Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 92 of 171
Found at i:29979853 original size:16 final size:15
Alignment explanation
Indices: 29979808--29979857 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
29979798 TAAACCTAAC
29979808 TAATTAATTATCAAAA
1 TAATTAATTA-CAAAA
*
29979824 T-A-TAATATATAAAA
1 TAATTAAT-TACAAAA
29979838 TAATTAATTACCAAAA
1 TAATTAATTA-CAAAA
29979854 TAAT
1 TAAT
29979858 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATTAATTACAAAA
Found at i:29981802 original size:45 final size:45
Alignment explanation
Indices: 29981731--29981855 Score: 164
Period size: 45 Copynumber: 2.8 Consensus size: 45
29981721 GCATAGCTCA
*
29981731 TCAAGCCAAGGATATCACCCTAAGTTTGATGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTAAGTTTGATGAGCCACCGCAATAC
* *
29981776 TCAAGCCAAGGATATCAGCCTTAGTTTGATGAGCCACCTCAATAC
1 TCAAGCCAAGGATATCAGCCTAAGTTTGATGAGCCACCGCAATAC
* * *
29981821 TCAATG-GAAGGATATCAAG-CTGAGTTTGACGAGCC
1 TCAA-GCCAAGGATATC-AGCCTAAGTTTGATGAGCC
29981856 CGGGCAATAC
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
45 69 0.96
46 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTAAGTTTGATGAGCCACCGCAATAC
Found at i:29985732 original size:4 final size:4
Alignment explanation
Indices: 29985723--29985775 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
29985713 AAACACATTA
* * * *
29985723 TCTT TCTT TCCT TC-T TCTT TCTT CCTC TCCT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
*
29985770 TTTT TC
1 TCTT TC
29985776 CCGTTTATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TCTT
Found at i:29987101 original size:18 final size:19
Alignment explanation
Indices: 29987078--29987113 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29987068 ACCTTTAATA
29987078 TTTACT-TCTTTTGTTAGT
1 TTTACTCTCTTTTGTTAGT
*
29987096 TTTACTCTCTTTTTTTAG
1 TTTACTCTCTTTTGTTAG
29987114 CTAAATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.11, C:0.14, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTACTCTCTTTTGTTAGT
Found at i:29989986 original size:374 final size:373
Alignment explanation
Indices: 29989289--29990029 Score: 1169
Period size: 374 Copynumber: 2.0 Consensus size: 373
29989279 AATTTACCTG
* * * *
29989289 CTCGACATATGCCTCAATCATTTGTCTGTACACAACTAGGGTTTTGACTTCTTGATTCCCGGACA
1 CTCGACATATGCCTCAATCATTTGTCTATACACAACTAGGGTTTCGACTTCTCGATTCCCGAACA
29989354 AGTACACCATCTAAAAAAAAAAGCAAACTTGTTAGGTAACATTTTCATAAAATGAAAATTCTTAA
66 AGTACACCATCTAAAAAAAAAAGCAAACTTGTTAGGTAACATTTTCATAAAATGAAAATTCTTAA
* *
29989419 TCGATGTTTTAATTTTTTAACCTATTTACAAGCGGAAAAACATATTGTTGGTGACTTAATGATGG
131 TCGATGTTTTAATTTTTTAACCTATTTACAAGCGGAAAAACATATTGTTGGTGACTCAATGATGC
* ** * ** *
29989484 CAGAAATGACGTCCTGTACAACGCCCAAGACTACAGTAATAACAGGCACCTGTTTATATCTTGTG
196 CAGAAATGACATCCTGTACAACGCCCAAGACTACAACAATAACAGGCACCTATCCATATCTTATG
* *
29989549 TATCATGTTTTGTCACCCAACAAAGCTCACAGTACAATGTTGATAATACTGTTGAATCCCAACTA
261 TATCATGTTTTGTCACCCAACAAAGCTCACAGTACAACGTTGATAATACTGTTGAACCCCAACTA
* *
29989614 TACGAATAGG-CAGCTTGAAAATCAGCCAACAAAGGTAAGTACCTCCTC
326 TACGAAT-GGACAGCTTGAAAATCAACCAACAAAGGCAAGTACCTCCTC
* * * *
29989662 CTCGACTTATGCCTCAATCATTTGTCTATACATAACTAGGGTTTCGACTTCTCGATTCCTGAATA
1 CTCGACATATGCCTCAATCATTTGTCTATACACAACTAGGGTTTCGACTTCTCGATTCCCGAACA
*
29989727 AGTACACCATCTGAAAAAAAAAGCAAACTTGTTAGGTAACATTTTCATAAAATGAAAATTCTTAA
66 AGTACACCATCTAAAAAAAAAAGCAAACTTGTTAGGTAACATTTTCATAAAATGAAAATTCTTAA
*
29989792 TCGATGTTTTAATTTTTTTAACCTATTTACAAGTGGAAAAACATATTGTTGGTGACTCAATGATG
131 TCGATGTTTTAA-TTTTTTAACCTATTTACAAGCGGAAAAACATATTGTTGGTGACTCAATGATG
* **
29989857 CCAGAAATGACATCCTGTATAGGGCCCAAGACTACAACAATAACAGGCACCTATCCATATCTTAT
195 CCAGAAATGACATCCTGTACAACGCCCAAGACTACAACAATAACAGGCACCTATCCATATCTTAT
* ** * *
29989922 GTATCATGTTTTGTCACCCGACAAAGCTCATGGTATAACGTTGATAATATTGTTGAACCCCAACT
260 GTATCATGTTTTGTCACCCAACAAAGCTCACAGTACAACGTTGATAATACTGTTGAACCCCAACT
*
29989987 ATATGAATGGACAGCTTGAAAATCAACCAACAAAGGCAAGTAC
325 ATACGAATGGACAGCTTGAAAATCAACCAACAAAGGCAAGTAC
29990030 ATCAAATGAA
Statistics
Matches: 334, Mismatches: 32, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
373 135 0.40
374 199 0.60
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (373 bp):
CTCGACATATGCCTCAATCATTTGTCTATACACAACTAGGGTTTCGACTTCTCGATTCCCGAACA
AGTACACCATCTAAAAAAAAAAGCAAACTTGTTAGGTAACATTTTCATAAAATGAAAATTCTTAA
TCGATGTTTTAATTTTTTAACCTATTTACAAGCGGAAAAACATATTGTTGGTGACTCAATGATGC
CAGAAATGACATCCTGTACAACGCCCAAGACTACAACAATAACAGGCACCTATCCATATCTTATG
TATCATGTTTTGTCACCCAACAAAGCTCACAGTACAACGTTGATAATACTGTTGAACCCCAACTA
TACGAATGGACAGCTTGAAAATCAACCAACAAAGGCAAGTACCTCCTC
Found at i:30002435 original size:21 final size:21
Alignment explanation
Indices: 30002411--30002456 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
30002401 TTTTACCGAT
*
30002411 ACAAGTGAAGCTTCTATAGAA
1 ACAAGTGAAACTTCTATAGAA
* *
30002432 ACAAGTGAAATTTCTATCGAA
1 ACAAGTGAAACTTCTATAGAA
30002453 ACAA
1 ACAA
30002457 ATCATGCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (21 bp):
ACAAGTGAAACTTCTATAGAA
Found at i:30005067 original size:35 final size:37
Alignment explanation
Indices: 30004997--30005068 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
30004987 TCGAAAAAAA
30004997 TTTCGAATTTCGAATTGTTCGAATCAAGTTAAATTTTT
1 TTTCGAATTTCGAA-TGTTCGAATCAAGTTAAATTTTT
* * *
30005035 TTTCGAATTTCG-A-GTTTGAATCGAGTTTAATTTT
1 TTTCGAATTTCGAATGTTCGAATCAAGTTAAATTTT
30005069 CGAATTCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 18 0.58
37 1 0.03
38 12 0.39
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (37 bp):
TTTCGAATTTCGAATGTTCGAATCAAGTTAAATTTTT
Found at i:30005274 original size:18 final size:15
Alignment explanation
Indices: 30005239--30005267 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30005229 CATCAACAAA
30005239 TTAAACCCAAATATT
1 TTAAACCCAAATATT
30005254 TTAAACCCAAATAT
1 TTAAACCCAAATAT
30005268 AATTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAACCCAAATATT
Found at i:30008450 original size:15 final size:15
Alignment explanation
Indices: 30008430--30008460 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30008420 TTTGGAAACC
30008430 ATCTCTAGCAACTTT
1 ATCTCTAGCAACTTT
30008445 ATCTCTAGCAACTTT
1 ATCTCTAGCAACTTT
30008460 A
1 A
30008461 CTACTCGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
ATCTCTAGCAACTTT
Found at i:30013184 original size:5 final size:5
Alignment explanation
Indices: 30013174--30013207 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
30013164 TTGCTTGGGA
*
30013174 TTTTC TTTTC TTTTC TTTTC CTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
30013208 TCTTGATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:30017018 original size:15 final size:14
Alignment explanation
Indices: 30016990--30017024 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
30016980 AAGTTATTTT
30016990 TAAATTAATTTTTAA
1 TAAA-TAATTTTTAA
30017005 TAAATAATTATTTAA
1 TAAATAATT-TTTAA
30017020 TAAAT
1 TAAAT
30017025 TTTTGAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAATAATTTTTAA
Found at i:30025047 original size:59 final size:58
Alignment explanation
Indices: 30024970--30025404 Score: 555
Period size: 59 Copynumber: 7.4 Consensus size: 58
30024960 TTTGACTATC
30024970 GGGGTAAAATGGTAATTTTTGGTGAAATCTGGGTTAAAAATGGGATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAAT-TGGGTTAAAAATGGGATTTTGGAAAGTTCG
* ** *** * * * **
30025029 GGGGCAAAATTATAATTTTTGGTGAAAATAAAGTTAAAAATAGAATTTAGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTG-AAATTGGGTTAAAAATGGGATTTTGGAAAGTTCG
* * *
30025088 GGGGTAAAATGGTAACTTTTAGTGAAATAGGGGTTAAAAATGGGATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAAT-TGGGTTAAAAATGGGATTTTGGAAAGTTCG
* *
30025147 GGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTAGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATT-GGGTTAAAAATGGGATTTTGGAAAGTTCG
* * * *
30025206 AGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGGATTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAAT-TGGGTTAAAAATGGGATTTTGGAAAGTTCG
* *
30025265 GGGGTAAAACGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGAAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATT-GGGTTAAAAATGGGATTTTGGAAAGTTCG
* * * * *
30025324 GGGATAAAATGGTATTTTTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTA-ATTTTTGGTGAAATTGGG-TTAAAAATGGGATTTTGGAAAGTTCG
30025384 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
30025405 AATAGTTTAG
Statistics
Matches: 321, Mismatches: 48, Indels: 14
0.84 0.13 0.04
Matches are distributed among these distances:
58 4 0.01
59 264 0.82
60 53 0.17
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATTGGGTTAAAAATGGGATTTTGGAAAGTTCG
Found at i:30025118 original size:29 final size:28
Alignment explanation
Indices: 30025085--30025406 Score: 116
Period size: 29 Copynumber: 11.0 Consensus size: 28
30025075 TTAGGAAAGT
30025085 TTAGGGGTAAAATGGTAACTTTTAGTGAAA
1 TTAGGGGTAAAATGGTAA-TTTT-GTGAAA
*
30025115 -TAGGGGTTAAAAATGG-GATTTTG-GAAA
1 TTAGGGG-T-AAAATGGTAATTTTGTGAAA
*
30025142 GTTCGGGGGTAAAATGGTAATTTTTGGTGAAA
1 -TT-AGGGGTAAAATGGTAA-TTTT-GTGAAA
* * *
30025174 TTAGGGTTAAAAATGG-GATTTT-AGAAA
1 TTAGGGGT-AAAATGGTAATTTTGTGAAA
*
30025201 GTTTGAGGGTAAAATGGTAATTTTTGATGAAA
1 -TTAG-GGGTAAAATGGTAA-TTTTG-TGAAA
* * *
30025233 -TCGGGGTTAAAAATGG-GATTTT-AGAAA
1 TTAGGGG-T-AAAATGGTAATTTTGTGAAA
* *
30025260 GTTCGGGGGTAAAACGGTAATTTTTGGTGAAA
1 -TT-AGGGGTAAAATGGTAA-TTTT-GTGAAA
* *
30025292 TT-GGGGTTAAAAATGG-GATTTTG-AAAA
1 TTAGGGG-T-AAAATGGTAATTTTGTGAAA
* *
30025319 GTTCGGGGATAAAATGGTATTTTTTTGGTGAAA
1 -TTAGGGG-TAAAATGGTA--ATTTT-GTGAAA
* *
30025352 -TCGGGATTAAAAATGG-AATTTTG-GAAA
1 TTAGGG-GT-AAAATGGTAATTTTGTGAAA
30025379 GTTCAGGGGTAAAATGGTAATTTT-TGAA
1 -TT-AGGGGTAAAATGGTAATTTTGTGAA
30025407 TAGTTTAGGG
Statistics
Matches: 222, Mismatches: 29, Indels: 83
0.66 0.09 0.25
Matches are distributed among these distances:
27 19 0.09
28 42 0.19
29 59 0.27
30 36 0.16
31 43 0.19
32 20 0.09
33 3 0.01
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (28 bp):
TTAGGGGTAAAATGGTAATTTTGTGAAA
Found at i:30028032 original size:115 final size:115
Alignment explanation
Indices: 30027829--30028081 Score: 384
Period size: 115 Copynumber: 2.2 Consensus size: 115
30027819 ATTTGGTCCA
* * * *
30027829 CTTCTCTATATCTCATCAAGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
* *
30027894 AGGAAGCTGGGTTCAAAGATTTGCTCACA-TTGAGCGTTGAGTTGGTGTT
66 AGGAAGCCGGGTTCAAAGATTTGCTCACATTTGAGCGTTGAGTTGGTATT
30027943 CTTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAG-AGTCTCA
1 C-TTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTA-TCTCA
* * *
30028007 TCAGGAAGCCGGGTTCGAAGTTTTGCTCGCATTTGAGCGTTGAGTTGGTATT
64 TCAGGAAGCCGGGTTCAAAGATTTGCTCACATTTGAGCGTTGAGTTGGTATT
*
30028059 CTTCTCTGTATCTCATTAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
30028082 ATGACCGCCT
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
114 2 0.02
115 104 0.83
116 20 0.16
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (115 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
AGGAAGCCGGGTTCAAAGATTTGCTCACATTTGAGCGTTGAGTTGGTATT
Found at i:30028288 original size:196 final size:196
Alignment explanation
Indices: 30027945--30028488 Score: 971
Period size: 196 Copynumber: 2.8 Consensus size: 196
30027935 TTGGTGTTCT
* * * * * *
30027945 TTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGAGTCTCATCA
1 TTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCA
30028010 GGAAGCCGGGTTCGAAGTTTTGCTCGCATTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCAT
66 GGAAGCCGGGTTCGAAGTTTTGCTCGCATTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCAT
*
30028075 TAGGAAGATGACCGCCTCGCTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCA
131 CAGGAAGATGACCGCCTCGCTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCA
30028140 C
196 C
*
30028141 TTCTCAGTGTCTCATCAGAAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCA
1 TTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCA
30028206 GGAAGCCGGGTTCGAAGTTTTGCTCGCATTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCAT
66 GGAAGCCGGGTTCGAAGTTTTGCTCGCATTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCAT
* *
30028271 CAGCAAGATGACCGCCTCACTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCA
131 CAGGAAGATGACCGCCTCGCTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCA
30028336 C
196 C
*
30028337 TTCTTAGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCA
1 TTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCA
* *
30028402 GGAAGCCGGGTTCGAACTTTTGCTCACATTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCAT
66 GGAAGCCGGGTTCGAAGTTTTGCTCGCATTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCAT
30028467 CAGGAAGATGACCGCCTCGCTT
131 CAGGAAGATGACCGCCTCGCTT
30028489 GTTGAACTAC
Statistics
Matches: 332, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
196 332 1.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (196 bp):
TTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACTTGCTTCTCAGTGTCTCATCA
GGAAGCCGGGTTCGAAGTTTTGCTCGCATTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCAT
CAGGAAGATGACCGCCTCGCTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCA
C
Found at i:30040711 original size:59 final size:56
Alignment explanation
Indices: 30040528--30040839 Score: 322
Period size: 58 Copynumber: 5.3 Consensus size: 56
30040518 TTGACTTTCG
*
30040528 GGGGTAAAATGGTAATTTTTTGTGTGAAATTTGGGTTAAAAACTGGGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAA-TTTTTG-GTGAAA-TAGGGTT-AAAA-T-GGATTTTGGAAAGTTCA
* ** * *
30040590 GGGGCAAAATGGTAATTTTTGGTGAAAATAGGGTTAAAATAAAATTTAGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTG-AAATAGGGTTAAAAT-GGATTTTGGAAAGTTCA
* * * *
30040648 GGGGTAAAATGATAACTTTTGGTGAAATCGGGATTAAAAATGCAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATAGGG-TT-AAAATG-GATTTTGGAAAGTTCA
* * *
30040707 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGGTTAAAATAGGATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAAT--AGGGTTAAAAT-GGATTTTGGAAAGTTCA
* *
30040765 GGGATAAAATGGTAATTTTTGGTGAAATTAGGGTCAAAA-GGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAA-TAGGGTTAAAATGGATTTTGGAAAGTTCA
* *
30040821 GGGATAAAATAGTAATTTT
1 GGGGTAAAATGGTAATTTT
30040840 GAATAGTTTA
Statistics
Matches: 216, Mismatches: 25, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
56 33 0.15
57 7 0.03
58 89 0.41
59 51 0.24
60 13 0.06
61 9 0.04
62 14 0.06
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (56 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATAGGGTTAAAATGGATTTTGGAAAGTTCA
Found at i:30040721 original size:117 final size:116
Alignment explanation
Indices: 30040524--30040839 Score: 374
Period size: 117 Copynumber: 2.7 Consensus size: 116
30040514 ATTTTTGACT
*
30040524 TTCGGGGGTAAAATGGTAATTTTTTGTGTGAAATTTGGGTTAAAAACTGGGATTTTGGAAAGTTC
1 TTCGGGGGTAAAATGGTAA-TTTTTG-GTGAAATTAGGGTTAAAAA-T-GGATTTTGGAAAGTTC
*
30040589 AGGGGCAAAATGGTAATTTTTGGTGAAAAT-AGGGTTAAAATA-AAATTTAGGAAAG
62 AGGGGTAAAATGGTAATTTTTGGTG-AAATCAGGGTTAAAATAGAAATTTA-GAAAG
* * * *
30040644 TTCGGGGGTAAAATGATAACTTTTGGTGAAA-TCGGGATTAAAAATGCAATTTTGGAAAGTTCAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGG-TTAAAAATG-GATTTTGGAAAGTTCAG
* * *
30040708 GGGTAAAATGGTAA-TTTTGGTGAAATCGGGGGTTAAAATAGGATTTTAGAAAG
64 GGGTAAAATGGTAATTTTTGGTGAAATC-AGGGTTAAAATAGAAATTTAGAAAG
** * *
30040761 TTTAGGGATAAAATGGTAATTTTTGGTGAAATTAGGG-TCAAAA-GGATTTTGGAAAGTTCAGGG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGATTTTGGAAAGTTCAGGG
* *
30040824 ATAAAATAGTAATTTT
66 GTAAAATGGTAATTTT
30040840 GAATAGTTTA
Statistics
Matches: 171, Mismatches: 18, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
114 28 0.16
115 8 0.05
116 14 0.08
117 76 0.44
118 22 0.13
119 5 0.03
120 18 0.11
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (116 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGATTTTGGAAAGTTCAGGG
GTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATAGAAATTTAGAAAG
Found at i:30041904 original size:3 final size:3
Alignment explanation
Indices: 30041896--30041976 Score: 54
Period size: 3 Copynumber: 26.0 Consensus size: 3
30041886 AATTTAAAAA
* * * **
30041896 ATT ATT ATT AATT ATT ATAT ATT ACT ATC ATT AAT ATT ATT GGT ATT
1 ATT ATT ATT -ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
30041943 ATTT ATT ATT ATA ATT AAT AAT AAT ATT ATT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30041977 GGTAGCATTT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
3 52 0.85
4 9 0.15
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:30041974 original size:31 final size:31
Alignment explanation
Indices: 30041906--30041976 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
30041896 ATTATTATTA
* * * *
30041906 ATTATTATATATTACTATCATTAATATTATT
1 ATTATTATTTATTACTATAATTAATAATAAT
** *
30041937 GGTATTATTTATTATTATAATTAATAATAAT
1 ATTATTATTTATTACTATAATTAATAATAAT
30041968 ATTATTATT
1 ATTATTATT
30041977 GGTAGCATTT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTATTATTTATTACTATAATTAATAATAAT
Found at i:30042308 original size:24 final size:24
Alignment explanation
Indices: 30042274--30042342 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
30042264 TTTTTTCTCC
30042274 TTTTTCAGAACAGGGTTTGTATTGA
1 TTTTTC-GAACAGGGTTTGTATTGA
30042299 TTTTTCGAACAGGGTTTGTATTGA
1 TTTTTCGAACAGGGTTTGTATTGA
** *
30042323 TTTTTAAAATAGGGTTTGTA
1 TTTTTCGAACAGGGTTTGTA
30042343 ACCCTTACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 35 0.85
25 6 0.15
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTTTCGAACAGGGTTTGTATTGA
Found at i:30042796 original size:16 final size:16
Alignment explanation
Indices: 30042759--30042803 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
30042749 TTATCAGGAC
30042759 ATTT-AATTTTATTTTAA
1 ATTTAAATTTTA--TTAA
30042776 ATTTAAATTTTATTAA
1 ATTTAAATTTTATTAA
*
30042792 GTTTAAATTTTA
1 ATTTAAATTTTA
30042804 GAAAAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 15 0.58
17 4 0.15
18 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTAAATTTTATTAA
Found at i:30048359 original size:21 final size:21
Alignment explanation
Indices: 30048330--30048381 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
30048320 GGAGTTTTTA
30048330 GTATCGGTAGAAG-CATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
30048351 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
30048372 GTATCGGTAG
1 GTATCGGTAG
30048382 TATTATCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:30051365 original size:158 final size:159
Alignment explanation
Indices: 30051085--30051388 Score: 430
Period size: 158 Copynumber: 1.9 Consensus size: 159
30051075 GTAACCATAT
* * * * * * * *
30051085 ATGCTCACATGAGATGTGAAATGGGCTTTGCTCACACGAGCTGTGGGTTGAGATGTTAGGTTACA
1 ATGCTCACACGAGATGCGAAATGGGCTCTACTCACACAAGCTGTGGGTCGAGACGTTAGGCTACA
* * * * *
30051150 TGATGCTGCTCACACGAGCTGTGGAGAATTAGCGACCAATGCAGGATCTCAACCATCGGTAGGAC
66 CGATGCTGCTCACACGAGCTGTGGAGAATCAGCAACCAATGCAAGACCTCAACCATCGGTAGGAC
*
30051215 ATCTAAGACCAGCACCAATATAACCTGTA
131 ATCCAAGACCAGCACCAATATAACCTGTA
* *
30051244 ATGCTCACACGAGCTGCGAAATGGG-TCTACTCATACAAGCTGTGGGTCGAGACGTTAGGCTACA
1 ATGCTCACACGAGATGCGAAATGGGCTCTACTCACACAAGCTGTGGGTCGAGACGTTAGGCTACA
* * *
30051308 CGATGCTGCTCGCACGAGCTGTGGAGAATCCGCAACCAATGCAAGACCTCAGCCATCGGTAGGAC
66 CGATGCTGCTCACACGAGCTGTGGAGAATCAGCAACCAATGCAAGACCTCAACCATCGGTAGGAC
30051373 ATCCAAGACCAGCACC
131 ATCCAAGACCAGCACC
30051389 TGGAACTGTA
Statistics
Matches: 126, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
158 104 0.83
159 22 0.17
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (159 bp):
ATGCTCACACGAGATGCGAAATGGGCTCTACTCACACAAGCTGTGGGTCGAGACGTTAGGCTACA
CGATGCTGCTCACACGAGCTGTGGAGAATCAGCAACCAATGCAAGACCTCAACCATCGGTAGGAC
ATCCAAGACCAGCACCAATATAACCTGTA
Found at i:30055178 original size:22 final size:22
Alignment explanation
Indices: 30055153--30055205 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
30055143 TTTACTACTG
* *
30055153 TTTGATGTTGTTTTGCTA-TCAT
1 TTTGTTGTTGTATTGCTACT-AT
30055175 TTTGTTGTTGTATTGCTACTAT
1 TTTGTTGTTGTATTGCTACTAT
30055197 TTTGTTGTT
1 TTTGTTGTT
30055206 ATTATTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.62
Consensus pattern (22 bp):
TTTGTTGTTGTATTGCTACTAT
Found at i:30056124 original size:10 final size:10
Alignment explanation
Indices: 30056109--30056140 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
30056099 TACATCAAGA
30056109 ACTTCAACTG
1 ACTTCAACTG
30056119 ACTTCAACTG
1 ACTTCAACTG
30056129 ACTTCAACTG
1 ACTTCAACTG
30056139 AC
1 AC
30056141 AATAACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.28
Consensus pattern (10 bp):
ACTTCAACTG
Found at i:30063789 original size:3 final size:3
Alignment explanation
Indices: 30063781--30063812 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
30063771 CCCATTGCCA
*
30063781 TCT TCT TCT TCT TCT TCT TCT TCT TCA TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
30063813 ATCATCTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:30063817 original size:9 final size:9
Alignment explanation
Indices: 30063779--30063821 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
30063769 GTCCCATTGC
30063779 CATCTTCTT
1 CATCTTCTT
*
30063788 CTTCTTCTT
1 CATCTTCTT
*
30063797 CTTCTTCTT
1 CATCTTCTT
*
30063806 CATCTTCAT
1 CATCTTCTT
30063815 CATCTTC
1 CATCTTC
30063822 CGTTCCTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.09, C:0.35, G:0.00, T:0.56
Consensus pattern (9 bp):
CATCTTCTT
Found at i:30065797 original size:40 final size:41
Alignment explanation
Indices: 30065753--30065829 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
30065743 ATATTCTCTC
* *
30065753 TAATTTGCTTCAT-AAAAAGGATATCAATCTA-TCAATCTAT
1 TAATTTACTTCATGAAAAA-GATACCAATCTATTCAATCTAT
30065793 TAATTTACTTCATGAAAAAGATACCAATCTATTCAAT
1 TAATTTACTTCATGAAAAAGATACCAATCTATTCAAT
30065830 TTGCTTCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 23 0.70
41 10 0.30
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (41 bp):
TAATTTACTTCATGAAAAAGATACCAATCTATTCAATCTAT
Found at i:30067511 original size:6 final size:6
Alignment explanation
Indices: 30067502--30067551 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
30067492 GTGAGAGAGA
30067502 CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG
1 CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG
30067550 CA
1 CA
30067552 GGATGTGCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (6 bp):
CATAGG
Found at i:30068084 original size:10 final size:10
Alignment explanation
Indices: 30068069--30068094 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30068059 AATATTATTT
30068069 AAAAATTTTA
1 AAAAATTTTA
30068079 AAAAATTTTA
1 AAAAATTTTA
30068089 AAAAAT
1 AAAAAT
30068095 GGTTTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:30070845 original size:32 final size:31
Alignment explanation
Indices: 30070784--30070850 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
30070774 TTTTAGGGTT
*
30070784 TTTTTAGGGTTTAGTTATTTATTTGTTTAGG
1 TTTTTAGGGTTTAGTTATTTAGTTGTTTAGG
*
30070815 ATTTTTAGGGTTTATTTATTTAGGTT-TTTAGG
1 -TTTTTAGGGTTTAGTTATTTA-GTTGTTTAGG
30070847 TTTT
1 TTTT
30070851 ATTTATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 4 0.12
32 26 0.81
33 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.21, T:0.63
Consensus pattern (31 bp):
TTTTTAGGGTTTAGTTATTTAGTTGTTTAGG
Found at i:30070846 original size:23 final size:24
Alignment explanation
Indices: 30070801--30070859 Score: 93
Period size: 23 Copynumber: 2.5 Consensus size: 24
30070791 GGTTTAGTTA
*
30070801 TTTATTTGTTTAGGATTTTTAGGG
1 TTTATTTATTTAGGATTTTTAGGG
*
30070825 TTTATTTATTTAGG-TTTTTAGGT
1 TTTATTTATTTAGGATTTTTAGGG
30070848 TTTATTTATTTA
1 TTTATTTATTTA
30070860 TAAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 20 0.61
24 13 0.39
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (24 bp):
TTTATTTATTTAGGATTTTTAGGG
Found at i:30072369 original size:21 final size:21
Alignment explanation
Indices: 30072345--30072401 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
30072335 AGTGCAAACC
* *
30072345 TCTATCGATACAAGTGACAGT
1 TCTACCGATACAAGTGACACT
*
30072366 TCTACCGATACAAGTGACTCT
1 TCTACCGATACAAGTGACACT
*
30072387 TCTACCGAAACAAGT
1 TCTACCGATACAAGT
30072402 CTTACTTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (21 bp):
TCTACCGATACAAGTGACACT
Found at i:30072544 original size:66 final size:65
Alignment explanation
Indices: 30072462--30072601 Score: 244
Period size: 66 Copynumber: 2.1 Consensus size: 65
30072452 CAACTTCTAC
*
30072462 CGATACAAGTACACAAACTATCGATACTTCTAAACACATAACTACCGATACTTGCTATTCAACTA
1 CGATACAAGTACACAAACTACCGATACTTCTAAACACATAACTACCGATACTTGCTATTCAACTA
*
30072527 TCGATACAAGTATACAAACTACCGATACTTCTAAACACATAACTACCGATACTTGCTATTCAACT
1 -CGATACAAGTACACAAACTACCGATACTTCTAAACACATAACTACCGATACTTGCTATTCAACT
30072592 A
65 A
30072593 CTGATACAA
1 C-GATACAA
30072602 CCCAAGTCAG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
65 1 0.01
66 70 0.99
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (65 bp):
CGATACAAGTACACAAACTACCGATACTTCTAAACACATAACTACCGATACTTGCTATTCAACTA
Found at i:30072593 original size:21 final size:22
Alignment explanation
Indices: 30072474--30072599 Score: 82
Period size: 21 Copynumber: 5.7 Consensus size: 22
30072464 ATACAAGTAC
* *
30072474 ACAAACTATCGATACTT-CTAAAC
1 ACAAACTACCGATACTTGCT--AT
30072497 ACATAACTACCGATACTTGCTAT
1 ACA-AACTACCGATACTTGCTAT
* * **
30072520 TC-AACTATCGATACAAG-TAT
1 ACAAACTACCGATACTTGCTAT
*
30072540 ACAAACTACCGATACTT-CTAAAC
1 ACAAACTACCGATACTTGCT--AT
30072563 ACATAACTACCGATACTTGCTAT
1 ACA-AACTACCGATACTTGCTAT
* *
30072586 TC-AACTACTGATAC
1 ACAAACTACCGATAC
30072600 AACCCAAGTC
Statistics
Matches: 81, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
20 4 0.05
21 35 0.43
23 11 0.14
24 27 0.33
25 4 0.05
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (22 bp):
ACAAACTACCGATACTTGCTAT
Found at i:30073208 original size:52 final size:53
Alignment explanation
Indices: 30073150--30073292 Score: 234
Period size: 52 Copynumber: 2.7 Consensus size: 53
30073140 TTCGCATTTG
*
30073150 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGAT-GGATTCGT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* *
30073202 GTAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGATTCAT
**
30073255 ATAACTCATAATGACACAGAGTCATCGGACCTTTAATC
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATC
30073293 TTTGGTACAA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 42 0.51
53 41 0.49
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCATGATAGGATTCAT
Found at i:30074168 original size:21 final size:22
Alignment explanation
Indices: 30074144--30074186 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
30074134 ACTTCCATCA
30074144 TTAAACTTTAATT-AACC-ATTT
1 TTAAAC-TTAATTGAACCTATTT
*
30074165 TTAATCTTAATTGAACCTATTT
1 TTAAACTTAATTGAACCTATTT
30074187 ATACTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAAACTTAATTGAACCTATTT
Found at i:30076006 original size:23 final size:24
Alignment explanation
Indices: 30075980--30076041 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
30075970 AATGTTCACA
** *
30075980 AACATGTTCATTTAAC-TTAATCG
1 AACATGTTCATCGAACATTAAACG
30076003 AACATGTTCA-CGAACATTAAACG
1 AACATGTTCATCGAACATTAAACG
30076026 AACATGTTCAT-GAACA
1 AACATGTTCATCGAACA
30076042 ATGTTAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (24 bp):
AACATGTTCATCGAACATTAAACG
Found at i:30078012 original size:23 final size:23
Alignment explanation
Indices: 30077938--30078151 Score: 142
Period size: 23 Copynumber: 9.5 Consensus size: 23
30077928 TAAACGGAAC
* * *
30077938 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
30077960 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
30077982 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
30078008 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
30078028 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30078047 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * * *
30078070 AATCGGAGAGGACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30078093 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
30078118 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
30078141 AATCAGAGAGC
1 AAACAGAGAGC
30078152 GCGCTAGTGT
Statistics
Matches: 149, Mismatches: 27, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 77 0.52
24 2 0.01
25 27 0.18
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:30078046 original size:39 final size:39
Alignment explanation
Indices: 30077992--30078066 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
30077982 GGGCAACAGA
*
30077992 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
30078031 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
30078067 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:30078109 original size:46 final size:46
Alignment explanation
Indices: 30078031--30078151 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
30078021 ACAAAGTACT
* * * *
30078031 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GACGTGCTAAACAGA
*
30078077 GAGGACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGACGTGCTAAACAGA
30078125 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
30078152 GCGCTAGTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
46 25 0.38
48 40 0.61
49 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGACGTGCTAAACAGA
Found at i:30082892 original size:6 final size:6
Alignment explanation
Indices: 30082881--30082911 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
30082871 TCTCAATCCC
30082881 TCGCAT TCGCAT TCGCAT TCGCAT TCGCAT T
1 TCGCAT TCGCAT TCGCAT TCGCAT TCGCAT T
30082912 TCCATTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (6 bp):
TCGCAT
Found at i:30083961 original size:2 final size:2
Alignment explanation
Indices: 30083954--30083981 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30083944 TAAAATTTAG
30083954 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
30083982 TAATTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30090565 original size:2 final size:2
Alignment explanation
Indices: 30090558--30090585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30090548 CCTTCAATTT
30090558 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
30090586 AAAACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30094337 original size:16 final size:16
Alignment explanation
Indices: 30094313--30094343 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30094303 ATTAAAGTAG
*
30094313 AAAATATAAATAATTC
1 AAAAAATAAATAATTC
30094329 AAAAAATAAATAATT
1 AAAAAATAAATAATT
30094344 AATAAAGTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATAAATAATTC
Found at i:30106867 original size:6 final size:6
Alignment explanation
Indices: 30106856--30106890 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
30106846 TATAACAAAA
30106856 TTTCTT TTTCTT TTCTCTT TTTC-T TTTCTT TTTCT
1 TTTCTT TTTCTT TT-TCTT TTTCTT TTTCTT TTTCT
30106891 CATTCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:30106874 original size:13 final size:13
Alignment explanation
Indices: 30106858--30106888 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30106848 TAACAAAATT
30106858 TCTTTTTCTTTTC
1 TCTTTTTCTTTTC
30106871 TCTTTTTCTTTTC
1 TCTTTTTCTTTTC
30106884 T-TTTT
1 TCTTTT
30106889 CTCATTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TCTTTTTCTTTTC
Found at i:30116362 original size:21 final size:22
Alignment explanation
Indices: 30116338--30116387 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
30116328 ACAACTTCTT
* *
30116338 CCGATACAAGTATGTA-AACTA
1 CCGATACAACTATATATAACTA
*
30116359 CCGATACATCTATATATAACTA
1 CCGATACAACTATATATAACTA
30116381 CCGATAC
1 CCGATAC
30116388 TCACAATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (22 bp):
CCGATACAACTATATATAACTA
Found at i:30117934 original size:16 final size:17
Alignment explanation
Indices: 30117915--30117954 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
30117905 TATTTAGCCT
30117915 TAATTAATTTTA-CTTA
1 TAATTAATTTTACCTTA
*
30117931 TAATCAA-TTTACCTTA
1 TAATTAATTTTACCTTA
30117947 TAA-TAATT
1 TAATTAATT
30117955 CATCCACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAATTTTACCTTA
Found at i:30122995 original size:16 final size:17
Alignment explanation
Indices: 30122974--30123007 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
30122964 TAATTACAAG
30122974 CAATTACAT-CCAAATT
1 CAATTACATGCCAAATT
30122990 CAATTACATGCCAAATT
1 CAATTACATGCCAAATT
30123007 C
1 C
30123008 TTGATCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (17 bp):
CAATTACATGCCAAATT
Found at i:30123210 original size:31 final size:30
Alignment explanation
Indices: 30123172--30123269 Score: 85
Period size: 31 Copynumber: 3.3 Consensus size: 30
30123162 TTAATATAAC
30123172 ATTTGGTATCTGAATTTGATATTTTTCCATA
1 ATTTGGTATCTGAATTTGATATTTTTCC-TA
* * **
30123203 ATTTGGTATTTAAACTTT--T-TTTGACCTA
1 ATTTGGTATCTGAA-TTTGATATTTTTCCTA
* * *
30123231 ATTTGGTACCTGAACTTGACACTTTTTCCTA
1 ATTTGGTATCTGAATTTGATA-TTTTTCCTA
30123262 ATTTGGTA
1 ATTTGGTA
30123270 CTTAAACTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
27 2 0.04
28 13 0.25
29 5 0.10
30 1 0.02
31 27 0.53
32 3 0.06
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTTGGTATCTGAATTTGATATTTTTCCTA
Found at i:30123264 original size:59 final size:59
Alignment explanation
Indices: 30123172--30123363 Score: 208
Period size: 62 Copynumber: 3.2 Consensus size: 59
30123162 TTAATATAAC
* * * *
30123172 ATTTGGTATCTGAATTTGATATTTTTCCATAATTTGGTATTTAAACTTTTTTT-G-ACCTA
1 ATTTGGTACCTGAACTTGACATTTTTCC-TAATTTGGTACTTAAACTTTTTTTGGAACC-A
30123231 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGAACCA
1 ATTTGGTACCTGAACTTGACA-TTTTTCCTAATTTGGTACTTAAACTTTTTTTGGAACCA
* * * * * **
30123291 AATTGGTACCTAAAACTTGGCATTTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGATTCA
1 ATTTGGTACCT-GAACTTGACA--TTTTTCCTAATTTGGTACTTAAACTTTTTTTGGAACCA
*
30123353 ATTTAGTACCT
1 ATTTGGTACCT
30123364 AAATTTATTA
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
59 41 0.36
60 19 0.17
61 11 0.10
62 43 0.38
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGACATTTTTCCTAATTTGGTACTTAAACTTTTTTTGGAACCA
Found at i:30123298 original size:60 final size:58
Alignment explanation
Indices: 30123174--30123345 Score: 202
Period size: 59 Copynumber: 2.9 Consensus size: 58
30123164 AATATAACAT
* * * * *
30123174 TTGGTATCTGAATTTGATATTTTTCCATAATTTGGTATTTAAACTTTTTTTGACCTAAT
1 TTGGTACCTGAACTTGACATTTTTCC-TAATTTGGTACTTAAACTTTTTTTGACCTAAA
30123233 TTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGAACC-AAA
1 TTGGTACCTGAACTTGACA-TTTTTCCTAATTTGGTACTTAAACTTTTTTT-G-ACCTAAA
* * *
30123293 TTGGTACCTAAAACTTGGCATTTTTTTCCTAATTTGGTACCTAAACTTTTTTT
1 TTGGTACCT-GAACTTGACA--TTTTTCCTAATTTGGTACTTAAACTTTTTTT
30123346 AGATTCAATT
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
59 39 0.39
60 19 0.19
61 11 0.11
62 30 0.30
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (58 bp):
TTGGTACCTGAACTTGACATTTTTCCTAATTTGGTACTTAAACTTTTTTTGACCTAAA
Found at i:30123644 original size:31 final size:31
Alignment explanation
Indices: 30123590--30123653 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
30123580 AACTTAAAAG
30123590 AAGTGTCAAGTTTAGGTACCAAATTAGGA-AA
1 AAGTGTCAAGTTTAGGTACCAAATT-GGACAA
*
30123621 AAGTGTCAAGTTT-GAGTATCAAATTGGACAA
1 AAGTGTCAAGTTTAG-GTACCAAATTGGACAA
30123652 AA
1 AA
30123654 AAATTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (31 bp):
AAGTGTCAAGTTTAGGTACCAAATTGGACAA
Found at i:30124432 original size:29 final size:29
Alignment explanation
Indices: 30124379--30124434 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
30124369 AGGATCCATT
* *
30124379 TAAAATTTAAAAAGATTTGAGTAAAAATA
1 TAAAATTTAAAAAAATTTGAATAAAAATA
30124408 TAAAATTTAAAAAAAATTT-AATAAAAA
1 TAAAATTT-AAAAAAATTTGAATAAAAA
30124435 CTAAGATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
TAAAATTTAAAAAAATTTGAATAAAAATA
Found at i:30134003 original size:16 final size:16
Alignment explanation
Indices: 30133982--30134014 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30133972 ATAGATAAAG
30133982 TGAGAGAAATTGTTTT
1 TGAGAGAAATTGTTTT
30133998 TGAGAGAAATTGTTTT
1 TGAGAGAAATTGTTTT
30134014 T
1 T
30134015 CATTATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGAGAGAAATTGTTTT
Found at i:30135497 original size:30 final size:29
Alignment explanation
Indices: 30135433--30135497 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
30135423 ATCAATAACT
30135433 CAAAAATATGTTAAAATTTTTAAAAAGGA
1 CAAAAATATGTTAAAATTTTTAAAAAGGA
* * **
30135462 TAAAAATATAGTTAAAATTTTTGAAAATTA
1 CAAAAATAT-GTTAAAATTTTTAAAAAGGA
30135492 CAAAAA
1 CAAAAA
30135498 ATTGAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (29 bp):
CAAAAATATGTTAAAATTTTTAAAAAGGA
Found at i:30135514 original size:18 final size:17
Alignment explanation
Indices: 30135482--30135516 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30135472 GTTAAAATTT
*
30135482 TTGAAAATTACAAAAAA
1 TTGAAAATTAAAAAAAA
30135499 TTGAAAATATAAAAAAAA
1 TTGAAAAT-TAAAAAAAA
30135517 AGTTTGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (17 bp):
TTGAAAATTAAAAAAAA
Found at i:30135645 original size:31 final size:31
Alignment explanation
Indices: 30135587--30135646 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
30135577 ACGTTGATCC
** **
30135587 AATGTTGATCAATGTTGATTGGCTGTTGACT
1 AATGTTGATCAACATTGATTGAATGTTGACT
*
30135618 AATGTTGATCACCATTGATTGAATGTTGA
1 AATGTTGATCAACATTGATTGAATGTTGA
30135647 TAGATCTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (31 bp):
AATGTTGATCAACATTGATTGAATGTTGACT
Found at i:30135685 original size:19 final size:18
Alignment explanation
Indices: 30135661--30135696 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30135651 TCTTTTTTTG
30135661 TATTTATAAAATATTTATA
1 TATTTATAAAAT-TTTATA
*
30135680 TATTTATATAATTTTAT
1 TATTTATAAAATTTTAT
30135697 TTTTTTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTATAAAATTTTATA
Found at i:30135742 original size:27 final size:27
Alignment explanation
Indices: 30135707--30135759 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
30135697 TTTTTTCTAG
*
30135707 TTTTCTAAAATT-TTAACAATACTTTTA
1 TTTTCTAAAATTATCAA-AATACTTTTA
*
30135734 TTTTTTAAAATTATCAAAATACTTTT
1 TTTTCTAAAATTATCAAAATACTTTT
30135760 TTGATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTTCTAAAATTATCAAAATACTTTTA
Found at i:30138887 original size:12 final size:11
Alignment explanation
Indices: 30138869--30138900 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
30138859 TCATAGGCAT
30138869 GAAAAAAAACA
1 GAAAAAAAACA
30138880 GAAAAAAAACA
1 GAAAAAAAACA
30138891 GAAAATAAAA
1 GAAAA-AAAA
30138901 GGGATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.03
Consensus pattern (11 bp):
GAAAAAAAACA
Found at i:30141781 original size:32 final size:32
Alignment explanation
Indices: 30141740--30141802 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
30141730 GGGTCTTCAC
*
30141740 TGGCGGCCCTTCTTTATTCATTAATTAGTATT
1 TGGCGGCCCTTCTTTATTAATTAATTAGTATT
30141772 TGGCGGCCCTTCTTTATTAATTAATTAGTAT
1 TGGCGGCCCTTCTTTATTAATTAATTAGTAT
30141803 ATATTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (32 bp):
TGGCGGCCCTTCTTTATTAATTAATTAGTATT
Found at i:30141944 original size:17 final size:17
Alignment explanation
Indices: 30141924--30141960 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
30141914 ATTATTATTA
*
30141924 TTAATTTTTTATTAAAT
1 TTAACTTTTTATTAAAT
30141941 TTAACTTTTTATTAAAT
1 TTAACTTTTTATTAAAT
30141958 TTA
1 TTA
30141961 TTGCCGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAACTTTTTATTAAAT
Found at i:30142181 original size:16 final size:14
Alignment explanation
Indices: 30142152--30142178 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30142142 TGACGGGAAT
30142152 TATGTGAATTTTTA
1 TATGTGAATTTTTA
30142166 TATGTGAATTTTT
1 TATGTGAATTTTT
30142179 TTAATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
TATGTGAATTTTTA
Found at i:30142547 original size:13 final size:13
Alignment explanation
Indices: 30142529--30142574 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
30142519 TTTAAAATTA
30142529 TTAAAATTATTTT
1 TTAAAATTATTTT
**
30142542 TTAAAATATAAATT
1 TTAAAAT-TATTTT
30142556 TT-AAATTATTTT
1 TTAAAATTATTTT
30142568 TTAAAAT
1 TTAAAAT
30142575 ATAAAAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 6 0.22
13 15 0.56
14 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:30142562 original size:26 final size:28
Alignment explanation
Indices: 30142521--30142626 Score: 135
Period size: 26 Copynumber: 3.7 Consensus size: 28
30142511 CAAATTATTT
30142521 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATT-AAATTATTTTTTAAAATA
30142550 T-AAATT-TTAAATTATTTTTTAAAATA
1 TAAAATTATTAAATTATTTTTTAAAATA
* *
30142576 TAAAAGTATTTAAATTATTTTTTTGAAATAA
1 TAAAATTA-TTAAATTA-TTTTTTAAAAT-A
*
30142607 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATTATTTT
30142627 AATTTCCAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
26 19 0.28
27 6 0.09
28 5 0.07
29 13 0.19
30 17 0.25
31 8 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
TAAAATTATTAAATTATTTTTTAAAATA
Found at i:30148274 original size:18 final size:18
Alignment explanation
Indices: 30148251--30148340 Score: 110
Period size: 18 Copynumber: 4.9 Consensus size: 18
30148241 AGGAATGCAT
*
30148251 TACTGGCTCGTAAGAGCA
1 TACTGGCTCGTTAGAGCA
*
30148269 TACTGGCTCGTTGGAGCA
1 TACTGGCTCGTTAGAGCA
*
30148287 TTACTGGC-CAGTAAGAGCA
1 -TACTGGCTC-GTTAGAGCA
*
30148306 TACTGGCTTGTTAGAGCA
1 TACTGGCTCGTTAGAGCA
*
30148324 TACTTGCTCGTTAGAGC
1 TACTGGCTCGTTAGAGC
30148341 GATATAATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
18 47 0.77
19 14 0.23
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (18 bp):
TACTGGCTCGTTAGAGCA
Found at i:30148301 original size:37 final size:37
Alignment explanation
Indices: 30148247--30148340 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
30148237 TGGAAGGAAT
*
30148247 GCATTACTGGCTCGTAAGAGCATACTGGCTCGTTGGA
1 GCATTACTGGCTCGTAAGAGCATACTGGCTCGTTAGA
*
30148284 GCATTACTGGC-CAGTAAGAGCATACTGGCTTGTTAGA
1 GCATTACTGGCTC-GTAAGAGCATACTGGCTCGTTAGA
* *
30148321 GCA-TACTTGCTCGTTAGAGC
1 GCATTACTGGCTCGTAAGAGC
30148341 GATATAATGT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
36 14 0.27
37 37 0.73
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (37 bp):
GCATTACTGGCTCGTAAGAGCATACTGGCTCGTTAGA
Found at i:30155388 original size:18 final size:18
Alignment explanation
Indices: 30155364--30155438 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
30155354 AGGAATACAT
*
30155364 TACTGGCTTTTAAGAGCA
1 TACTGGCTCTTAAGAGCA
* *
30155382 CACTGGCTCATAAGAGCA
1 TACTGGCTCTTAAGAGCA
* *
30155400 TATTGGCT-TGTTAGAGCA
1 TACTGGCTCT-TAAGAGCA
*
30155418 TTACTGGCTCGTAAGAGCA
1 -TACTGGCTCTTAAGAGCA
30155437 TA
1 TA
30155439 TTGGTTCGTT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
18 30 0.68
19 14 0.32
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (18 bp):
TACTGGCTCTTAAGAGCA
Found at i:30155433 original size:37 final size:36
Alignment explanation
Indices: 30155367--30155454 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 36
30155357 AATACATTAC
30155367 TGGCTT-TTAAGAGCACACTGGCTCATAAGAGCATAT
1 TGGCTTGTT-AGAGCACACTGGCTCATAAGAGCATAT
* *
30155403 TGGCTTGTTAGAGCATTACTGGCTCGTAAGAGCATAT
1 TGGCTTGTTAGAGCA-CACTGGCTCATAAGAGCATAT
30155440 TGG-TTCGTTAGAGCA
1 TGGCTT-GTTAGAGCA
30155455 ATATATTGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
36 14 0.30
37 33 0.70
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (36 bp):
TGGCTTGTTAGAGCACACTGGCTCATAAGAGCATAT
Found at i:30155452 original size:18 final size:18
Alignment explanation
Indices: 30155394--30155454 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
30155384 CTGGCTCATA
30155394 AGAGCATATTGGCTT-GTT
1 AGAGCATATTGG-TTCGTT
* * *
30155412 AGAGCATTACTGGCTCGTA
1 AGAGCA-TATTGGTTCGTT
30155431 AGAGCATATTGGTTCGTT
1 AGAGCATATTGGTTCGTT
30155449 AGAGCA
1 AGAGCA
30155455 ATATATTGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (18 bp):
AGAGCATATTGGTTCGTT
Found at i:30156941 original size:38 final size:35
Alignment explanation
Indices: 30156899--30156981 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 35
30156889 GTCAACAAGA
30156899 AAGTTTTTTCTTGTACACAATACAATTCATTGTTCAAT
1 AAGTTTTTT-TTG-ACACAATA-AATTCATTGTTCAAT
***
30156937 AAGTTTCTCTTTTGAGTTAATAAATTCATTGTTCAAT
1 AAGTTT-T-TTTTGACACAATAAATTCATTGTTCAAT
*
30156974 AACTTTTT
1 AAGTTTTT
30156982 AGATTGTGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
35 1 0.03
36 1 0.03
37 20 0.51
38 11 0.28
39 4 0.10
40 2 0.05
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (35 bp):
AAGTTTTTTTTGACACAATAAATTCATTGTTCAAT
Found at i:30163581 original size:22 final size:22
Alignment explanation
Indices: 30163555--30163601 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
30163545 CTTACATTGA
30163555 GTTTTTTTTAATCATTTTGCA-
1 GTTTTTTTTAATCATTTTGCAT
30163576 GTTTTTTTTAATCATTTTGCAT
1 GTTTTTTTTAATCATTTTGCAT
30163598 GTTT
1 GTTT
30163602 ATTTCATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (22 bp):
GTTTTTTTTAATCATTTTGCAT
Found at i:30164035 original size:16 final size:16
Alignment explanation
Indices: 30164014--30164044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30164004 CATGTTAGAG
30164014 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
30164030 CATATATATTTGAAA
1 CATATAAATTTGAAA
30164045 AGTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:30164147 original size:9 final size:9
Alignment explanation
Indices: 30164123--30164240 Score: 51
Period size: 10 Copynumber: 12.2 Consensus size: 9
30164113 AAAATTATTA
*
30164123 TTTTAGAAAA
1 TTTTA-AAAT
30164133 TTTTAAAAT
1 TTTTAAAAT
**
30164142 TTTTAACTT
1 TTTTAAAAT
*
30164151 TCTTTATATAT
1 T-TTTA-AAAT
*
30164162 TCTTTAGAATTT
1 T-TTTA-AA-AT
30164174 TTTTTAAAAT
1 TTT-TAAAAT
*
30164184 TTTTATAATT
1 TTTTA-AAAT
*
30164194 TTTTAAAAA
1 TTTTAAAAT
* *
30164203 ATAT-AAAT
1 TTTTAAAAT
30164211 TTTT-AAAT
1 TTTTAAAAT
30164219 TTTTATAAAT
1 TTTTA-AAAT
30164229 ATTTTAAAAT
1 -TTTTAAAAT
30164239 TT
1 TT
30164241 ATTTTTTGTA
Statistics
Matches: 83, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
8 13 0.16
9 19 0.23
10 29 0.35
11 18 0.22
12 4 0.05
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:30164203 original size:21 final size:21
Alignment explanation
Indices: 30164164--30164204 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30164154 TTATATATTC
**
30164164 TTTAGAATTTTTTTTAAAATT
1 TTTAGAATTTTTTAAAAAATT
*
30164185 TTTATAATTTTTTAAAAAAT
1 TTTAGAATTTTTTAAAAAAT
30164205 ATAAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTAGAATTTTTTAAAAAATT
Found at i:30164241 original size:18 final size:17
Alignment explanation
Indices: 30164174--30164242 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 17
30164164 TTTAGAATTT
*
30164174 TTTTTAAAATTTTTATAAT
1 TTTTTAAAA--TTTATAAA
**
30164193 TTTTTAAAAAATATAAA
1 TTTTTAAAATTTATAAA
*
30164210 TTTTTAAATTTTTATAAA
1 TTTTTAAA-ATTTATAAA
30164228 TATTTTAAAATTTAT
1 T-TTTTAAAATTTAT
30164243 TTTTTGTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
17 13 0.32
18 12 0.29
19 16 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTAAAATTTATAAA
Found at i:30168082 original size:29 final size:29
Alignment explanation
Indices: 30168040--30168333 Score: 164
Period size: 29 Copynumber: 10.2 Consensus size: 29
30168030 GAGGCCCTCG
*
30168040 AACTTATCC-AAAATCATATTTTACCCCTA
1 AACTT-TCCAAAAATCACATTTTACCCCTA
* *
30168069 AACTTTCCAAAAATCACATTTTGACCCTTG
1 AACTTTCCAAAAATCACATTTT-ACCCCTA
*
30168099 AACTTTCC-AAAATTACATTTTTACCCCTA
1 AACTTTCCAAAAATCACA-TTTTACCCCTA
* ** *
30168128 AA-TTTCTCAAAAATTACATTTTTGCCCTCG
1 AACTTTC-CAAAAATCACATTTTACCCCT-A
* * *
30168158 AAC-TTCC-AAAATTACATTTTACCTCTG
1 AACTTTCCAAAAATCACATTTTACCCCTA
* * *
30168185 AAC-TTCCAAAAATTATATTTTTGCTCCC-A
1 AACTTTCCAAAAATCACA-TTTTAC-CCCTA
* ** *
30168214 AACTTT-CAAAAATTACATTTTGACCTTTG
1 AACTTTCCAAAAATCACATTTT-ACCCCTA
* * *
30168243 AAC-TTCTAAAAAGCACGTTTTGACCCCTA
1 AACTTTCCAAAAATCACATTTT-ACCCCTA
* * *
30168272 AACTTT-TAAAAATTACATTTTGA-CCTTA
1 AACTTTCCAAAAATCACATTTT-ACCCCTA
* *
30168300 AA-TTTTCAAAAATTACATTTTAGCCCC-A
1 AACTTTCCAAAAATCACATTTTA-CCCCTA
30168328 AACTTT
1 AACTTT
30168334 TGCCAAAATT
Statistics
Matches: 212, Mismatches: 34, Indels: 38
0.75 0.12 0.13
Matches are distributed among these distances:
27 12 0.06
28 61 0.29
29 102 0.48
30 37 0.17
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AACTTTCCAAAAATCACATTTTACCCCTA
Found at i:30168342 original size:58 final size:56
Alignment explanation
Indices: 30168099--30168343 Score: 219
Period size: 58 Copynumber: 4.2 Consensus size: 56
30168089 TTGACCCTTG
* * *
30168099 AACTTTCCAAAATTACATTTTTACCCCTAAATTTCTCAAAAATTACATTTTTGCCCTCG
1 AACTTTCCAAAATTACATTTTGA-CCTTAAATTT-TCAAAAATTACATTTTTGCCC-CA
* * * *
30168158 AAC-TTCCAAAATTACATTTT-ACCTCTGAACTTCCAAAAATTATATTTTTGCTCCCA
1 AACTTTCCAAAATTACATTTTGACCT-TAAATTTTCAAAAATTACATTTTTGC-CCCA
* * * ** *
30168214 AACTTTCAAAAATTACATTTTGACCTTTGAA-CTTCTAAAAAGCAC-GTTTTGACCCCTA
1 AACTTTCCAAAATTACATTTTGACC-TTAAATTTTC-AAAAATTACATTTTTG-CCCC-A
** *
30168272 AACTTTTAAAAATTACATTTTGACCTTAAATTTTCAAAAATTACATTTTAGCCCCA
1 AACTTTCCAAAATTACATTTTGACCTTAAATTTTCAAAAATTACATTTTTGCCCCA
30168328 AACTTTTGCCAAAATT
1 AAC-TTT-CCAAAATT
30168344 GTATTTTGCC
Statistics
Matches: 152, Mismatches: 22, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
56 27 0.18
57 52 0.34
58 69 0.45
59 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (56 bp):
AACTTTCCAAAATTACATTTTGACCTTAAATTTTCAAAAATTACATTTTTGCCCCA
Found at i:30170740 original size:192 final size:192
Alignment explanation
Indices: 30170413--30170797 Score: 752
Period size: 192 Copynumber: 2.0 Consensus size: 192
30170403 TGTTATTCTA
30170413 CCAGAAAGTAGTTGTAATTTATTTACTTAGAATAAATTTTATTTTATGGGAATTATGATCTTTAT
1 CCAGAAAGTAGTTGTAATTTATTTACTTAGAATAAATTTTATTTTATGGGAATTATGATCTTTAT
30170478 CGATTTTTTATAGAAATAATTTATTTTCCTACTGAAAGTAAATAAATCGTTTTTCTTTGTGTGTT
66 CGATTTTTTATAGAAATAATTTATTTTCCTACTGAAAGTAAATAAATCGTTTTTCTTTGTGTGTT
30170543 TTGGTTCATATGCTTGAACTCACACTCGACGTGATTTGTGGAACAAGAATAACGAAAAAGAT
131 TTGGTTCATATGCTTGAACTCACACTCGACGTGATTTGTGGAACAAGAATAACGAAAAAGAT
30170605 CCAGAAAGTAGTTGTAATTTATTTACTTAGAATAAATTTTATTTTATGGGAATTATGATCTTTAT
1 CCAGAAAGTAGTTGTAATTTATTTACTTAGAATAAATTTTATTTTATGGGAATTATGATCTTTAT
* *
30170670 CGATTTTTTATAGAGATAATTTATTTTCTTACTGAAAGTAAATAAATCGTTTTTCTTTGTGTGTT
66 CGATTTTTTATAGAAATAATTTATTTTCCTACTGAAAGTAAATAAATCGTTTTTCTTTGTGTGTT
30170735 TTGGTTCATATGCTTGAACTCACACTCGACGTGATTTGTGGAACAAGAATAACGAAAAAGAT
131 TTGGTTCATATGCTTGAACTCACACTCGACGTGATTTGTGGAACAAGAATAACGAAAAAGAT
30170797 C
1 C
30170798 GTTTGGTTGA
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 191 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (192 bp):
CCAGAAAGTAGTTGTAATTTATTTACTTAGAATAAATTTTATTTTATGGGAATTATGATCTTTAT
CGATTTTTTATAGAAATAATTTATTTTCCTACTGAAAGTAAATAAATCGTTTTTCTTTGTGTGTT
TTGGTTCATATGCTTGAACTCACACTCGACGTGATTTGTGGAACAAGAATAACGAAAAAGAT
Found at i:30171303 original size:79 final size:80
Alignment explanation
Indices: 30171215--30171386 Score: 231
Period size: 80 Copynumber: 2.2 Consensus size: 80
30171205 AAAATTTTTA
** * *
30171215 CCAACTTTTAAGAGACTCC-AA-CTTTTTTTTTAGTTTTTAAGAGCTTAAATATTTGTACGAGAC
1 CCAACTTTTAAGAGA-TCCTAATCTTTTTTTTTAACTTTTAAGAACCTAAATATTTGTACGAGAC
*
30171278 TCAAAAATATTTTTCT
65 TCAAAAACATTTTTCT
* *
30171294 CCAACTTTTAAGAGATCCTAATTTTTTTTTTTAACTTTTAAGAACCTAAATTTTTGTACGAGACT
1 CCAACTTTTAAGAGATCCTAATCTTTTTTTTTAACTTTTAAGAACCTAAATATTTGTACGAGACT
*
30171359 TAAAAACATTTTTCT
66 CAAAAACATTTTTCT
* *
30171374 CAAAGTTTTAAGA
1 CCAACTTTTAAGA
30171387 AACCTAAAGC
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
78 3 0.04
79 17 0.21
80 61 0.75
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (80 bp):
CCAACTTTTAAGAGATCCTAATCTTTTTTTTTAACTTTTAAGAACCTAAATATTTGTACGAGACT
CAAAAACATTTTTCT
Found at i:30171409 original size:5 final size:5
Alignment explanation
Indices: 30171399--30171424 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30171389 CCTAAAGCTC
30171399 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
30171425 TGTAGGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:30176895 original size:24 final size:24
Alignment explanation
Indices: 30176867--30176929 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
30176857 AGAAATAATC
30176867 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
30176891 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
30176915 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
30176930 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:30178604 original size:26 final size:28
Alignment explanation
Indices: 30178575--30178628 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
30178565 TAAACTTTGA
*
30178575 TTTAA-TG-TGCAATTGTATACATGAAC
1 TTTAATTGATGCAATTATATACATGAAC
30178601 TTTAATTTGATGCAATTATATACATGAA
1 TTTAA-TTGATGCAATTATATACATGAA
30178629 GCTCCAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
28 2 0.08
29 17 0.71
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (28 bp):
TTTAATTGATGCAATTATATACATGAAC
Found at i:30178615 original size:29 final size:29
Alignment explanation
Indices: 30178559--30178669 Score: 96
Period size: 31 Copynumber: 3.7 Consensus size: 29
30178549 ATCTCAAAAT
* * *
30178559 TATACATAAACTTTGATTTAATGTGCAATTG
1 TATACATGAACTTTAATTTGA--TGCAATTG
*
30178590 TATACATGAACTTTAATTTGATGCAATTA
1 TATACATGAACTTTAATTTGATGCAATTG
** * *
30178619 TATACATGAAGCTCCAATTGTGATTCAAATG
1 TATACATGAA-CTTTAATT-TGATGCAATTG
*
30178650 TATACTTGAAACTTTAATTT
1 TATACATG-AACTTTAATTT
30178670 CGATTTAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
29 17 0.26
30 7 0.11
31 39 0.60
32 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (29 bp):
TATACATGAACTTTAATTTGATGCAATTG
Found at i:30180516 original size:16 final size:18
Alignment explanation
Indices: 30180477--30180510 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30180467 TAAGTTTATA
30180477 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
30180494 ATATTTATATATTATGT
1 ATATTTATATATTATGT
30180511 AATTTAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:30181382 original size:96 final size:96
Alignment explanation
Indices: 30181207--30181395 Score: 247
Period size: 96 Copynumber: 2.0 Consensus size: 96
30181197 AAATTTTAGA
* * ** * ** *
30181207 AAAGGATATTTGATTATCTCGATTTGACGAAAGGTTGCACCTAGTAAGTTAAGGTGCAAATTTTC
1 AAAGGATATTCGATTATCTCGATTTGAAGAAAACTTGCACCTAGTAAATTAAGGCACAAAATTTC
30181272 AAAACCGAAGATAAAGAAACATTGCCTCGATT
66 AAAACCGAAGATAAA-AAACATTGCCTCGATT
*
30181304 AAAGG-TATTCGATTATTTCGATTTGAAGAAAACTTGCACCTAGTAAATTAAGGCACAAAATTTC
1 AAAGGATATTCGATTATCTCGATTTGAAGAAAACTTGCACCTAGTAAATTAAGGCACAAAATTTC
* *
30181368 GAAACTCGAA-ATAAAAAATATTGCCTCG
66 AAAAC-CGAAGATAAAAAACATTGCCTCG
30181396 GTTTTAAAGT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 12 0.15
96 59 0.74
97 9 0.11
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (96 bp):
AAAGGATATTCGATTATCTCGATTTGAAGAAAACTTGCACCTAGTAAATTAAGGCACAAAATTTC
AAAACCGAAGATAAAAAACATTGCCTCGATT
Found at i:30181830 original size:59 final size:60
Alignment explanation
Indices: 30181748--30181934 Score: 224
Period size: 59 Copynumber: 3.2 Consensus size: 60
30181738 GATAAAAAAG
* * * * *
30181748 GAATTCTTGGACGTCCGGGGGT-AAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATA
*
30181807 GAATTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTTTGGAAA-TTTTAGGGGT-AAAAATG
1 GAATTTTTGGAAGTTCGAGGGTAAAAATGGTAATTTTT-GAAAGTTTT-GGGGTCAAAAATA
* **
30181866 GAATATTTGGAAGTTTAAGGGTAAAAAT-GTAATTTTTGAAAGTTTTGGGGTC-AAAATA
1 GAATTTTTGGAAGTTCGAGGGTAAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATA
*
30181924 TAATTTTTGGA
1 GAATTTTTGGA
30181935 CAATTTAGGG
Statistics
Matches: 110, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
58 24 0.22
59 71 0.65
60 15 0.14
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (60 bp):
GAATTTTTGGAAGTTCGAGGGTAAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATA
Found at i:30181832 original size:29 final size:29
Alignment explanation
Indices: 30181778--30181934 Score: 149
Period size: 29 Copynumber: 5.3 Consensus size: 29
30181768 GTAAAATGGT
*
30181778 AATTTTTGAAAGTTTTGA-GGTCAAAAATAG
1 AATTTTTGGAAG-TTTGAGGGT-AAAAATAG
* *
30181808 AATTTTTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTTGAGGGTAAAAATAG
* * *
30181837 AATTTTTGGAAATTTTAGGGGTAAAAATGG
1 AATTTTTGGAAGTTTGA-GGGTAAAAATAG
* *
30181867 AATATTTGGAAGTTTAAGGGTAAAAAT-G
1 AATTTTTGGAAGTTTGAGGGTAAAAATAG
* * *
30181895 TAATTTTTGAAAGTTTTG-GGGTCAAAATAT
1 -AATTTTTGGAAG-TTTGAGGGTAAAAATAG
30181925 AATTTTTGGA
1 AATTTTTGGA
30181935 CAATTTAGGG
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
28 1 0.01
29 63 0.59
30 43 0.40
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
AATTTTTGGAAGTTTGAGGGTAAAAATAG
Found at i:30184492 original size:201 final size:201
Alignment explanation
Indices: 30184115--30184701 Score: 885
Period size: 201 Copynumber: 2.9 Consensus size: 201
30184105 ACTTGGCCTT
* * * * **
30184115 CTTCTCAGTATCTCATCAGGAGGATGACCGCGTCTCTTGTTTTGATTCACTTCTCTATGT-T-TC
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCACTTCTC-A-GTATCTC
* * * * * * *
30184178 AACAGGAAAACGGATTTGGTTCACTTCTCCGTATCTCATCAGGATGCTAATCA-TTTATTACTTC
64 ATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * * *
30184242 GACCTGCTTCTCAGTATCTCATTAGGAAGCTAGGGTTCGAAGATTTGCTCACTTTGAGCGTCGAG
129 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCCTCGAG
30184307 TTGGCATA
194 TTGGCATA
* *
30184315 CTTCTCTGTATCTCATCAGGAAGATCACCGCCTCACTTGTTTCAATTCGCTTCTCAGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCACTTCTCAGTATCTCAT
30184380 CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* *
30184445 CCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCCTCGAGTT
30184510 GGCATA
196 GGCATA
*
30184516 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTATTTCAATTCACTTCTCAGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCACTTCTCAGTATCTCAT
*
30184581 CAGGAAGACGAATTTGG-TCAACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
66 CAGGAAGACGAATTTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
** *
30184645 ATTTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATTGAG
130 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG
30184702 TCTAGTTTCA
Statistics
Matches: 353, Mismatches: 30, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
198 2 0.01
199 2 0.01
200 98 0.28
201 251 0.71
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCACTTCTCAGTATCTCAT
CAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCCTCGAGTT
GGCATA
Found at i:30188757 original size:457 final size:457
Alignment explanation
Indices: 30187895--30189721 Score: 3170
Period size: 457 Copynumber: 4.0 Consensus size: 457
30187885 CGGATTAATC
* *
30187895 GTGTTGGCCTAGTACGCATCTCATGAAATTTTCAAAGACTATCAAGTACAGAATCAATGGCTTAT
1 GTGTTGGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAGGATCAATGGCTTAT
* *
30187960 TAGGAATTGGAGGTACCAAGATGGTAGCTTTGGATAAATAATCTTTGACCTTATTAAAGGTTTCC
66 TAGGAATTGGAGGTACCAAGATGGGAGCTTTGGATAAATAATCTTTGACCTTGTTAAAGGTTTCC
30188025 TGACATTCATCATCCCATACACCCGAGTTACGCTTTTTAAGCAGGCGGAAGATAGGATCGCATTT
131 TGACATTCATCATCCCATACACCCGAGTTACGCTTTTTAAGCAGGCGGAAGATAGGATCGCATTT
* * * *
30188090 CTCGGTTAACTTTAAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGAACTTCTT
196 CTCAGTTAACTGTGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGGACTTCTT
* *
30188155 TTTGCTTGCTTGGTAGTGGTAGCTCCTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
261 TTTGCGTGCTTGGTGGTGGTAGCTCCTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
* * *
30188220 CATTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGACGCCAAAAGTGCATTTTATCGGGTT
326 CTTTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGGCGCCAAAAGTGCATTTTGTCGGGTT
** *
30188285 TAGCACTAATTGATATTTCCTTAATCTTCCAAATAGCTTTCTCAGGATTCTTACATGCTCTTCCT
391 TAGCTTTAGTTGATATTTCCTTAATCTTCCAAATAGCTTTCTCAGGATTCTTACATGCTCTTCCT
30188350 CT
456 CT
*
30188352 GTGTTAGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAGGATCAATGGCTTAT
1 GTGTTGGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAGGATCAATGGCTTAT
30188417 TAGGAATTGGAGGTACCAAGATGGGAGCTTTGGATAAATAATCTTTGACCTTGTTAAAGGTTTCC
66 TAGGAATTGGAGGTACCAAGATGGGAGCTTTGGATAAATAATCTTTGACCTTGTTAAAGGTTTCC
* * * * *
30188482 TAACATTTATCATCTCATACACCTGGGTTACGCTTTTTAAGCAGGCGGAAGATAGGATCGCATTT
131 TGACATTCATCATCCCATACACCCGAGTTACGCTTTTTAAGCAGGCGGAAGATAGGATCGCATTT
30188547 CTCAGTTAACTGTGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGGACTTCTT
196 CTCAGTTAACTGTGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGGACTTCTT
30188612 TTTGCGTGCTTGGTGGTGGTAGCTCCTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
261 TTTGCGTGCTTGGTGGTGGTAGCTCCTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
*
30188677 CTTTTGTTGACCACAAAGCCTAATAGTTTTCCTGACATGGCGCCAAAAGTGCATTTTGTCGGGTT
326 CTTTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGGCGCCAAAAGTGCATTTTGTCGGGTT
**
30188742 TAGCTTTAGTTGATATTTCCTTAATCTTCCAAATAGCTTTCTTGGGATTCTTACATGCTCTTCCT
391 TAGCTTTAGTTGATATTTCCTTAATCTTCCAAATAGCTTTCTCAGGATTCTTACATGCTCTTCCT
30188807 CCT
456 -CT
30188810 -TGTTGGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAGGATCAATGGCTTAT
1 GTGTTGGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAGGATCAATGGCTTAT
* *
30188874 TAGGAATTGAAGGTACCAAGATGGGAGCTTTGGATAAATAATCTTTCACCTTGTTAAAGGTTTCC
66 TAGGAATTGGAGGTACCAAGATGGGAGCTTTGGATAAATAATCTTTGACCTTGTTAAAGGTTTCC
*
30188939 TGACATTCATCATCCCATACACCCGAGTTACGCTTTTTAAGCAGGCGAAAGATAGGATCGCATTT
131 TGACATTCATCATCCCATACACCCGAGTTACGCTTTTTAAGCAGGCGGAAGATAGGATCGCATTT
* *
30189004 CTCGGTTAACTGAGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGGACTTCTT
196 CTCAGTTAACTGTGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGGACTTCTT
* *
30189069 TTTGCGTGCTTGGTGGTAGTAGCTCTTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
261 TTTGCGTGCTTGGTGGTGGTAGCTCCTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
* *
30189134 CTTTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGGTGCCAAAAGTGCATTTTGTTGGGTT
326 CTTTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGGCGCCAAAAGTGCATTTTGTCGGGTT
30189199 TAGCTTTAGTTGATATTTCCTTAATCTTCCAAATAGCTTTCTCAGGATTCTTACATGCTCTTCCT
391 TAGCTTTAGTTGATATTTCCTTAATCTTCCAAATAGCTTTCTCAGGATTCTTACATGCTCTTCCT
*
30189264 CC
456 CT
* *
30189266 ATGTTGGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAAGATCAATGGCTTAT
1 GTGTTGGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAGGATCAATGGCTTAT
*
30189331 TAGGAATTGGAGGTACCAAGATGAGAGCTTTGGATAAATAATCTTTGACCTTGTTAAAGGTTTCC
66 TAGGAATTGGAGGTACCAAGATGGGAGCTTTGGATAAATAATCTTTGACCTTGTTAAAGGTTTCC
* * * *
30189396 TGACATTCATCATCTCATACACCCGGGTTGCGCTTTTTAAGCAGGCGGAAGATAGGATCACATTT
131 TGACATTCATCATCCCATACACCCGAGTTACGCTTTTTAAGCAGGCGGAAGATAGGATCGCATTT
* * *
30189461 CTCAATTAACTATGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCAGACTTCTT
196 CTCAGTTAACTGTGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGGACTTCTT
* *
30189526 TTTGCGTGCTTAGTGGTGGTAGCTCCTGTATGGATTTGACTTTATCCGGGTCAATTTCAATTCCT
261 TTTGCGTGCTTGGTGGTGGTAGCTCCTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
30189591 CTTTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGGCGCCAAAAGTGCATTTTGTCGGGTT
326 CTTTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGGCGCCAAAAGTGCATTTTGTCGGGTT
** ** *
30189656 TAGCTTTAGTTGATATTAACTTAATCTTCCAAATAATTTTCTCAGGATTCTTACATGCCCTTCCT
391 TAGCTTTAGTTGATATTTCCTTAATCTTCCAAATAGCTTTCTCAGGATTCTTACATGCTCTTCCT
30189721 C
456 C
30189722 CATCTGGGAA
Statistics
Matches: 1299, Mismatches: 69, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
456 1 0.00
457 1296 1.00
458 2 0.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (457 bp):
GTGTTGGCCTAGTACGCATCCCATGAAATTTTCAAAGACTATCAAGTACAGGATCAATGGCTTAT
TAGGAATTGGAGGTACCAAGATGGGAGCTTTGGATAAATAATCTTTGACCTTGTTAAAGGTTTCC
TGACATTCATCATCCCATACACCCGAGTTACGCTTTTTAAGCAGGCGGAAGATAGGATCGCATTT
CTCAGTTAACTGTGAAATGAACCGAGCAATGTAATTTAGTCTTCCTAAAAACCCTCGGACTTCTT
TTTGCGTGCTTGGTGGTGGTAGCTCCTGTATGGCTTTGACTTTATCCGGGTCAATTTCAATTCCT
CTTTTGTTGACCACAAAGCCTAACAGTTTTCCTGACATGGCGCCAAAAGTGCATTTTGTCGGGTT
TAGCTTTAGTTGATATTTCCTTAATCTTCCAAATAGCTTTCTCAGGATTCTTACATGCTCTTCCT
CT
Found at i:30198074 original size:29 final size:28
Alignment explanation
Indices: 30198024--30198084 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
30198014 AAAATGAGAC
*
30198024 TTTTGGATACCCGGGGGTAAAGTAGTAA
1 TTTTGGATACCCGGGGGCAAAGTAGTAA
* * *
30198052 TTTTGGATTCTCGAGGGGCAAAGTGGTAA
1 TTTTGGATACCCG-GGGGCAAAGTAGTAA
30198081 TTTT
1 TTTT
30198085 AGGAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.25, C:0.10, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTTGGATACCCGGGGGCAAAGTAGTAA
Found at i:30198247 original size:59 final size:59
Alignment explanation
Indices: 30198183--30198823 Score: 321
Period size: 58 Copynumber: 10.9 Consensus size: 59
30198173 GGACATTCGG
*
30198183 GGGTAAAATGGTAATTTTTAAAAGTTTCGAGGTCAAAAATAGAATTTTTGGAAGTTTAA
1 GGGTAAAATGGTAATTTTTAAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAA
* * * * * **
30198242 GGGTAAAATGG-AATTTTTGGAAATTTTAGGGGT-AAAAATGGAATATTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTT-AAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAA
* * * *
30198300 GGGTAAAAAT-ATAATTTTTGAAAA-TTTCGAGGTTAAAAATGGAATTTTTAGAAGTTTGA
1 GGGT-AAAATGGTAATTTTT-AAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAA
* * * *
30198359 GGGTAAAAATGG-AATTTTTGAAAGTTTTGGGGTCAAAATAT--AATTTTTGGACAATTATGCAA
1 GGGT-AAAATGGTAATTTTTAAAAGTTTCGAGGTCAAAA-ATGGAATTTTTGGA-AGTT-T--AA
* * ** * ** * * *
30198421 TCGGAATTGAAAATGAG-ACTTTTGGATA-CCT-GAGGGC-AAAATGGTAA-TTTTGG-ACTCTG
1 --GG--GT-AAAATG-GTAATTTTTAAAAGTTTCGAGGTCAAAAATGG-AATTTTTGGAAGT-TT
30198480 AA
58 AA
* * * * * ** * * *
30198482 GGGGTAAAATGGTAATTTTGGAAAAATTT--AGGGCTAAAAT-G-ATATTTCAAACATATAG
1 -GGGTAAAATGGTAATTTT-TAAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAA-GTTTAA
* ** * * *
30198540 GGGTAAAACGGTAATTTTTAGAAA-AATCG-GGATCAAAAATGGAATTTTTGGACGCTTGA
1 GGGTAAAATGGTAATTTTTA-AAAGTTTCGAGG-TCAAAAATGGAATTTTTGGAAGTTTAA
* * * **
30198599 GGGTAAAATGGTAATTTTCAAAAGTTTCGGGGTCAAAAATGAAATTTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTAAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAA
** * * *
30198658 GGGTAAAATGG-AATTTTTGGAAGTTT-AAGGGT-AAAAATGGAATTTTTGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTAAAAGTTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTTAA
* * * * *
30198715 GGGTAAAAAT-GTAATTTTGAGAAGTCTT-GAGGT-TAAAATGGAATTTTTAGAAGTTTGA
1 GGGT-AAAATGGTAATTTTTAAAAGT-TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAA
*
30198773 GGGTAAAAAT-GTAATTTTTAAAAGTTTCGAGGTTAAAATAT--AATTTTTGGA
1 GGGT-AAAATGGTAATTTTTAAAAGTTTCGAGGTCAAAA-ATGGAATTTTTGGA
30198824 TAATTTAGGG
Statistics
Matches: 449, Mismatches: 91, Indels: 85
0.72 0.15 0.14
Matches are distributed among these distances:
56 4 0.01
57 65 0.14
58 163 0.36
59 160 0.36
60 15 0.03
61 2 0.00
62 1 0.00
63 4 0.01
64 6 0.01
65 10 0.02
66 10 0.02
67 9 0.02
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTAAAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAA
Found at i:30198269 original size:29 final size:30
Alignment explanation
Indices: 30198157--30198829 Score: 195
Period size: 29 Copynumber: 22.8 Consensus size: 30
30198147 AAAATCAGGA
* * * *
30198157 TAAAAAAGGAATTTTTGGACA-TTCGGGGG
1 TAAAAATGGAATTTTTGGAAATTTTGAGGG
* *
30198186 T-AAAATGGTAATTTTT-AAAAGTTTCGA-GG
1 TAAAAATGG-AATTTTTGGAAA-TTTTGAGGG
* * *
30198215 TCAAAAATAGAATTTTTGG-AAGTTTAAGGG
1 T-AAAAATGGAATTTTTGGAAATTTTGAGGG
30198245 T-AAAATGGAATTTTTGGAAATTTT-AGGGG
1 TAAAAATGGAATTTTTGGAAATTTTGA-GGG
* * *
30198274 TAAAAATGGAATATTTGG-AAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAATTTTGAGGG
** * * *
30198303 TAAAAATATAATTTTTGAAAATTTCGAGGT
1 TAAAAATGGAATTTTTGGAAATTTTGAGGG
* *
30198333 TAAAAATGGAATTTTTAG-AAGTTTGAGGG
1 TAAAAATGGAATTTTTGGAAATTTTGAGGG
30198362 TAAAAATGGAATTTTT-GAAAGTTTTG-GGG
1 TAAAAATGGAATTTTTGGAAA-TTTTGAGGG
* ** * *
30198391 TCAAAATATAATTTTTGGACAATTATGCAATCGGAAT
1 TAAAAATGGAATTTTTGGA-AATTTTG--A--GG--G
* * * **
30198428 TGAAAAT-GAGACTTTTGGATA-CCTGAGGG
1 TAAAAATGGA-ATTTTTGGAAATTTTGAGGG
* * *
30198457 -CAAAATGGTAA-TTTTGG--ACTCTGAAGGGG
1 TAAAAATGG-AATTTTTGGAAATTTTG-A-GGG
*
30198486 T-AAAATGGTAA-TTTTGGAAAAATTT-AGGG
1 TAAAAATGG-AATTTTTGG-AAATTTTGAGGG
* ** * *
30198515 CT-AAAAT-G-ATATTTCAAACATATAG-GGG
1 -TAAAAATGGAATTTTTGGAA-ATTTTGAGGG
* * ** * *
30198543 T-AAAACGGTAATTTTTAGAAAAATCG-GGA
1 TAAAAATGG-AATTTTTGGAAATTTTGAGGG
***
30198572 TCAAAAATGGAATTTTTGG-ACGCTTGAGGG
1 T-AAAAATGGAATTTTTGGAAATTTTGAGGG
** *
30198602 T-AAAATGGTAA-TTTTCAAAAGTTTCG-GGG
1 TAAAAATGG-AATTTTTGGAAA-TTTTGAGGG
* * *
30198631 TCAAAAATGAAATTTTTGG-AAGTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAATTTTGAGGG
* *
30198661 T-AAAATGGAATTTTTGG-AAGTTTAAGGG
1 TAAAAATGGAATTTTTGGAAATTTTGAGGG
*
30198689 TAAAAATGGAATTTTT-GAAAGTTT-AGGGG
1 TAAAAATGGAATTTTTGGAAATTTTGA-GGG
* * *
30198718 TAAAAATGTAA-TTTTGAGAAGTCTTGA-GG
1 TAAAAATGGAATTTTTG-GAAATTTTGAGGG
* * *
30198747 TTAAAATGGAATTTTTAG-AAGTTTGAGGG
1 TAAAAATGGAATTTTTGGAAATTTTGAGGG
* * * *
30198776 TAAAAATGTAATTTTT-AAAAGTTTCGAGGT
1 TAAAAATGGAATTTTTGGAAA-TTTTGAGGG
30198806 TAAAATAT--AATTTTTGGATAATTT
1 TAAAA-ATGGAATTTTTGGA-AATTT
30198830 AGGGACCTTT
Statistics
Matches: 486, Mismatches: 95, Indels: 125
0.69 0.13 0.18
Matches are distributed among these distances:
26 1 0.00
27 11 0.02
28 93 0.19
29 201 0.41
30 125 0.26
31 31 0.06
32 3 0.01
33 1 0.00
35 4 0.01
36 2 0.00
37 14 0.03
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (30 bp):
TAAAAATGGAATTTTTGGAAATTTTGAGGG
Found at i:30198291 original size:117 final size:118
Alignment explanation
Indices: 30198157--30198411 Score: 333
Period size: 117 Copynumber: 2.2 Consensus size: 118
30198147 AAAATCAGGA
* * *
30198157 TAAAAAAGGAATTTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTT-AAAAGTTTCGAGGTCAA
1 TAAAAATGGAATTTTTGGACAGTTCGAGGGTAAAAAT-ATAATTTTTGAAAA-TTTCGAGGTCAA
*
30198219 AAATAGAATTTTTGGAAGTTTAAGGGT-AAAATGGAATTTTTGGAAA-TTTTAGGGG
64 AAATAGAATTTTTAGAAGTTTAAGGGTAAAAATGGAATTTTT-GAAAGTTTT-GGGG
* *
30198274 TAAAAATGGAATATTTGGA-AGTTCGAGGGTAAAAATATAATTTTTGAAAATTTCGAGGTTAAAA
1 TAAAAATGGAATTTTTGGACAGTTCGAGGGTAAAAATATAATTTTTGAAAATTTCGAGGTCAAAA
* *
30198338 ATGGAATTTTTAGAAGTTTGAGGGTAAAAATGGAATTTTTGAAAGTTTTGGGG
66 ATAGAATTTTTAGAAGTTTAAGGGTAAAAATGGAATTTTTGAAAGTTTTGGGG
* **
30198391 TCAAAATATAATTTTTGGACA
1 TAAAAATGGAATTTTTGGACA
30198412 ATTATGCAAT
Statistics
Matches: 120, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
116 1 0.01
117 91 0.76
118 28 0.23
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (118 bp):
TAAAAATGGAATTTTTGGACAGTTCGAGGGTAAAAATATAATTTTTGAAAATTTCGAGGTCAAAA
ATAGAATTTTTAGAAGTTTAAGGGTAAAAATGGAATTTTTGAAAGTTTTGGGG
Found at i:30198689 original size:87 final size:88
Alignment explanation
Indices: 30198575--30198823 Score: 321
Period size: 87 Copynumber: 2.9 Consensus size: 88
30198565 ATCGGGATCA
* * *
30198575 AAAATGGAATTTTTGGACGCTTGAGGGT-AAAATGGTAATTTTCAAAAGTTTCGGGGTCAAAAAT
1 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGTAATTTTTAAAAGTTTCGGGGT-AAAAAT
*
30198639 GAAATTTTTGGAAGT-TTGGGGGT
65 GAAATTTTTGGAAGTCTTGAGGGT
* * *
30198662 AAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGG-AATTTTTGAAAGTTTAGGGGTAAAAATG
1 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGTAATTTTTAAAAGTTTCGGGGTAAAAATG
* *
30198726 TAA-TTTTGAGAAGTCTTGAGGTT
66 AAATTTTTG-GAAGTCTTGAGGGT
* * *
30198749 AAAATGGAATTTTTAGAAGTTTGAGGGTAAAAAT-GTAATTTTTAAAAGTTTCGAGGTTAAAAT-
1 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGTAATTTTTAAAAGTTTCGGGGTAAAAATG
30198812 ATAATTTTTGGA
66 A-AATTTTTGGA
30198824 TAATTTAGGG
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
85 5 0.04
86 15 0.11
87 108 0.77
88 12 0.09
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (88 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGTAATTTTTAAAAGTTTCGGGGTAAAAATG
AAATTTTTGGAAGTCTTGAGGGT
Found at i:30200619 original size:14 final size:14
Alignment explanation
Indices: 30200602--30200631 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30200592 AATTTGGGCT
30200602 TTTGTAATTGGACA
1 TTTGTAATTGGACA
*
30200616 TTTGTATTTGGACA
1 TTTGTAATTGGACA
30200630 TT
1 TT
30200632 AATTTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (14 bp):
TTTGTAATTGGACA
Found at i:30200643 original size:6 final size:6
Alignment explanation
Indices: 30200632--30200727 Score: 76
Period size: 6 Copynumber: 16.7 Consensus size: 6
30200622 TTTGGACATT
* *
30200632 AATTTA ATTTTA AATTTA ATTTTA AATTTA TAA--TA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * * *
30200678 TATGTA AATTTA AATTTA AA-ATA AATTCA ACTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
30200724 AATT
1 AATT
30200728 CTGTTGGGCC
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 51 0.75
7 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:30200656 original size:23 final size:23
Alignment explanation
Indices: 30200630--30200696 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
30200620 TATTTGGACA
30200630 TTAATTTAATTTTAAATTTAATT
1 TTAATTTAATTTTAAATTTAATT
**
30200653 TTAAATTT-ATAATAAATTTAAATT
1 TT-AATTTAATTTTAAATTT-AATT
* *
30200677 TT-ATGTAAATTTAAATTTAA
1 TTAATTTAATTTTAAATTTAA
30200697 AATAAATTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
22 5 0.14
23 19 0.54
24 11 0.31
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TTAATTTAATTTTAAATTTAATT
Found at i:30200672 original size:17 final size:17
Alignment explanation
Indices: 30200632--30200727 Score: 102
Period size: 17 Copynumber: 5.6 Consensus size: 17
30200622 TTTGGACATT
* *
30200632 AATTTAATTTTAAATTTA
1 AATTTAAATTTAAA-ATA
* *
30200650 ATTTTAAATTTATAATA
1 AATTTAAATTTAAAATA
* **
30200667 AATTTAAATTTTATGTA
1 AATTTAAATTTAAAATA
30200684 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
30200701 AATTCAACTTTAAAATA
1 AATTTAAATTTAAAATA
30200718 AATTTAAATT
1 AATTTAAATT
30200728 CTGTTGGGCC
Statistics
Matches: 62, Mismatches: 16, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
17 51 0.82
18 11 0.18
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:30201661 original size:21 final size:21
Alignment explanation
Indices: 30201631--30201685 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
30201621 CTCGAACCCT
*
30201631 AAATCTTAAATCCCAAA-TCTC
1 AAATCATAAATCCCAAACTC-C
*
30201652 AAATCATAAATCTCAAACTCC
1 AAATCATAAATCCCAAACTCC
30201673 AAACTCA-AAATCC
1 AAA-TCATAAATCC
30201686 TGAATCCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATCATAAATCCCAAACTCC
Found at i:30201662 original size:14 final size:14
Alignment explanation
Indices: 30201630--30201668 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
30201620 TCTCGAACCC
* *
30201630 TAAATCTTAAATCC
1 TAAATCTCAAATCA
*
30201644 CAAATCTCAAATCA
1 TAAATCTCAAATCA
30201658 TAAATCTCAAA
1 TAAATCTCAAA
30201669 CTCCAAACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAATCTCAAATCA
Found at i:30201691 original size:28 final size:28
Alignment explanation
Indices: 30201643--30201697 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
30201633 ATCTTAAATC
*
30201643 CCAAATCTCAAATCATAAATCTCAAACT
1 CCAAATCTCAAATCATAAATCCCAAACT
* *
30201671 CCAAA-CTCAAAATCCTGAATCCCAAAC
1 CCAAATCTC-AAATCATAAATCCCAAAC
30201698 CTGGAACCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (28 bp):
CCAAATCTCAAATCATAAATCCCAAACT
Found at i:30201741 original size:7 final size:7
Alignment explanation
Indices: 30201731--30201774 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
30201721 AAAGTTAAAA
30201731 GTTTAAG
1 GTTTAAG
30201738 GTTTAAG
1 GTTTAAG
30201745 GTTTAAG
1 GTTTAAG
30201752 GTTT--G
1 GTTTAAG
30201757 GATTTAAG
1 G-TTTAAG
30201765 GTTTAAG
1 GTTTAAG
30201772 GTT
1 GTT
30201775 CGAGATTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
7 27 0.79
8 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (7 bp):
GTTTAAG
Found at i:30216996 original size:97 final size:96
Alignment explanation
Indices: 30216816--30216999 Score: 208
Period size: 97 Copynumber: 1.9 Consensus size: 96
30216806 ATAGTTTGTG
* * ** * *
30216816 GGTCATTGAAGGATTTATCTCCATATCTAAGTTCAAATATAAGTTGGAAACATGAACTTGAAGCA
1 GGTCATTGAAGGATTTATCTCCATACCTAAGCTCAAATATAAGTCAGAAACAAGAACTTCAAGCA
**
30216881 AAATGAAGGGCTGGAGCAACATGGATATACA
66 AAATGAAGGGCTAAAGCAACATGGATATACA
* * * ** *
30216912 GGTCATTGCAGGGTCTTATCTCCATACCTATGCTCGGATATAAGTCAGAAACAAGTACTTCAAGC
1 GGTCATTGAAGGAT-TTATCTCCATACCTAAGCTCAAATATAAGTCAGAAACAAGAACTTCAAGC
*
30216977 AAAATGAAGAG-TCAAAGCAACAT
65 AAAATGAAGGGCT-AAAGCAACAT
30217000 AAATTAGCAG
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
96 13 0.18
97 58 0.82
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (96 bp):
GGTCATTGAAGGATTTATCTCCATACCTAAGCTCAAATATAAGTCAGAAACAAGAACTTCAAGCA
AAATGAAGGGCTAAAGCAACATGGATATACA
Found at i:30217573 original size:17 final size:16
Alignment explanation
Indices: 30217537--30217575 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
30217527 TTTTGTTTGA
30217537 GTTTTA-TTTATAAAT
1 GTTTTATTTTATAAAT
*
30217552 ATTTTATTTTATGAAAT
1 GTTTTATTTTAT-AAAT
30217569 GTTTTAT
1 GTTTTAT
30217576 AAAATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 5 0.25
16 5 0.25
17 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (16 bp):
GTTTTATTTTATAAAT
Found at i:30222434 original size:24 final size:24
Alignment explanation
Indices: 30222405--30222477 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
30222395 AATGACTCGT
*
30222405 CTGGAAGAAACAGTCATGTCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
* *
30222429 CTGGAAGAAGCAGTCACGTAAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
* * *
30222453 CAGGAAGAAGCAGCCATGGCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
30222477 C
1 C
30222478 AATTACACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.37, C:0.23, G:0.29, T:0.11
Consensus pattern (24 bp):
CTGGAAGAAGCAGTCATGTCAGCA
Found at i:30228756 original size:23 final size:23
Alignment explanation
Indices: 30228682--30228895 Score: 151
Period size: 23 Copynumber: 9.5 Consensus size: 23
30228672 TAAACGGAAC
* * *
30228682 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
30228704 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
30228726 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
30228752 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
30228772 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30228791 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30228814 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30228837 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
30228862 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
30228885 AATCAAAGAGC
1 AAACAGAGAGC
30228896 GCGCTAGTGT
Statistics
Matches: 152, Mismatches: 24, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 78 0.51
24 2 0.01
25 29 0.19
26 8 0.05
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:30228790 original size:39 final size:39
Alignment explanation
Indices: 30228736--30228810 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
30228726 GGGCAACAGA
*
30228736 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
30228775 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
30228811 GCTAATCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:30228849 original size:48 final size:46
Alignment explanation
Indices: 30228775--30228895 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
30228765 ACAAAGTACT
* *
30228775 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
30228821 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
*
30228869 GAGCACACACAGTGCTAATCAAAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
30228896 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 25 0.37
48 42 0.62
49 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:30231254 original size:26 final size:26
Alignment explanation
Indices: 30231178--30231255 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
30231168 GTCAACTATA
* * * * *
30231178 CACCGACTTGAAGCTTGCTATTTAAT
1 CACCGGCTCGAAGCCTGCTATATATT
*
30231204 CACCGGCTCGAAGCCTGCTACATATT
1 CACCGGCTCGAAGCCTGCTATATATT
30231230 CACCGGCTC-AAGGCCTGCTATATATT
1 CACCGGCTCGAA-GCCTGCTATATATT
30231256 TGTTTACGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 2 0.05
26 42 0.95
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (26 bp):
CACCGGCTCGAAGCCTGCTATATATT
Found at i:30232126 original size:22 final size:21
Alignment explanation
Indices: 30232085--30232130 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
30232075 TTTATTCATC
30232085 TTAATTTTTAATCATTTTAATA
1 TTAATTTTTAATCATTTTAA-A
30232107 TTAA-TTTTAAGTC-TTCTTAAA
1 TTAATTTTTAA-TCATT-TTAAA
30232128 TTA
1 TTA
30232131 CATCAAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATTTTTAATCATTTTAAA
Found at i:30235626 original size:14 final size:16
Alignment explanation
Indices: 30235607--30235638 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
30235597 GATCATCAAT
30235607 ATCATTAA-A-CCAAG
1 ATCATTAATATCCAAG
30235621 ATCATTAATATCCAAG
1 ATCATTAATATCCAAG
30235637 AT
1 AT
30235639 AACTTAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (16 bp):
ATCATTAATATCCAAG
Found at i:30236454 original size:31 final size:31
Alignment explanation
Indices: 30236419--30236572 Score: 191
Period size: 31 Copynumber: 5.0 Consensus size: 31
30236409 ACACATAATG
* ** *
30236419 CCTGATACAATATAAACACCGGTACAAAGTA
1 CCTGATATAATATAGTCACCGGTACATAGTA
* **
30236450 CCTGATATAGTATAGTCACCAATACATAGTA
1 CCTGATATAATATAGTCACCGGTACATAGTA
* *
30236481 CCTAATATAATATAGTCACTGGTACATAGTA
1 CCTGATATAATATAGTCACCGGTACATAGTA
*
30236512 CTTGATATAATATAGTCACCGGTACATAGTA
1 CCTGATATAATATAGTCACCGGTACATAGTA
* * *
30236543 CCTGATACAATATAATCACAGGTACATAGT
1 CCTGATATAATATAGTCACCGGTACATAGT
30236573 CTTGATACTT
Statistics
Matches: 104, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (31 bp):
CCTGATATAATATAGTCACCGGTACATAGTA
Found at i:30236569 original size:62 final size:62
Alignment explanation
Indices: 30236419--30236579 Score: 216
Period size: 62 Copynumber: 2.6 Consensus size: 62
30236409 ACACATAATG
* * * * *
30236419 CCTGATACAATATAAACACCGGTACAAAGTACCTGATATAGTATAGTCACCAATACATAGTA
1 CCTGATACAATATAATCACAGGTACATAGTACTTGATATAATATAGTCACCAATACATAGTA
* * * * **
30236481 CCTAATATAATATAGTCACTGGTACATAGTACTTGATATAATATAGTCACCGGTACATAGTA
1 CCTGATACAATATAATCACAGGTACATAGTACTTGATATAATATAGTCACCAATACATAGTA
30236543 CCTGATACAATATAATCACAGGTACATAGT-CTTGATA
1 CCTGATACAATATAATCACAGGTACATAGTACTTGATA
30236580 CTTTAAAACC
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 7 0.08
62 78 0.92
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (62 bp):
CCTGATACAATATAATCACAGGTACATAGTACTTGATATAATATAGTCACCAATACATAGTA
Found at i:30244538 original size:23 final size:22
Alignment explanation
Indices: 30244508--30244632 Score: 110
Period size: 23 Copynumber: 5.5 Consensus size: 22
30244498 ACGCTAGCGC
30244508 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGTTT-GCACTGT-GTGT
30244531 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGTTT-GCACTGT-GTGT
* * * *
30244554 GCCTACTGATTTGCGCTATGTGC
1 GCTTACTG-TTTGCACTGTGTGT
* *
30244577 GCCTACTGATTGCACTGTGTGT
1 GCTTACTGTTTGCACTGTGTGT
* *
30244599 GCCTACTGGATTGCACTGTGTGT
1 GCTTACT-GTTTGCACTGTGTGT
30244622 GCTTACTGTTT
1 GCTTACTGTTT
30244633 CCCCAGCACT
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
22 20 0.22
23 66 0.73
24 4 0.04
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (22 bp):
GCTTACTGTTTGCACTGTGTGT
Found at i:30244629 original size:45 final size:46
Alignment explanation
Indices: 30244511--30244629 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 46
30244501 CTAGCGCGCT
*
30244511 TACTG-TTTCGCACT-TCGTGTGCTTACTGTTTCGCACTTCGTGTGCC
1 TACTGATTT-GCACTAT-GTGTGCTTACTGATTCGCACTTCGTGTGCC
* * *
30244557 TACTGATTTGCGCTATGTGCGCCTACTGATT-GCACTGT-GTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACT-TCGTGTGCC
*
30244602 TACTGGA-TTGCACTGTGTGTGCTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
30244630 TTTCCCCAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
45 33 0.54
46 24 0.39
47 4 0.07
ACGTcount: A:0.12, C:0.24, G:0.25, T:0.39
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTCGCACTTCGTGTGCC
Found at i:30250216 original size:17 final size:17
Alignment explanation
Indices: 30250194--30250232 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
30250184 AGGTGGAGAA
* *
30250194 CTTGTTTGTTGAGAGTT
1 CTTGTTTGTAGAGAATT
30250211 CTTGTTTGTAGAGAATT
1 CTTGTTTGTAGAGAATT
30250228 CTTGT
1 CTTGT
30250233 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.08, G:0.26, T:0.51
Consensus pattern (17 bp):
CTTGTTTGTAGAGAATT
Found at i:30252489 original size:159 final size:156
Alignment explanation
Indices: 30252202--30252514 Score: 436
Period size: 159 Copynumber: 2.0 Consensus size: 156
30252192 CTAGTCTCTC
* * * * *
30252202 TCAATTTTGAAATTGAGCAATTTGGTCCCTTTAAAAATATCAGAGCAATTTAATCCTTGTCAATT
1 TCAATTTTGAAATTGAGCAAATTAGTCCCTTTAAAAAAATCAGAGCAATTTAATCCCTATCAATT
* * *
30252267 TTGAAAGTGAGCAACTATGGATAGTTAATCACGATGTTAATATTTTCCATCAATTATATATTATT
66 TTGAAAGTGAGCAACTATGGACAATTAATCACGATGTTAATATTTTCCATCAATTATAAATTATT
30252332 T-TGATTGGT-GTAATATCAAATTTAGA
131 TGT-ATTGGTAG-AATATCAAATTTAGA
30252358 TCAATTTTGAAATTGAGCAAATTAGTCCCTCTTAAAAAAATCAGAGCAATTTAATATCCCTATCA
1 TCAATTTTGAAATTGAGCAAATTAGTCCCT-TTAAAAAAATCAGAGCAATTT-A-ATCCCTATCA
* *
30252423 ATTTTGAAAGTGAGCATCTGA-GGACAATTAATCACGATGTTAATA-TTTCTCATCAATTGTAAA
63 ATTTTGAAAGTGAGCAACT-ATGGACAATTAATCACGATGTTAATATTTTC-CATCAATTATAAA
*
30252486 TTATTTGTATTGGTAGATTATCAAATTTA
126 TTATTTGTATTGGTAGAATATCAAATTTA
30252515 TCCCTTAAAG
Statistics
Matches: 139, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
156 28 0.20
157 20 0.14
158 5 0.04
159 83 0.60
160 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (156 bp):
TCAATTTTGAAATTGAGCAAATTAGTCCCTTTAAAAAAATCAGAGCAATTTAATCCCTATCAATT
TTGAAAGTGAGCAACTATGGACAATTAATCACGATGTTAATATTTTCCATCAATTATAAATTATT
TGTATTGGTAGAATATCAAATTTAGA
Done.