final size:10
Alignment explanation
Indices: 3198165--3198233 Score: 81
Period size: 10 Copynumber: 7.1 Consensus size: 10
3198155 GCTGATGGAA
3198165 AACCGGTTTG
1 AACCGGTTTG
*
3198175 -ACCAGTTTTG
1 AACC-GGTTTG
3198185 AACCGGTTTG
1 AACCGGTTTG
*
3198195 -ACCGGTCTG
1 AACCGGTTTG
3198204 AACCGGTTTG
1 AACCGGTTTG
*
3198214 -ACCGGTCTG
1 AACCGGTTTG
3198223 AACCGGTTTG
1 AACCGGTTTG
3198233 A
1 A
3198234 CCGATCTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
9 19 0.39
10 27 0.55
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:3198207 original size:19 final size:19
Alignment explanation
Indices: 3198165--3198254 Score: 126
Period size: 19 Copynumber: 4.7 Consensus size: 19
3198155 GCTGATGGAA
* *
3198165 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
3198185 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
3198204 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
* *
3198223 AACCGGTTTGACCGATCTA
1 AACCGGTTTGACCGGTCTG
*
3198242 AACCGGGTTGACC
1 AACCGGTTTGACC
3198255 CGACCCGACT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
19 52 0.80
20 13 0.20
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3198270 original size:17 final size:17
Alignment explanation
Indices: 3198248--3198305 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
3198238 TCTAAACCGG
3198248 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
3198265 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
* *
3198282 GTTGACCCGATCCGACC
1 GTTGACCCGACCCGACT
3198299 GTTGACC
1 GTTGACC
3198306 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.40, G:0.24, T:0.19
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:3202577 original size:39 final size:40
Alignment explanation
Indices: 3202505--3202584 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
3202495 AGAGTAGAAG
3202505 CAAAATAACCTGCCATACATGCATTATACTACTTGTATAT
1 CAAAATAACCTGCCATACATGCATTATACTACTTGTATAT
*
3202545 CAAAATAACCTGCCAT-CATGCATTATATTACTTGTATAT
1 CAAAATAACCTGCCATACATGCATTATACTACTTGTATAT
3202584 C
1 C
3202585 TTGCCAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 23 0.59
40 16 0.41
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (40 bp):
CAAAATAACCTGCCATACATGCATTATACTACTTGTATAT
Found at i:3203182 original size:2 final size:2
Alignment explanation
Indices: 3203175--3203201 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3203165 TAATAGTACC
3203175 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3203202 GAATCAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3205066 original size:24 final size:24
Alignment explanation
Indices: 3205024--3205092 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
3205014 GTGCCACATA
* *
3205024 TTTGTCCCAACGGATCACATAGGT
1 TTTGTCCCAAAGGACCACATAGGT
* *
3205048 TTTTTCCCGAAGGACCACATA-GT
1 TTTGTCCCAAAGGACCACATAGGT
*
3205071 TTTGTCCTAAAGGACCACATAG
1 TTTGTCCCAAAGGACCACATAG
3205093 AACCCTCAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (24 bp):
TTTGTCCCAAAGGACCACATAGGT
Found at i:3205247 original size:14 final size:15
Alignment explanation
Indices: 3205228--3205260 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3205218 ATCGAATAAT
3205228 TTCAAAT-TCACATA
1 TTCAAATGTCACATA
*
3205242 TTCAAATGTCACATT
1 TTCAAATGTCACATA
3205257 TTCA
1 TTCA
3205261 TAATCATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (15 bp):
TTCAAATGTCACATA
Found at i:3211632 original size:21 final size:21
Alignment explanation
Indices: 3211608--3211702 Score: 59
Period size: 21 Copynumber: 4.3 Consensus size: 21
3211598 CACCACAACT
3211608 CACATAATTG-CACCGAAGTG-C
1 CACATAATTGTC-CCGAAG-GAC
*
3211629 CACATATTTGTCCCGAAGGAC
1 CACATAATTGTCCCGAAGGAC
* * *
3211650 CACATAGGTTTTTTACCGAAGGAC
1 CACATA---ATTGTCCCGAAGGAC
* *
3211674 AACATAGTTTTGTCCCGAAGGAC
1 CACATA--ATTGTCCCGAAGGAC
3211697 CACATA
1 CACATA
3211703 GAACCCTCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 22 0.35
22 1 0.02
23 20 0.32
24 18 0.29
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (21 bp):
CACATAATTGTCCCGAAGGAC
Found at i:3211691 original size:23 final size:23
Alignment explanation
Indices: 3211620--3211703 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
3211610 CATAATTGCA
3211620 CCGAAGTG-CCACATA--TTTGTC
1 CCGAAG-GACCACATAGTTTTGTC
* *
3211641 CCGAAGGACCACATAGGTTTTTTA
1 CCGAAGGACCACATA-GTTTTGTC
*
3211665 CCGAAGGACAACATAGTTTTGTC
1 CCGAAGGACCACATAGTTTTGTC
3211688 CCGAAGGACCACATAG
1 CCGAAGGACCACATAG
3211704 AACCCTCAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
23 21 0.40
24 18 0.34
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CCGAAGGACCACATAGTTTTGTC
Found at i:3212305 original size:18 final size:18
Alignment explanation
Indices: 3212278--3212326 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
3212268 TTCTCATCGA
*
3212278 TGGTATCGATACCCACTC
1 TGGTACCGATACCCACTC
3212296 TGGTACCGATACCCACTC
1 TGGTACCGATACCCACTC
3212314 TGGTACCGATACC
1 TGGTACCGATACC
3212327 ATTTTGGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.24
Consensus pattern (18 bp):
TGGTACCGATACCCACTC
Found at i:3217803 original size:16 final size:15
Alignment explanation
Indices: 3217784--3217813 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3217774 ACTTATTCCC
3217784 TTTTTCTTCTATTTTT
1 TTTTTCTTCT-TTTTT
3217800 TTTTTCTTCTTTTT
1 TTTTTCTTCTTTTT
3217814 CTCTTCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTCTTTTTT
Found at i:3220016 original size:57 final size:57
Alignment explanation
Indices: 3219926--3221044 Score: 1702
Period size: 57 Copynumber: 19.6 Consensus size: 57
3219916 GTCCAATACA
* * ** *
3219926 GAAATTCATACACTGAGTATGA-TTCTTAACATTTTAGCGTAAGAAACAACCTATTT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
3219982 GAAATTTATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
3220039 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGTCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3220096 GAAATTCAAACACTTAGTATGATTTCTAAACATTTTAGCGTACGAAACGCCCTATTT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* ** *
3220153 GAAATTCATACACTTAGTATGATTTCTTAATATTTTAGCGTACGAAACAACCTATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3220210 GAAATTCATACAGTTAGTATGATTTCTTAACATTTTAGCGTATGAAACTCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
3220267 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATTT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * **
3220324 GAAATTCATACACTTAGTATGGTTTCTTAACATTTTAGCGTACGAAACACTTTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3220381 AAAATTCATACACTTAGTATGATTTCTAAACATTTTAGCGTACGAAACGCCCTATTT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * *
3220438 GAAATTCATACACTTAGTATGATTTCTTAACATTTTGGCATACGAAACGACCTATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
3220495 AAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
3220552 GAAATTAATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3220609 GAAATTCATACACTTAGTATGATTTCATAACATTTTAGCGTATGAAACGCCATATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3220666 GAAATTCATACACTTCA-TATGAGTTCTTACCATTTTAGCGTACGAAACGCTCTATCT
1 GAAATTCATACACTT-AGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * *
3220723 AAAATTCATACACTTAGTGTGATTTCTTATCATTTTAGCGTACGAAACGCTCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
3220780 GAAATTCATACACTTAGTGTGATTTCTTATCATTTTAGCGTACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * **
3220837 GAAATTAATACACTTAGTATGATTTATTAACATTTTAGAATACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3220894 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGGGTACAAAATGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3220951 GAAATTCATACTCTTAGTATGAATTCTTAACATTTTAGCGTACGAAACACCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
3221008 GAAATTCATACACGTAGTATGATTTCTTAACATTTTA
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTA
3221045 CACACTTAGT
Statistics
Matches: 964, Mismatches: 96, Indels: 5
0.91 0.09 0.00
Matches are distributed among these distances:
56 21 0.02
57 942 0.98
58 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (57 bp):
GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
Found at i:3221516 original size:20 final size:20
Alignment explanation
Indices: 3221466--3221516 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
3221456 ATGATGCTTG
*
3221466 GTATCGATACCCTTACCATC
1 GTATCGATACTCTTACCATC
3221486 GTATCGATACTCTTACCATC
1 GTATCGATACTCTTACCATC
3221506 GTATCGATACT
1 GTATCGATACT
3221517 ACTATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (20 bp):
GTATCGATACTCTTACCATC
Found at i:3221583 original size:116 final size:115
Alignment explanation
Indices: 3221391--3221612 Score: 286
Period size: 116 Copynumber: 1.9 Consensus size: 115
3221381 CCCTATAATG
* * * * ** *
3221391 GTATTGATACTACTATTCTATGGTATCGATACTCCCTTCTGGTATTGATACCAATTTTTGATTCA
1 GTATCGATACTACTATTCTATGGAACCGATACTCCCTTCCGGTATCAATACCAATTTTAGATTCA
* *
3221456 ATGATGCTTGGTATCGATACCCTTACCATCGTATCGATACTCTTACCATC
66 ATGATGATTGGTATCGAAACCCTTACCATCGTATCGATACTCTTACCATC
* *
3221506 GTATCGATACTACTATATATTATGGAACCGATAC-CCCTTCCGGTATCAATACCCATTTTAGATT
1 GTATCGATACTACTAT-T-CTATGGAACCGATACTCCCTTCCGGTATCAATACCAATTTTAGATT
* *
3221570 CGATG-TAGATTGGTATCGAAACCCTTACCATGGTATCGATACT
64 CAATGAT-GATTGGTATCGAAACCCTTACCATCGTATCGATACT
3221613 ACCTTGTTGG
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
115 16 0.18
116 63 0.69
117 12 0.13
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (115 bp):
GTATCGATACTACTATTCTATGGAACCGATACTCCCTTCCGGTATCAATACCAATTTTAGATTCA
ATGATGATTGGTATCGAAACCCTTACCATCGTATCGATACTCTTACCATC
Found at i:3230368 original size:17 final size:17
Alignment explanation
Indices: 3230346--3230398 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
3230336 TCAATAAATT
*
3230346 TAGTTCACTAATTAAAC
1 TAGTTCATTAATTAAAC
*
3230363 TAGTTCATTCATTAAAC
1 TAGTTCATTAATTAAAC
**
3230380 TAGTAAATTAATTAAAC
1 TAGTTCATTAATTAAAC
3230397 TA
1 TA
3230399 TTTTCTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:3231038 original size:282 final size:282
Alignment explanation
Indices: 3230534--3231071 Score: 878
Period size: 282 Copynumber: 1.9 Consensus size: 282
3230524 AATGTTTTAT
*
3230534 ATTTCTAGATTTCATACAGATGTGTTTGGTTCCTAAAATAAATTGAAAATTATTCCTCTATCTCT
1 ATTTCTAGATTTCATACAGACGTGTTTGGTTCCTAAAATAAATTGAAAATTATTCCTCTATCTCT
** * * *
3230599 TATCTTTCCAACATCTTTTTAATCACCTCAATCCGATATCGAGAACTTGAGATATGAACATTTTA
66 TAGATTTCCAAAACCTTTTCAATCACCTCAATCCGATATCGAGAACTTGAGATATGAACATTTTA
* *
3230664 TCGAAGACACTACAGGCTGGAATTTCACTACGGGAATTGCATGCAAGGAAGGCTTGAACATCCAA
131 TCGAAGACACTACAGGCTGGAATTTCACTACGGGAATTGCATACAAGGAAGGATTGAACATCCAA
3230729 AGGAGTCTCCAAATTCATTCATACAAGTGAATGGACGAATTGGATGAGCTTGAACCAAGGATAAA
196 AGGAGTCTCCAAATTCATTCATACAAGTGAATGGACGAATTGGATGAGCTTGAACCAAGGATAAA
3230794 AAATTTAGTCAGTTTGTTTTCC
261 AAATTTAGTCAGTTTGTTTTCC
* * * * *
3230816 ATTTCTAGATTTGATACATACGTGTTTGGTTCCTAAAATCAATTGGAAATTATTCCTCTATCTTT
1 ATTTCTAGATTTCATACAGACGTGTTTGGTTCCTAAAATAAATTGAAAATTATTCCTCTATCTCT
* * * *
3230881 TAGATTTCCAAAACCTTTTCAATCACCTTAATCCGATATCGGGAGCTTGAGATATGATCATTTTA
66 TAGATTTCCAAAACCTTTTCAATCACCTCAATCCGATATCGAGAACTTGAGATATGAACATTTTA
* * *
3230946 TCGAGGACACTAGAGGTTGGAATTTCACTACGGGAATTGCATACAAGGAAGGATTGAACATCCAA
131 TCGAAGACACTACAGGCTGGAATTTCACTACGGGAATTGCATACAAGGAAGGATTGAACATCCAA
* *
3231011 AGGAGTCTCCAAATTCATTCATACAAGTGCATGGACGAATTGGATGATCTTGAACCAAGGA
196 AGGAGTCTCCAAATTCATTCATACAAGTGAATGGACGAATTGGATGAGCTTGAACCAAGGA
3231072 ATAGACTTTT
Statistics
Matches: 234, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
282 234 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (282 bp):
ATTTCTAGATTTCATACAGACGTGTTTGGTTCCTAAAATAAATTGAAAATTATTCCTCTATCTCT
TAGATTTCCAAAACCTTTTCAATCACCTCAATCCGATATCGAGAACTTGAGATATGAACATTTTA
TCGAAGACACTACAGGCTGGAATTTCACTACGGGAATTGCATACAAGGAAGGATTGAACATCCAA
AGGAGTCTCCAAATTCATTCATACAAGTGAATGGACGAATTGGATGAGCTTGAACCAAGGATAAA
AAATTTAGTCAGTTTGTTTTCC
Found at i:3236236 original size:20 final size:20
Alignment explanation
Indices: 3236207--3236246 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3236197 AGGAAAAAAC
* *
3236207 TTTTAAAAAACCCAAGAGAA
1 TTTTAAAAAAACCAAAAGAA
*
3236227 TTTTATAAAAACCAAAAGAA
1 TTTTAAAAAAACCAAAAGAA
3236247 AGAAGTGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (20 bp):
TTTTAAAAAAACCAAAAGAA
Found at i:3236317 original size:20 final size:20
Alignment explanation
Indices: 3236292--3236348 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3236282 TTTGGTTCAC
*
3236292 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
*
3236312 GGAATAAAAGATTACCTGTG
1 GGAATAAAAGATTACCAGTG
3236332 GGAATAAAAGATTACCA
1 GGAATAAAAGATTACCA
3236349 TGGAATATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:3236355 original size:18 final size:19
Alignment explanation
Indices: 3236292--3236355 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 19
3236282 TTTGGTTCAC
*
3236292 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCA-TG
*
3236312 GGAATAAAAGATTACCTGTG
1 GGAATAAAAGATTACC-ATG
3236332 GGAATAAAAGATTACCAT-
1 GGAATAAAAGATTACCATG
3236350 GGAATA
1 GGAATA
3236356 TGATTACTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.15
19 1 0.03
20 33 0.82
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCATG
Found at i:3237852 original size:15 final size:15
Alignment explanation
Indices: 3237832--3237871 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
3237822 TCGGATGTTA
*
3237832 CGGGTACCCGGTAAT
1 CGGGTACCCGGGAAT
3237847 CGGGTACCCGGGAAT
1 CGGGTACCCGGGAAT
3237862 CGGGTACCCG
1 CGGGTACCCG
3237872 ATACCCGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.38, T:0.15
Consensus pattern (15 bp):
CGGGTACCCGGGAAT
Found at i:3242839 original size:14 final size:14
Alignment explanation
Indices: 3242812--3242866 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
3242802 TATTTTAAAA
*
3242812 TATTAAA-ATAATT
1 TATTAAATATTATT
*
3242825 TATTTAATATTATT
1 TATTAAATATTATT
*
3242839 TATGTCAATATTA-T
1 TAT-TAAATATTATT
3242853 TATTAAAATATTAT
1 TATT-AAATATTAT
3242867 ATCTACAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 7 0.21
14 19 0.56
15 8 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
TATTAAATATTATT
Found at i:3243039 original size:22 final size:21
Alignment explanation
Indices: 3242989--3243048 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
3242979 ATTATTTATT
*
3242989 AAAATAATATTATTAAAATATG
1 AAAATTATA-TATTAAAATATG
3243011 AAAATTATTATATTAAAATAAT-
1 AAAATTA-TATATTAAAAT-ATG
* *
3243033 AATATTATATTTTAAA
1 AAAATTATATATTAAA
3243049 GAGTATACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 8 0.24
22 21 0.64
23 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATTATATATTAAAATATG
Found at i:3252604 original size:112 final size:112
Alignment explanation
Indices: 3252407--3252637 Score: 417
Period size: 112 Copynumber: 2.1 Consensus size: 112
3252397 CCACCTCAAG
3252407 GTATTCTCTTTTTCCTCCATTTAGGATTAGGGAGGTTTTTTAATGAGGTCCTTGAGGTGGTGTAC
1 GTATTCTCTTTTTCCTCCATTTAGGATTAGGGAGGTTTTTTAATGAGGTCCTTGAGGTGGTGTAC
**
3252472 TTTGTACCCCTTTTATACAAAGTACCCTCTTTCAAAAAAAAATTGCA
66 TTTGTACCCCTTTTATACAAAGTACCAGCTTTCAAAAAAAAATTGCA
*
3252519 GTATTCTCTTTTTCCTCCATTTAGGATTAGGGAGGTTTTTTAATGAGGTCCTTGAGGTGGTGTAT
1 GTATTCTCTTTTTCCTCCATTTAGGATTAGGGAGGTTTTTTAATGAGGTCCTTGAGGTGGTGTAC
*
3252584 TTTGTACCCCTTTTATACAAAGTACCAGGTTTCAAAAAAAAATTGCA
66 TTTGTACCCCTTTTATACAAAGTACCAGCTTTCAAAAAAAAATTGCA
*
3252631 GTTTTCT
1 GTATTCT
3252638 TCTAAACAGA
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (112 bp):
GTATTCTCTTTTTCCTCCATTTAGGATTAGGGAGGTTTTTTAATGAGGTCCTTGAGGTGGTGTAC
TTTGTACCCCTTTTATACAAAGTACCAGCTTTCAAAAAAAAATTGCA
Found at i:3254582 original size:7 final size:7
Alignment explanation
Indices: 3254567--3254596 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3254557 AGAAATTAAG
*
3254567 AAATTTA
1 AAATATA
3254574 AAATATA
1 AAATATA
3254581 AAATATA
1 AAATATA
3254588 AAATATA
1 AAATATA
3254595 AA
1 AA
3254597 TAATTATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATATA
Found at i:3255190 original size:20 final size:21
Alignment explanation
Indices: 3255148--3255190 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3255138 AAGCCTTTTG
*
3255148 AATCATAGAAGTTGAAAAATA
1 AATCATAGAACTTGAAAAATA
* *
3255169 AATCATAGACCTT-AAAATTA
1 AATCATAGAACTTGAAAAATA
3255189 AA
1 AA
3255191 AATTCGACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCATAGAACTTGAAAAATA
Found at i:3259330 original size:2 final size:2
Alignment explanation
Indices: 3259323--3259371 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3259313 CTGTCCCTGT
3259323 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3259365 TC TC TC T
1 TC TC TC T
3259372 ATATTACATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3264229 original size:64 final size:63
Alignment explanation
Indices: 3264125--3264243 Score: 141
Period size: 64 Copynumber: 1.9 Consensus size: 63
3264115 TTGTTTAAGG
* * **
3264125 TGCATCGCTGCACATGGAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGCCATCGA
1 TGCATCGATGCACAAGGAGTGCATCGATGCACCAATTTAAAAA-AAAACATCGAATGCCATCGA
* * * *
3264189 TGCATCGATGCATAAGGAGTGCATCGATGCACCCCA-TTAAATACAAACATCGAAT
1 TGCATCGATGCACAAGGAGTGCATCGATGCA-CCAATTTAAAAAAAAACATCGAAT
3264244 AAGATTTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 11 0.24
64 34 0.74
65 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (63 bp):
TGCATCGATGCACAAGGAGTGCATCGATGCACCAATTTAAAAAAAAACATCGAATGCCATCGA
Found at i:3264897 original size:103 final size:103
Alignment explanation
Indices: 3264718--3265249 Score: 1001
Period size: 103 Copynumber: 5.2 Consensus size: 103
3264708 GTAGAGGGTC
* *
3264718 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3264783 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
3264821 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3264886 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3264924 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3264989 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
3265027 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
3265092 TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3265130 TATGGGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
3265195 TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3265233 TATGTGGTCCTTAGGGA
1 TATGTGGTCCTTCGGGA
3265250 GAACTTTATA
Statistics
Matches: 421, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 421 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3265287 original size:23 final size:23
Alignment explanation
Indices: 3265261--3265328 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
3265251 AACTTTATAT
*
3265261 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
3265284 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
3265307 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3265329 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3272140 original size:103 final size:103
Alignment explanation
Indices: 3271961--3272493 Score: 978
Period size: 103 Copynumber: 5.2 Consensus size: 103
3271951 GTAGAGGGTC
*
3271961 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3272026 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3272064 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3272129 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3272167 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
3272232 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATTA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
3272270 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
3272335 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
3272373 TATGGGGTCCTTCGGGACGTATATGTATTCTTTGGAATAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
3272438 TTGATCTTTGGCATATGTATATGACTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
3272476 TATGTGGT-CTTAGGGACA
1 TATGTGGTCCTTCGGGACA
3272494 ACTTTATATG
Statistics
Matches: 416, Mismatches: 14, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
102 8 0.02
103 408 0.98
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3272529 original size:23 final size:23
Alignment explanation
Indices: 3272503--3272570 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
3272493 AACTTTATAT
* *
3272503 GGCACTTCCGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
3272526 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
3272549 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3272571 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3274106 original size:21 final size:19
Alignment explanation
Indices: 3274059--3274112 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
3274049 TTTATTGTGC
3274059 AAAGGATCGATCCCTCGAA
1 AAAGGATCGATCCCTCGAA
* *
3274078 AAAAGATCGATCCTTCGACCA
1 AAAGGATCGATCCCTCGA--A
3274099 AAAGGATCGATCCC
1 AAAGGATCGATCCC
3274113 AAACTTTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.17
Consensus pattern (19 bp):
AAAGGATCGATCCCTCGAA
Found at i:3274118 original size:70 final size:70
Alignment explanation
Indices: 3274005--3274181 Score: 228
Period size: 70 Copynumber: 2.5 Consensus size: 70
3273995 GTCAGTTCCA
* * * *
3274005 GAAAAAGGATCAATCCCTCGACCAAAAGGATTGATCCCAAACTTTTTATTGTGCAAAGGATCGAT
1 GAAAAAAGATCAATCCCTCGACCAAAAGGATCGATCCCAAACTTTCTATTGTGCAAAGAATCGAT
3274070 CCCTC
66 CCCTC
* *
3274075 GAAAAAAGATCGATCCTTCGACCAAAAGGATCGATCCCAAACTTTCTATTGTGCAAAGAATCGAT
1 GAAAAAAGATCAATCCCTCGACCAAAAGGATCGATCCCAAACTTTCTATTGTGCAAAGAATCGAT
*
3274140 CCCTTT
66 CCC-TC
** * * **
3274146 TTAAAATGATCAATCCCTCTAGGAAAAGGATCGATC
1 GAAAAAAGATCAATCCCTCGACCAAAAGGATCGATC
3274182 TCTTCGTTGT
Statistics
Matches: 91, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
70 62 0.68
71 29 0.32
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (70 bp):
GAAAAAAGATCAATCCCTCGACCAAAAGGATCGATCCCAAACTTTCTATTGTGCAAAGAATCGAT
CCCTC
Found at i:3275211 original size:65 final size:64
Alignment explanation
Indices: 3275136--3275272 Score: 161
Period size: 65 Copynumber: 2.1 Consensus size: 64
3275126 GTACACTTGG
* * *
3275136 GTGCATCGGTACACT-AATTACATTCGATATTTCAA-AAGAGCCAAGAGTGTATCGATACATGGT
1 GTGCATCGGTACA-TAAAATACATTCGATATTTCAATAA-AACCAAGAGTGCATCGATACATGG-
3275199 CT
63 CT
* * * * *
3275201 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATGGCT
1 GTGCATCGGTACATAAAATACATTCGATATTTCAATAAAACCAAGAGTGCATCGATACATGGCT
3275265 GTGCATCG
1 GTGCATCG
3275273 ATGCATGGCT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
64 11 0.18
65 49 0.79
66 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCGATATTTCAATAAAACCAAGAGTGCATCGATACATGGCT
Found at i:3275270 original size:18 final size:18
Alignment explanation
Indices: 3275247--3275290 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
3275237 AAAATCAGGA
3275247 GTGCATCGATGCATGGCT
1 GTGCATCGATGCATGGCT
3275265 GTGCATCGATGCATGGCT
1 GTGCATCGATGCATGGCT
3275283 GTGCATCG
1 GTGCATCG
3275291 GTACACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.23, G:0.34, T:0.27
Consensus pattern (18 bp):
GTGCATCGATGCATGGCT
Found at i:3275664 original size:13 final size:14
Alignment explanation
Indices: 3275646--3275681 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3275636 TTTAAGATTT
3275646 TCTTTGAAAATC-A
1 TCTTTGAAAATCAA
3275659 TCTTTG-AAATCAA
1 TCTTTGAAAATCAA
3275672 T-TTTGAAAAT
1 TCTTTGAAAAT
3275682 TACTCCCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (14 bp):
TCTTTGAAAATCAA
Found at i:3276018 original size:29 final size:28
Alignment explanation
Indices: 3275961--3276042 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
3275951 TTCAAACAAA
*
3275961 CCAAAC-ATCCAAA-ATATATTCAAAA-
1 CCAAACAATCCAAACAAATATTCAAAAT
3275986 -CAAACAATCCAAACTAAATATTCAAAAT
1 CCAAACAATCCAAAC-AAATATTCAAAAT
*
3276014 CCAAACAA-ACAAAGCCAAATATTCAAAAT
1 CCAAACAATCCAAA--CAAATATTCAAAAT
3276043 GTTTAAACAC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
24 5 0.10
25 7 0.15
27 11 0.23
28 4 0.08
29 20 0.42
30 1 0.02
ACGTcount: A:0.57, C:0.23, G:0.01, T:0.18
Consensus pattern (28 bp):
CCAAACAATCCAAACAAATATTCAAAAT
Found at i:3279145 original size:103 final size:103
Alignment explanation
Indices: 3278920--3279134 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
3278910 GTCGAGGGTC
*
3278920 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATACATAC
1 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
3278985 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3279023 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
3279088 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3279126 TATGTGGTC
1 TATGTGGTC
3279135 CTTATGGACA
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3279220 original size:23 final size:23
Alignment explanation
Indices: 3279144--3279221 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
3279134 CCTTATGGAC
*
3279144 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
3279168 ATTCTACGTGGCACTCCGGTACA
1 ATTATATGTGGCACTACGGTGCA
*
3279191 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
3279214 ATTATATG
1 ATTATATG
3279222 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:3283913 original size:19 final size:19
Alignment explanation
Indices: 3283889--3283927 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3283879 ATGCAATTGG
3283889 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
*
3283908 TGCATCGATGCATAATGCA
1 TGCATCGATGCATAAGGCA
3283927 T
1 T
3283928 CCCAGTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATAAGGCA
Found at i:3283987 original size:19 final size:20
Alignment explanation
Indices: 3283960--3284033 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
3283950 ATGTATTTTA
* *
3283960 TGCACCGATGCAC-ATGTAG
1 TGCATCGATGCACGATGCAG
* *
3283979 TGCATCGATGCACCGATAGGGAA
1 TGCATCGATGCA-CGAT--GCAG
* *
3284002 TGCATCGATACACTATGCAG
1 TGCATCGATGCACGATGCAG
3284022 TGCATCGATGCA
1 TGCATCGATGCA
3284034 TACCTTCATT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 11 0.26
20 14 0.33
21 2 0.05
22 3 0.07
23 13 0.30
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACGATGCAG
Found at i:3284960 original size:102 final size:103
Alignment explanation
Indices: 3284777--3284993 Score: 364
Period size: 102 Copynumber: 2.1 Consensus size: 103
3284767 GTCGAGGGTC
*
3284777 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTAGTGAGACACATAC
* * *
3284842 TTGATCCTTGGCATATGTATATGATTCTTAATG-ATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
3284879 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTAGTGAGACACATAC
*
3284944 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3284982 TATGTGGTCCTT
1 TATGTGGTCCTT
3284994 ATTGACATTA
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 91 0.86
103 15 0.14
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3285076 original size:23 final size:23
Alignment explanation
Indices: 3285000--3285077 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 23
3284990 CCTTATTGAC
* *
3285000 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTTCGGTGCA
* *
3285024 ATTCTACGTGGCAC-TCTGGTGCA
1 ATTATATGTGGCACTTC-GGTGCA
3285047 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
3285070 ATTATATG
1 ATTATATG
3285078 AGATGTGGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 40 0.87
24 5 0.11
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTTCGGTGCA
Found at i:3286752 original size:44 final size:44
Alignment explanation
Indices: 3286662--3286768 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
3286652 CGATGCACTG
* * *
3286662 CATAGTGTATCGAGGCACATTCAAGGAATGCATCAGTGCACCTT
1 CATAGTGTATCGATGCATATTCAAGGAATGCATCAGTACACCTT
* **
3286706 CATAGTGTATCGATTCATATTCAAGGAATGCATTTGTAC-CCTTT
1 CATAGTGTATCGATGCATATTCAAGGAATGCATCAGTACACC-TT
* *
3286750 CATAATTTATCGATGCATA
1 CATAGTGTATCGATGCATA
3286769 GTGCACAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.04
44 51 0.96
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CATAGTGTATCGATGCATATTCAAGGAATGCATCAGTACACCTT
Found at i:3293002 original size:20 final size:20
Alignment explanation
Indices: 3292979--3293021 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3292969 AGCAGAGTAT
3292979 GGCTTGAATTAATTTTAGAG
1 GGCTTGAATTAATTTTAGAG
3292999 GGCTTGAATTAATTTTAGAG
1 GGCTTGAATTAATTTTAGAG
3293019 GGC
1 GGC
3293022 ATGCATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (20 bp):
GGCTTGAATTAATTTTAGAG
Found at i:3293029 original size:20 final size:20
Alignment explanation
Indices: 3292983--3293030 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3292973 GAGTATGGCT
*
3292983 TGAATTAATTTTAGAGGGCT
1 TGAATTAATTTTAGAGGGCA
3293003 TGAATTAATTTTAGAGGGCA
1 TGAATTAATTTTAGAGGGCA
*
3293023 TGCATTAA
1 TGAATTAA
3293031 GTATGGACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (20 bp):
TGAATTAATTTTAGAGGGCA
Found at i:3309996 original size:15 final size:15
Alignment explanation
Indices: 3309976--3310054 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 15
3309966 AAATAATTAA
3309976 AATAATATATTTTAT
1 AATAATATATTTTAT
3309991 AATAATATATTTTAT
1 AATAATATATTTTAT
* * *
3310006 AATTATTTATTATAT
1 AATAATATATTTTAT
**
3310021 TTTAA-ATCA--TTA-
1 AATAATAT-ATTTTAT
3310033 AATTAATATATTTTAT
1 AA-TAATATATTTTAT
3310049 AATAAT
1 AATAAT
3310055 TTTTATATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
13 6 0.12
14 3 0.06
15 37 0.77
16 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:3310011 original size:21 final size:21
Alignment explanation
Indices: 3309987--3310092 Score: 69
Period size: 21 Copynumber: 5.0 Consensus size: 21
3309977 ATAATATATT
3309987 TTATAATAATATATTTTATAA
1 TTATAATAATATATTTTATAA
* *
3310008 TTAT-TTATTATATTTTA-AA
1 TTATAATAATATATTTTATAA
*
3310027 TCATTAAATTAATATATTTTATAA
1 TTA-T-AA-TAATATATTTTATAA
* **
3310051 -TA-ATTTTTATATTTTAATAA
1 TTATAATAATATATTTT-ATAA
*
3310071 TTA-AATAATATATATTAATAA
1 TTATAATAATATAT-TTTATAA
3310092 T
1 T
3310093 ATTAAAATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
19 13 0.20
20 17 0.27
21 18 0.28
22 2 0.03
23 12 0.19
24 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATAATAATATATTTTATAA
Found at i:3310021 original size:20 final size:21
Alignment explanation
Indices: 3309996--3310092 Score: 83
Period size: 20 Copynumber: 4.7 Consensus size: 21
3309986 TTTATAATAA
3309996 TATATTTT-ATAATTATTTAT
1 TATATTTTAATAATTATTTAT
* * *
3310016 TATATTTTAAATCATTAAATTAA
1 TATATTTT-AATAATT-ATTTAT
*
3310039 TATATTTT-ATAATAATTT-T
1 TATATTTTAATAATTATTTAT
** *
3310058 TATATTTTAATAATTAAATAA
1 TATATTTTAATAATTATTTAT
*
3310079 TATATATTAATAAT
1 TATATTTTAATAAT
3310093 ATTAAAATAA
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 8 0.13
20 18 0.30
21 17 0.28
22 5 0.08
23 12 0.20
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTTTAATAATTATTTAT
Found at i:3310092 original size:41 final size:42
Alignment explanation
Indices: 3309991--3310093 Score: 147
Period size: 43 Copynumber: 2.5 Consensus size: 42
3309981 TATATTTTAT
* *
3309991 AATAATATATTTTATAATTATTTATTATATTTTAAATCATTA
1 AATAATATATTTTATAATAATTTATTATATTTTAAATAATTA
3310033 AATTAATATATTTTATAATAATTT-TTATATTTT-AATAATTA
1 AA-TAATATATTTTATAATAATTTATTATATTTTAAATAATTA
*
3310074 AATAATATATATTAATAATA
1 AATAATATAT-TTTATAATA
3310094 TTAAAATAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
40 8 0.14
41 17 0.30
42 11 0.20
43 20 0.36
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (42 bp):
AATAATATATTTTATAATAATTTATTATATTTTAAATAATTA
Found at i:3310100 original size:24 final size:24
Alignment explanation
Indices: 3310065--3310131 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
3310055 TTTTATATTT
3310065 TAATAATT-AAATAATATATATTAA
1 TAAT-ATTAAAATAATATATATTAA
3310089 TAATATTAAAATAA-A-ATATTAA
1 TAATATTAAAATAATATATATTAA
3310111 -AATATTAAATATAATATATAT
1 TAATATTAAA-ATAATATATAT
3310132 GTATATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.23
22 11 0.28
23 5 0.13
24 14 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATATTAAAATAATATATATTAA
Found at i:3310101 original size:21 final size:22
Alignment explanation
Indices: 3310059--3310129 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 22
3310049 AATAATTTTT
* *
3310059 ATATTTTAATAAT-TAAATAAT-
1 ATATATTAATAATATTAA-AATA
3310080 ATATATTAATAATATTAAAATA
1 ATATATTAATAATATTAAAATA
*
3310102 AAATATTAA-AATATTAAATATA
1 ATATATTAATAATATTAAA-ATA
3310124 ATATAT
1 ATATAT
3310130 ATGTATATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
21 24 0.56
22 19 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATATTAATAATATTAAAATA
Found at i:3310106 original size:13 final size:13
Alignment explanation
Indices: 3310090--3310114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3310080 ATATATTAAT
3310090 AATATTAAAATAA
1 AATATTAAAATAA
3310103 AATATTAAAATA
1 AATATTAAAATA
3310115 TTAAATATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATTAAAATAA
Found at i:3321629 original size:64 final size:63
Alignment explanation
Indices: 3321543--3321752 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 63
3321533 TGCACTAAGA
* * *
3321543 GTGCATCGATACATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTT
** *
3321606 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAATGCATCGATGCATGGT
1 -GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT
3321670 AT
63 -T
* * * ** *
3321672 GTGCATCGATGAATGAAATGCATTCAATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG-T
3321735 T
63 T
3321736 AGTGCATCGATGCATCA
1 -GTGCATCGATGCATCA
3321753 CTTTGATAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTT
Found at i:3324385 original size:23 final size:22
Alignment explanation
Indices: 3324355--3324434 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
3324345 GCATGGCCTT
3324355 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
3324377 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
3324399 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
3324421 ATGCATCGATGCAC
1 GTGCATCGATGCAC
3324435 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:3324409 original size:44 final size:42
Alignment explanation
Indices: 3324333--3324453 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 42
3324323 AAAACCCGAT
* ** *
3324333 GGATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-GTCAGGTGTATCGATGCACATTCAA
* *
3324375 GGCGTGCATCGGTGCACCT-TCATGGTGTATCGATGCACATTCAA
1 GG-ATGCATCGATGCA-CTGTCA-GGTGTATCGATGCACATTCAA
*
3324419 GGATGCATCGATGCACTGTTAGGTGTATCGATGCA
1 GGATGCATCGATGCACTGTCAGGTGTATCGATGCA
3324454 TGAAGCACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
42 18 0.28
43 25 0.38
44 21 0.32
45 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTCAGGTGTATCGATGCACATTCAA
Found at i:3324450 original size:20 final size:21
Alignment explanation
Indices: 3324359--3324453 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
3324349 GGCCTTGTGC
*
3324359 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
3324382 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
3324403 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
3324425 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
3324445 ATCGATGCA
1 ATCGATGCA
3324454 TGAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 22 0.37
22 14 0.23
23 13 0.22
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:3330283 original size:18 final size:17
Alignment explanation
Indices: 3330229--3330277 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3330219 TTGGACCCTT
* *
3330229 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3330247 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3330265 AGTGCATTCGATG
1 AGTGCA-TCGATG
3330278 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3330447 original size:65 final size:64
Alignment explanation
Indices: 3330249--3330458 Score: 241
Period size: 65 Copynumber: 3.2 Consensus size: 64
3330239 TGCACTAAGA
* * **
3330249 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
*
3330313 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
3330376 AT-
63 -TG
* * *
3330378 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGTATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
3330442 G
64 G
*
3330443 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3330459 CTTTGATAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 51 0.41
65 65 0.52
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:3330800 original size:25 final size:25
Alignment explanation
Indices: 3330771--3330822 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3330761 ACTAATTCAT
*
3330771 TAATTTTCTAATAAACAATTAAAAA
1 TAATTTTATAATAAACAATTAAAAA
3330796 TAATTTTATAATAAACAATTAAAAA
1 TAATTTTATAATAAACAATTAAAAA
3330821 TA
1 TA
3330823 CTAACTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (25 bp):
TAATTTTATAATAAACAATTAAAAA
Found at i:3330902 original size:45 final size:44
Alignment explanation
Indices: 3330853--3330938 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 44
3330843 TTGCTACACC
*
3330853 CAAAAA-TCAAACCTTAATTATTATGATAATGTATTTATGAATGAA
1 CAAAAACT-AAACCTTAATTATTAT-ATAATGTATTTAAGAATGAA
* *
3330898 CAAAAACTAAACTTTAATTATTATTTAATGTATTTAAGAAT
1 CAAAAACTAAACCTTAATTATTATATAATGTATTTAAGAAT
3330939 TGTTATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 15 0.41
45 21 0.57
46 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (44 bp):
CAAAAACTAAACCTTAATTATTATATAATGTATTTAAGAATGAA
Found at i:3331215 original size:2 final size:2
Alignment explanation
Indices: 3331208--3331237 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3331198 AAAAGAATTC
3331208 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
3331238 TGACCACCTA
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:3335574 original size:113 final size:111
Alignment explanation
Indices: 3335438--3335720 Score: 426
Period size: 111 Copynumber: 2.5 Consensus size: 111
3335428 TAAAGAAAAA
* * *
3335438 AATTCGGTTTGGTTAATCAAACCAAAATTTATTTAAAAATTATTAACCGAACCAAATTAACCAAA
1 AATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACC--A
*
3335503 ACCTTTTTGAAAATTATTAA-CCGAATTAATCGAAGAAAAAATTCAGTT
64 A-CTTTTTGAAAAGTATTAACCCGAATTAATCGAAGAAAAAATTCAGTT
* * *
3335551 AATTCGGTTCGGTTAATCGAACCAAATTTTATTTGAAAATTATTAAACGAACCAAATTAACCAAT
1 AATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAC
* *
3335616 TTTTTTAAAAGTATTAACCCGAATTAATCGAAGCAAAAATTCAGTT
66 TTTTTGAAAAGTATTAACCCGAATTAATCGAAGAAAAAATTCAGTT
* *
3335662 AATTCGGTTCGGTTAATCGATCCAAAATTTATTTGAAAATTATTAACTGAA-CAAATTAA
1 AATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAA
3335721 TTTGAAAATT
Statistics
Matches: 156, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
110 23 0.15
111 76 0.49
113 57 0.37
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (111 bp):
AATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAC
TTTTTGAAAAGTATTAACCCGAATTAATCGAAGAAAAAATTCAGTT
Found at i:3335736 original size:15 final size:15
Alignment explanation
Indices: 3335692--3335736 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3335682 TCCAAAATTT
3335692 ATTTGAAAATTATTA
1 ATTTGAAAATTATTA
*
3335707 A-CTGAACAA--ATTA
1 ATTTGAA-AATTATTA
3335720 ATTTGAAAATTATTA
1 ATTTGAAAATTATTA
3335735 AT
1 AT
3335737 CGGACAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
13 7 0.29
14 8 0.33
15 9 0.38
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTTGAAAATTATTA
Found at i:3335828 original size:136 final size:137
Alignment explanation
Indices: 3335563--3335886 Score: 427
Period size: 136 Copynumber: 2.3 Consensus size: 137
3335553 TTCGGTTCGG
* * * * * *
3335563 TTAATCGAACCAAATTTTATTTGAAAATTATTAAACGAACCA-AATTAACCAATTTTTTTAAAAG
1 TTAACCGAACCAAA-TTAATTTGAAAATTATTAACCGAA-CAGAATTAATCTA-TTTTTT-AAAT
* * * * *
3335627 TATTAACCCGAATTAATCGAAGCAAAAATTCAGTTAATTCGGTTCGGTTAATCGATCCAAAATTT
62 TACTCA-TCGAATTAATCGAAGCAAAAATTCAGTTAAATCGGTTCGGTTAATCGAACCAAAATTT
3335692 ATTTGAAAATTA
126 ATTTGAAAATTA
* * *
3335704 TTAACTGAA-CAAATTAATTTGAAAATTATTAATCGGACAGAATTAATCTATTTTTTAAATTACT
1 TTAACCGAACCAAATTAATTTGAAAATTATTAACCGAACAGAATTAATCTATTTTTTAAATTACT
* *
3335768 CATCGAATTAATCGAAGCAAAAATTCGGTTAAATCGGTTCGGTTAATCGAACTAAAATTTATTTG
66 CATCGAATTAATCGAAGCAAAAATTCAGTTAAATCGGTTCGGTTAATCGAACCAAAATTTATTTG
3335833 AAAATTA
131 AAAATTA
* *
3335840 TTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACTGAATTAA
1 TTAACCGAACCAAATTAATTTGAAAATTATTAACCGAACAGAATTAA
3335887 CCAAATTTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
136 73 0.45
137 40 0.25
138 8 0.05
139 29 0.18
140 4 0.02
141 7 0.04
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (137 bp):
TTAACCGAACCAAATTAATTTGAAAATTATTAACCGAACAGAATTAATCTATTTTTTAAATTACT
CATCGAATTAATCGAAGCAAAAATTCAGTTAAATCGGTTCGGTTAATCGAACCAAAATTTATTTG
AAAATTA
Found at i:3335860 original size:29 final size:29
Alignment explanation
Indices: 3335823--3335886 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
3335813 ATCGAACTAA
*
3335823 AATTTATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
3335852 AATTAATTTGAAAATTATTAACCGAACTG
1 AATTAATTTGAAAATTATTAACCGAACCG
3335881 AATTAA
1 AATTAA
3335887 CCAAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:3337507 original size:29 final size:30
Alignment explanation
Indices: 3337474--3337538 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
3337464 TGCTGGAAAT
*
3337474 TTAAAGGA-AAATAATTAAAAT-ACATAAAA
1 TTAAAGGACAAA-AATTAAAATAACAAAAAA
* *
3337503 TTAAATGACAAAAATTTAAATAACAAAAAA
1 TTAAAGGACAAAAATTAAAATAACAAAAAA
*
3337533 ATAAAG
1 TTAAAG
3337539 TGCATAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.66, C:0.05, G:0.06, T:0.23
Consensus pattern (30 bp):
TTAAAGGACAAAAATTAAAATAACAAAAAA
Found at i:3337537 original size:15 final size:15
Alignment explanation
Indices: 3337481--3337537 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
3337471 AATTTAAAGG
3337481 AAAATAATTAAA-ATAC
1 AAAA-AATTAAATA-AC
* *
3337497 ATAAAATTAAATGAC
1 AAAAAATTAAATAAC
*
3337512 AAAAATTTAAATAAC
1 AAAAAATTAAATAAC
*
3337527 AAAAAAATAAA
1 AAAAAATTAAA
3337538 GTGCATAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 30 0.91
16 3 0.09
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAAAATTAAATAAC
Found at i:3339412 original size:21 final size:20
Alignment explanation
Indices: 3339384--3339423 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3339374 CCAAATCTCA
3339384 CATAATTTG-CACCGAAGTGC
1 CATAATTTGTC-CCGAAGTGC
3339404 CATATATTTGTCCCGAAGTG
1 CATA-ATTTGTCCCGAAGTG
3339424 TAACACCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 13 0.72
22 1 0.06
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
CATAATTTGTCCCGAAGTGC
Found at i:3340094 original size:23 final size:23
Alignment explanation
Indices: 3340039--3340118 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
3340029 CAGCTCGTAA
* *
3340039 TTTGCACCGCAGTGCCACATAA-
1 TTTGCACCGAAGTGCCACAAAAG
3340061 TTAT-C-CCGAAG-GACCACAAAAG
1 TT-TGCACCGAAGTG-CCACAAAAG
* * *
3340083 TTTGCATCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACAAAAG
3340106 TTTGCACCGAAGT
1 TTTGCACCGAAGT
3340119 ACGACATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 6 0.13
23 25 0.54
24 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACAAAAG
Found at i:3340125 original size:23 final size:23
Alignment explanation
Indices: 3340066--3340126 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
3340056 CATAATTATC
* * *
3340066 CCGAAGGACCACAAAAGTTTGCA
1 CCGAAGTACCACATAGGTTTGCA
* *
3340089 TCGAAGTGCCACATAGGTTTGCA
1 CCGAAGTACCACATAGGTTTGCA
*
3340112 CCGAAGTACGACATA
1 CCGAAGTACCACATA
3340127 TTTGTCTTGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CCGAAGTACCACATAGGTTTGCA
Found at i:3345891 original size:21 final size:21
Alignment explanation
Indices: 3345865--3345922 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
3345855 TGACTGTAGC
3345865 AGTGCATCGATACACTATAGA
1 AGTGCATCGATACACTATAGA
3345886 AGTGCATCGATACACTATAGA
1 AGTGCATCGATACACTATAGA
3345907 AGTGCATCGATACACT
1 AGTGCATCGATACACT
3345923 GTAATACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCGATACACTATAGA
Found at i:3349242 original size:23 final size:23
Alignment explanation
Indices: 3349183--3349266 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
3349173 TCGTAATTTA
*
3349183 CACCGAAGTGCCACATAA-TTTT
1 CACCGAAGTGCCACATAAGTTTG
* *
3349205 C-CCGAAAG-ACTACATAAGTTTG
1 CACCG-AAGTGCCACATAAGTTTG
*
3349227 CACCGAAGTGCCACATAGGTTTG
1 CACCGAAGTGCCACATAAGTTTG
* *
3349250 CACCAAAGTGCGACATA
1 CACCGAAGTGCCACATA
3349267 TTTGTCCTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 10 0.20
22 11 0.22
23 29 0.58
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
CACCGAAGTGCCACATAAGTTTG
Found at i:3353348 original size:413 final size:413
Alignment explanation
Indices: 3352581--3353407 Score: 1600
Period size: 413 Copynumber: 2.0 Consensus size: 413
3352571 TAATTTCTTC
3352581 CAATGAGAGACTTTCAAGAATATTTTATCTCCAACGTCAAACTCAATATTTTTTCTCTTTAAATC
1 CAATGAGAGACTTTCAAGAATATTTTATCTCCAACGTCAAACTCAATATTTTTTCTCTTTAAATC
3352646 CGCATATGACTTATGCCTATCGGCTGCCACTTTGAGATTATGTTGAATCACTTGAACTTTCTCTT
66 CGCATATGACTTATGCCTATCGGCTGCCACTTTGAGATTATGTTGAATCACTTGAACTTTCTCTT
*
3352711 CTACCTCCTTAATCAAATCAGGACCAAGAACATCCCGATCCTTAAGGTCATACCAATTCAGTGGT
131 CTACCTCCTTAATCAAATCAGGACCAAGAACATCCCGATCCTTAAGCTCATACCAATTCAGTGGT
3352776 GTACGACACCTTCTCCCGTATAAAGCCTCATAAGGAGCCATCATAATACTTGGCTGATAGCTATT
196 GTACGACACCTTCTCCCGTATAAAGCCTCATAAGGAGCCATCATAATACTTGGCTGATAGCTATT
*
3352841 ATCGTAGGCAAACTCTGCAAGAGGCAAATATTTTTCCAAAGATCCTTTAAACTTGATAACACATG
261 ATCGTAGGCAAACTCTGCAAGAGGCAAATATTTTTCCAAAGATCCTTTAAACTCGATAACACATG
*
3352906 CCCTTAACATATCTTCCAAGATTTGGATAGTCTGCTCAGACTAACCATCTGTCTGAGGGTTAAAG
326 CCCTTAACATATCTTCCAAGATTTGGATAGTCCGCTCAGACTAACCATCTGTCTGAGGGTTAAAG
*
3352971 GATGTACTAAATTTCAATTGAGT
391 GATGTAATAAATTTCAATTGAGT
*
3352994 CAATGAGAGACTTTCAAGAATATTTTATCTCCAACGTCGAACTCAATATTTTTTCTCTTTAAATC
1 CAATGAGAGACTTTCAAGAATATTTTATCTCCAACGTCAAACTCAATATTTTTTCTCTTTAAATC
*
3353059 CGCATATGACTTATGCCTATCGGTTGCCACTTTGAGATTATGTTGAATCACTTGAACTTTCTCTT
66 CGCATATGACTTATGCCTATCGGCTGCCACTTTGAGATTATGTTGAATCACTTGAACTTTCTCTT
3353124 CTACCTCCTTAATCAAATCAGGACCAAGAACATCCCGATCCTTAAGCTCATACCAATTCAGTGGT
131 CTACCTCCTTAATCAAATCAGGACCAAGAACATCCCGATCCTTAAGCTCATACCAATTCAGTGGT
3353189 GTACGACACCTTCTCCCGTATAAAGCCTCATAAGGAGCCATCATAATACTTGGCTGATAGCTATT
196 GTACGACACCTTCTCCCGTATAAAGCCTCATAAGGAGCCATCATAATACTTGGCTGATAGCTATT
3353254 ATCGTAGGCAAACTCTGCAAGAGGCAAATATTTTTCCAAAGATCCTTTAAACTCGATAACACATG
261 ATCGTAGGCAAACTCTGCAAGAGGCAAATATTTTTCCAAAGATCCTTTAAACTCGATAACACATG
3353319 CCCTTAACATATCTTCCAAGATTTGGATAGTCCGCTCAGACTAACCATCTGTCTGAGGGTTAAAG
326 CCCTTAACATATCTTCCAAGATTTGGATAGTCCGCTCAGACTAACCATCTGTCTGAGGGTTAAAG
3353384 GATGTAATAAATTTCAATTGAGT
391 GATGTAATAAATTTCAATTGAGT
3353407 C
1 C
3353408 CCTAAAGCTC
Statistics
Matches: 408, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
413 408 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (413 bp):
CAATGAGAGACTTTCAAGAATATTTTATCTCCAACGTCAAACTCAATATTTTTTCTCTTTAAATC
CGCATATGACTTATGCCTATCGGCTGCCACTTTGAGATTATGTTGAATCACTTGAACTTTCTCTT
CTACCTCCTTAATCAAATCAGGACCAAGAACATCCCGATCCTTAAGCTCATACCAATTCAGTGGT
GTACGACACCTTCTCCCGTATAAAGCCTCATAAGGAGCCATCATAATACTTGGCTGATAGCTATT
ATCGTAGGCAAACTCTGCAAGAGGCAAATATTTTTCCAAAGATCCTTTAAACTCGATAACACATG
CCCTTAACATATCTTCCAAGATTTGGATAGTCCGCTCAGACTAACCATCTGTCTGAGGGTTAAAG
GATGTAATAAATTTCAATTGAGT
Found at i:3357880 original size:23 final size:23
Alignment explanation
Indices: 3357852--3357910 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3357842 TTTTTTTCCT
*
3357852 GAAGGACCACATATGATTATCCC
1 GAAGGACCACATAGGATTATCCC
* *
3357875 -AGAGGACCACATAGGCTTGTCCC
1 GA-AGGACCACATAGGATTATCCC
3357898 GAAGGACCACATA
1 GAAGGACCACATA
3357911 AAATCATCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (23 bp):
GAAGGACCACATAGGATTATCCC
Found at i:3359047 original size:23 final size:23
Alignment explanation
Indices: 3359021--3359069 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
3359011 ATAAAGAACC
3359021 AAAATAAACTC-AAATATACCATT
1 AAAATAAACTCTAAATAT-CCATT
*
3359044 AAAATAAAGTCTAAATATCCATT
1 AAAATAAACTCTAAATATCCATT
3359067 AAA
1 AAA
3359070 CCAACAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAATATCCATT
Found at i:3368911 original size:23 final size:23
Alignment explanation
Indices: 3368885--3368933 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3368875 ATAAAGAACC
*
3368885 AAAATAAACTC-AAATATACCTTT
1 AAAATAAACTCTAAATAT-CCATT
*
3368908 AAAATAAAGTCTAAATATCCATT
1 AAAATAAACTCTAAATATCCATT
3368931 AAA
1 AAA
3368934 CTAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTCTAAATATCCATT
Found at i:3381925 original size:19 final size:21
Alignment explanation
Indices: 3381882--3381930 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3381872 TTCTTTGAAG
3381882 TATAATATTATGAATATATTT
1 TATAATATTATGAATATATTT
* *
3381903 TATAATTTTA-GATTATA-TT
1 TATAATATTATGAATATATTT
3381922 TAT-ATATTA
1 TATAATATTA
3381931 AATAACATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 5 0.20
19 5 0.20
20 6 0.24
21 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TATAATATTATGAATATATTT
Found at i:3393372 original size:35 final size:35
Alignment explanation
Indices: 3393323--3393394 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
3393313 AGAACAAAAA
3393323 TATAATTAACATAACCATTGAAATATTGGATAAAC
1 TATAATTAACATAACCATTGAAATATTGGATAAAC
*
3393358 TATAATTAATATAACCATTGAAATATTGGATAAAC
1 TATAATTAACATAACCATTGAAATATTGGATAAAC
3393393 TA
1 TA
3393395 CCCGTTCAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (35 bp):
TATAATTAACATAACCATTGAAATATTGGATAAAC
Found at i:3394151 original size:16 final size:17
Alignment explanation
Indices: 3394123--3394166 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3394113 CGATTAATTT
3394123 TAAAATATTATTTATGA
1 TAAAATATTATTTATGA
* *
3394140 TAAAAT-TTATTTTTTA
1 TAAAATATTATTTATGA
3394156 TAAAATATTAT
1 TAAAATATTAT
3394167 GTGAGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAAATATTATTTATGA
Found at i:3395130 original size:21 final size:23
Alignment explanation
Indices: 3395078--3395130 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
3395068 TATAATATTC
*
3395078 AATTTAAAATTATTTCACAATAA
1 AATTTAAAAATATTTCACAATAA
* *
3395101 AAATT-AAAAT-TTTCAC-TTAA
1 AATTTAAAAATATTTCACAATAA
3395121 AATTTAAAAA
1 AATTTAAAAA
3395131 ATGCCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 7 0.28
21 10 0.40
22 4 0.16
23 4 0.16
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTTAAAAATATTTCACAATAA
Found at i:3395404 original size:20 final size:22
Alignment explanation
Indices: 3395356--3395411 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
3395346 AACAACAACA
3395356 AAAAAT-TGACGTTATTACTATGC
1 AAAAATATGACGTTATTAC-AT-C
3395379 AAAAATATGACGTTATTA-AT-
1 AAAAATATGACGTTATTACATC
3395399 AAAAATATGACGT
1 AAAAATATGACGT
3395412 AAATACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.41
22 2 0.06
23 6 0.19
24 11 0.34
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (22 bp):
AAAAATATGACGTTATTACATC
Found at i:3396708 original size:12 final size:12
Alignment explanation
Indices: 3396691--3396717 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3396681 CTTCCTCCTT
3396691 TCTCATTTTCCC
1 TCTCATTTTCCC
3396703 TCTCATTTTCCC
1 TCTCATTTTCCC
3396715 TCT
1 TCT
3396718 TCAAGTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (12 bp):
TCTCATTTTCCC
Found at i:3401528 original size:19 final size:19
Alignment explanation
Indices: 3401506--3401543 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3401496 GGTGTTAATC
3401506 ATGTGTTTTTAAGACACCT
1 ATGTGTTTTTAAGACACCT
3401525 ATGTGTTTTTAAGACACCT
1 ATGTGTTTTTAAGACACCT
3401544 TAAGACCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (19 bp):
ATGTGTTTTTAAGACACCT
Found at i:3402514 original size:16 final size:16
Alignment explanation
Indices: 3402493--3402539 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
3402483 AAATAAAAAT
*
3402493 AGTAACAACTAGAATC
1 AGTAACAGCTAGAATC
*
3402509 AGTAACAGCTAGAAAC
1 AGTAACAGCTAGAATC
3402525 AGTAACAGCTAGAAT
1 AGTAACAGCTAGAAT
3402540 GTCATAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (16 bp):
AGTAACAGCTAGAATC
Found at i:3403034 original size:32 final size:32
Alignment explanation
Indices: 3402998--3403142 Score: 166
Period size: 32 Copynumber: 4.5 Consensus size: 32
3402988 ACAGAGTTAT
* *
3402998 TATTGTATTAAGATAATGCACAGTAGAGCCAA
1 TATTGCATTAAGATAATGCACAATAGAGCCAA
* *
3403030 TATTGCATTCAA-ATAAAGCACAATAGAACCAA
1 TATTGCATT-AAGATAATGCACAATAGAGCCAA
* *
3403062 TATTGCATTCAGATAATGTACAATAGAGCCAA
1 TATTGCATTAAGATAATGCACAATAGAGCCAA
* * * ** *
3403094 TATTACATTCAGATAATGCACCATAGAGTTAG
1 TATTGCATTAAGATAATGCACAATAGAGCCAA
3403126 TATTGCATTAAGATAAT
1 TATTGCATTAAGATAAT
3403143 TTACAAGATC
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
31 1 0.01
32 92 0.97
33 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (32 bp):
TATTGCATTAAGATAATGCACAATAGAGCCAA
Found at i:3403103 original size:64 final size:64
Alignment explanation
Indices: 3402998--3403148 Score: 185
Period size: 64 Copynumber: 2.4 Consensus size: 64
3402988 ACAGAGTTAT
* * * *
3402998 TATTGTATTAAGATAATGCACAGTAGAGCCAATATTGCATTCAAATAAAGCACAATAGAACCAA
1 TATTGCATTAAGATAATGTACAATAGAGCCAATATTACATTCAAATAAAGCACAATAGAACCAA
* * * * *** *
3403062 TATTGCATTCAGATAATGTACAATAGAGCCAATATTACATTCAGATAATGCACCATAGAGTTAG
1 TATTGCATTAAGATAATGTACAATAGAGCCAATATTACATTCAAATAAAGCACAATAGAACCAA
*
3403126 TATTGCATTAAGATAATTTACAA
1 TATTGCATTAAGATAATGTACAA
3403149 GATCGTTAGT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 73 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (64 bp):
TATTGCATTAAGATAATGTACAATAGAGCCAATATTACATTCAAATAAAGCACAATAGAACCAA
Found at i:3416307 original size:21 final size:21
Alignment explanation
Indices: 3416281--3416344 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3416271 TTTTGGTGCA
*
3416281 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
3416302 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
3416323 GAAGAGGAACCGATTCCCCCCA
1 G-AG-GGAACCGATCCCCCCCA
3416345 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 2 0.06
23 15 0.43
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:3421161 original size:38 final size:38
Alignment explanation
Indices: 3421110--3421182 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
3421100 TACTTACGAG
*
3421110 GAGTAAGTTAGCAGGATGTATGTTCCGATGTAGCAATT
1 GAGTAAGTTAGCAGGATGTATGTTCCAATGTAGCAATT
*
3421148 GAGTAAGTTAGCAGGGTGTATGTTCCAATGTAGCA
1 GAGTAAGTTAGCAGGATGTATGTTCCAATGTAGCA
3421183 GTTCTGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (38 bp):
GAGTAAGTTAGCAGGATGTATGTTCCAATGTAGCAATT
Done.