Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold187
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: 2169796
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 45208 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:1234804 original size:28 final size:28
Alignment explanation
Indices: 1234764--1234837 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1234754 GGAATAAAGC
*
1234764 CGGGGTTGGAGTATCCTCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCTC-CGAGAAATAA
1234792 CGGGGTTGGAGTATCC-CCGATGAAATAA
1 CGGGGTTGGAGTATCCTCCGA-GAAATAA
**
1234820 CAAGGTTGGAGTATCCTC
1 CGGGGTTGGAGTATCCTC
1234838 GACTATGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 36 0.90
29 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCTCCGAGAAATAA
Found at i:1234955 original size:52 final size:51
Alignment explanation
Indices: 1234823--1235208 Score: 219
Period size: 52 Copynumber: 7.4 Consensus size: 51
1234813 GAAATAACAA
* * * * * *
1234823 GGTTGGAGTATCCTCGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGAAAATAAAACCGG
* * * * *
1234875 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGAAAATAAAACCGG
* *
1234927 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGA-AAATAAAACCGG
* * * * * * **
1234979 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGG
** * ** ** *
1235030 GGTTGGAGTATCCCC---TCGGAAATAACGGGGTTAGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TTAGTGT-T--TTGAAAATAAAACCGG
* * * * *
1235085 GGTTGGGGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGAAAATAAAACCGG
* * *
1235139 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAACCGG
* *
1235190 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
1235209 GTGGAGAATT
Statistics
Matches: 253, Mismatches: 59, Indels: 45
0.71 0.17 0.13
Matches are distributed among these distances:
48 5 0.02
49 2 0.01
51 70 0.28
52 94 0.37
53 26 0.10
54 26 0.10
55 19 0.08
56 1 0.00
57 3 0.01
58 6 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGG
Found at i:1235036 original size:51 final size:51
Alignment explanation
Indices: 1234823--1235044 Score: 228
Period size: 52 Copynumber: 4.3 Consensus size: 51
1234813 GAAATAACAA
* * * *
1234823 GGTTGGAGTATCCTCGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGGAAATAAAACCGG
* * * * * * *
1234875 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTATTTTGGAAATAAAACCGG
* * * *
1234927 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTGGAAATAAAACCGG
* * * * **
1234979 GATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAACCGG
1235030 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1235045 TCGGAAATAA
Statistics
Matches: 138, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
51 36 0.26
52 91 0.66
53 11 0.08
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAACCGG
Found at i:1235204 original size:263 final size:262
Alignment explanation
Indices: 1234713--1235213 Score: 747
Period size: 263 Copynumber: 1.9 Consensus size: 262
1234703 TCGAAAATAA
* * * *
1234713 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* * * *
1234778 CCTCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGACTA
66 CCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTA
*
1234843 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
* *
1234908 GTTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
195 GTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
1234973 AAC
260 AAC
* *
1234976 CGGGATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
** * * *
1235041 CCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATG-ATCAACGGGGTTGGGGTATCCCCGATTG
66 CCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACTA
* *
1235105 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAATTA
130 TGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTA
*
1235169 GTGTCTT-GAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
193 GTGT-TTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
1235214 GAATTGAGAA
Statistics
Matches: 213, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
261 2 0.01
262 23 0.11
263 146 0.69
264 42 0.20
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (262 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTAT
GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
TTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
AC
Found at i:1238115 original size:54 final size:51
Alignment explanation
Indices: 1238003--1238181 Score: 177
Period size: 51 Copynumber: 3.5 Consensus size: 51
1237993 ATAACGGGGC
* * * * *
1238003 TGGAGTATCCCCGGTTGTGAGAAA-TCGATGATTAGAAAA-AAAATC-GGGAT
1 TGGAGTATCCCCGATTGTGAGAAATTAG-TGTTTTGAAAATAAAATCAGAG-T
* *
1238053 TGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGT
1 TGGAGTATCCCCGATTGTG-AGAAATTAGTG--TTTTGAAAATAAAATCAGAGT
* *
1238107 TGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGT
1 TGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCAGAGT
*
1238158 TGGAATATCCCCGATTGTGGAGAA
1 TGGAGTATCCCCGATTGT-GAGAA
1238182 TTGAGAAACT
Statistics
Matches: 108, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
50 18 0.17
51 42 0.39
52 6 0.06
53 16 0.15
54 24 0.22
55 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (51 bp):
TGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCAGAGT
Found at i:1240558 original size:33 final size:33
Alignment explanation
Indices: 1240520--1240586 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1240510 AAAATTTCCA
***
1240520 AATGTATAGATACAAAGATCCATGTATCGATAC
1 AATGTATAGATACAAAGAAAAATGTATCGATAC
* *
1240553 AATGTATCGATACATAGAAAAATGTATCGATAC
1 AATGTATAGATACAAAGAAAAATGTATCGATAC
1240586 A
1 A
1240587 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATAGATACAAAGAAAAATGTATCGATAC
Found at i:1240559 original size:13 final size:13
Alignment explanation
Indices: 1240541--1240566 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1240531 ACAAAGATCC
1240541 ATGTATCGATACA
1 ATGTATCGATACA
1240554 ATGTATCGATACA
1 ATGTATCGATACA
1240567 TAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1240630 original size:19 final size:18
Alignment explanation
Indices: 1240606--1240673 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1240596 CAGTAGCTAA
1240606 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1240625 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1240640 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1240657 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1240674 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1240646 original size:13 final size:13
Alignment explanation
Indices: 1240628--1240652 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1240618 ACAATACTTA
1240628 TGTATCGATACAT
1 TGTATCGATACAT
1240641 TGTATCGATACA
1 TGTATCGATACA
1240653 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1240650 original size:32 final size:32
Alignment explanation
Indices: 1240609--1240671 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1240599 TAGCTAATTA
*
1240609 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1240641 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1240672 AATTGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1240753 original size:21 final size:21
Alignment explanation
Indices: 1240729--1240785 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1240719 CATTTGTAGG
*
1240729 ATGTATCGATGCATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1240750 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1240771 ATGTATCGATACATT
1 ATGTATCGATACATT
1240786 TGGATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1245488 original size:13 final size:13
Alignment explanation
Indices: 1245470--1245494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1245460 TACTATGAAC
1245470 ATGTATCGATACA
1 ATGTATCGATACA
1245483 ATGTATCGATAC
1 ATGTATCGATAC
1245495 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1245493 original size:32 final size:33
Alignment explanation
Indices: 1245452--1245515 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1245442 CTTTTCAAGG
*
1245452 TGTATCGATACTATG-AACATGTATCGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
*
1245484 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
1245516 TTTGGTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:1251443 original size:67 final size:66
Alignment explanation
Indices: 1251316--1251512 Score: 182
Period size: 67 Copynumber: 2.9 Consensus size: 66
1251306 AGCCTTTCTG
* * * * * * * *
1251316 CACCACTACTCTACATAGTAGAACCAA-TGATGACAAGAACAACTAAGCACAGTACCTAGAGTTA
1 CACCACTACTCTGCATGGCAAAACCAATTGA-AACAAGAGCAATTGAGCACAGTA-CTAGAGTTA
1251380 CTA
64 CTA
* * * * * * *
1251383 CATCACTGCTCTGCATGGCAGAACCAA-TGACGATAAGAGCATTTGAGCACAGTATCTAGAGTTG
1 CACCACTACTCTGCATGGCAAAACCAATTGA-AACAAGAGCAATTGAGCACAGTA-CTAGAGTTA
*
1251447 CTG
64 CTA
*
1251450 CACCACTACTCTGTATGGCAAAACCAATTGAAACAAGAGCAATTGAGCACAGTACTTAGAGTT
1 CACCACTACTCTGCATGGCAAAACCAATTGAAACAAGAGCAATTGAGCACAGTAC-TAGAGTT
1251513 CTCCCCTAAT
Statistics
Matches: 107, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
66 1 0.01
67 103 0.96
68 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (66 bp):
CACCACTACTCTGCATGGCAAAACCAATTGAAACAAGAGCAATTGAGCACAGTACTAGAGTTACT
A
Found at i:1253309 original size:3 final size:3
Alignment explanation
Indices: 1253301--1253358 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1253291 GTTACTTTTT
1253301 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1253349 ATA ATA ATA A
1 ATA ATA ATA A
1253359 ATATCTATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1304214 original size:19 final size:21
Alignment explanation
Indices: 1304190--1304243 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1304180 GAGTTATCCA
*
1304190 AATGTATCGCT-CA-TTGTAG
1 AATGTATCGATACATTTGTAG
*
1304209 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1304230 AATGTATCGATACA
1 AATGTATCGATACA
1304244 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.32
20 2 0.06
21 19 0.61
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1304352 original size:13 final size:13
Alignment explanation
Indices: 1304334--1304359 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1304324 CATTTTTCTG
1304334 TGTATCGATACAT
1 TGTATCGATACAT
1304347 TGTATCGATACAT
1 TGTATCGATACAT
1304360 GGTCTTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1310743 original size:27 final size:26
Alignment explanation
Indices: 1310694--1310749 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1310684 TTTGAAATTT
* *
1310694 ATATATTAAAAATTATAATTATTTAA
1 ATATATTAAAAATTAAAAATATTTAA
*
1310720 ATATATTAAACTATTAAAAATATTTAA
1 ATATATTAAA-AATTAAAAATATTTAA
1310747 ATA
1 ATA
1310750 AATAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATTAAAAATTAAAAATATTTAA
Found at i:1312211 original size:14 final size:15
Alignment explanation
Indices: 1312187--1312219 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1312177 CTCTTTTTAT
1312187 TTTTCATTTTAATAA
1 TTTTCATTTTAATAA
*
1312202 TTTT-ATTTTATTAA
1 TTTTCATTTTAATAA
1312216 TTTT
1 TTTT
1312220 TATTCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTTAATAA
Found at i:1312220 original size:15 final size:15
Alignment explanation
Indices: 1312185--1312223 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1312175 ATCTCTTTTT
1312185 ATTTTTCATTTTAATA
1 ATTTTT-ATTTTAATA
*
1312201 A-TTTTATTTTATTA
1 ATTTTTATTTTAATA
1312215 ATTTTTATT
1 ATTTTTATT
1312224 CTAAAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 11 0.52
16 1 0.05
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTATTTTAATA
Found at i:1312557 original size:20 final size:20
Alignment explanation
Indices: 1312534--1312571 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1312524 TAACTGATAA
*
1312534 AATATTTAATTTTATCATAT
1 AATATTTAATTTCATCATAT
*
1312554 AATATTTAGTTTCATCAT
1 AATATTTAATTTCATCAT
1312572 CATCATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (20 bp):
AATATTTAATTTCATCATAT
Found at i:1312864 original size:13 final size:14
Alignment explanation
Indices: 1312833--1312873 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1312823 GTTGAATTTT
*
1312833 ATTATTTTAAATGTA
1 ATTATATTAAAT-TA
1312848 ATTATA-TAAATTA
1 ATTATATTAAATTA
1312861 ATTATATTAAATT
1 ATTATATTAAATT
1312874 TTTAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 11 0.46
15 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTATATTAAATTA
Found at i:1315791 original size:2 final size:2
Alignment explanation
Indices: 1315779--1315815 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1315769 GAAATTTAAA
* *
1315779 AC AC CC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1315816 AAAGGAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1319378 original size:19 final size:19
Alignment explanation
Indices: 1319338--1319379 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1319328 ATATAACTTT
* *
1319338 TATAAATGAGTCTTATATA
1 TATAAATGAGTATTATAAA
1319357 TATAAATGA-TATTGATAAA
1 TATAAATGAGTATT-ATAAA
1319376 TATA
1 TATA
1319380 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (19 bp):
TATAAATGAGTATTATAAA
Found at i:1320973 original size:18 final size:19
Alignment explanation
Indices: 1320950--1320999 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1320940 CCAAATATAT
1320950 ATTTTAAT-ATTGATT-TTA
1 ATTTTAATCATT-ATTGTTA
1320968 ATTTTAATCATTATTGTTA
1 ATTTTAATCATTATTGTTA
*
1320987 TTTTTAATC-TTAT
1 ATTTTAATCATTAT
1321000 AGGAACTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTTTAATCATTATTGTTA
Found at i:1322113 original size:34 final size:35
Alignment explanation
Indices: 1322075--1322141 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1322065 CCTTACAACA
1322075 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTTT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTTT
1322109 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1322142 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTTT
Found at i:1322619 original size:13 final size:13
Alignment explanation
Indices: 1322601--1322690 Score: 72
Period size: 13 Copynumber: 6.0 Consensus size: 13
1322591 CAATTTTTTG
1322601 TGTATCGATACAT
1 TGTATCGATACAT
1322614 TGTATCGATACATACTTT
1 TGTATCGATAC--A---T
1322632 GTGTATCGATACAT
1 -TGTATCGATACAT
1322646 TGTATCGATACATACTTT
1 TGTATCGATAC--A---T
1322664 GTGTATCGATACAT
1 -TGTATCGATACAT
1322678 TGTATCGATACAT
1 TGTATCGATACAT
1322691 ACTTTGTGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 35 0.54
14 2 0.03
15 2 0.03
17 2 0.03
18 2 0.03
19 22 0.34
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1322638 original size:19 final size:19
Alignment explanation
Indices: 1322614--1322708 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
1322604 ATCGATACAT
1322614 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
1322633 TGTATCGATAC--A---T-
1 TGTATCGATACATACTTTG
1322646 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
1322665 TGTATCGATAC--A---T-
1 TGTATCGATACATACTTTG
1322678 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
1322697 TGTATCGATACA
1 TGTATCGATACA
1322709 AGTTTGGCTA
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
15 2 0.03
17 2 0.03
18 2 0.03
19 34 0.53
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTTTG
Found at i:1322638 original size:32 final size:32
Alignment explanation
Indices: 1322581--1322708 Score: 229
Period size: 32 Copynumber: 4.0 Consensus size: 32
1322571 TACAAGCCAA
**
1322581 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATAC-ATACTTTGTGTATCGATACAT
1322614 TGTATCGATACATACTTTGTGTATCGATACAT
1 TGTATCGATACATACTTTGTGTATCGATACAT
1322646 TGTATCGATACATACTTTGTGTATCGATACAT
1 TGTATCGATACATACTTTGTGTATCGATACAT
1322678 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
1322709 AGTTTGGCTA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 82 0.88
33 11 0.12
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:1323373 original size:15 final size:17
Alignment explanation
Indices: 1323355--1323388 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1323345 TTTCTTTTAA
1323355 TTTTG-ACATTAA-AAT
1 TTTTGCACATTAATAAT
1323370 TTTTGCACATTAATAAT
1 TTTTGCACATTAATAAT
1323387 TT
1 TT
1323389 ATTTTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTTGCACATTAATAAT
Found at i:1324765 original size:35 final size:36
Alignment explanation
Indices: 1324719--1324789 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1324709 GAGAGTGGTT
1324719 GACACAATACTT-ATGAGTGGGAAATGGAAAAGGTC
1 GACACAATACTTAATGAGTGGGAAATGGAAAAGGTC
1324754 GACACAATACTTAATGAGTGGGAAATGGAAAAGGTC
1 GACACAATACTTAATGAGTGGGAAATGGAAAAGGTC
1324790 ATATACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 12 0.34
36 23 0.66
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (36 bp):
GACACAATACTTAATGAGTGGGAAATGGAAAAGGTC
Found at i:1325082 original size:23 final size:23
Alignment explanation
Indices: 1325029--1325075 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1325019 TAATTATAAA
1325029 AATAAAT-ATAAAAATAATATTTT
1 AATAAATAAT-AAAATAATATTTT
1325052 AATAAATAATAAAAT-ATATTTT
1 AATAAATAATAAAATAATATTTT
1325074 AA
1 AA
1325076 ATTAATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 12 0.52
24 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAAATAATAAAATAATATTTT
Found at i:1327267 original size:22 final size:20
Alignment explanation
Indices: 1327213--1327269 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
1327203 CCCTTAGACT
*
1327213 ATGCCCTAGATTATGTCTTG
1 ATGCCTTAGATTATGTCTTG
* *
1327233 ATGCCTAAAATTATGTCTATTG
1 ATGCCTTAGATTATGTC--TTG
1327255 ATGCCTTAGATTATG
1 ATGCCTTAGATTATG
1327270 ATAAAGATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
22 16 0.53
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (20 bp):
ATGCCTTAGATTATGTCTTG
Found at i:1327297 original size:54 final size:51
Alignment explanation
Indices: 1327186--1327298 Score: 118
Period size: 54 Copynumber: 2.1 Consensus size: 51
1327176 AAAATAATTA
* ** *
1327186 CAAAATTATGTTTTGATCCCTTAGACTATGCCCTAGATTATGTCTTGATGC
1 CAAAATTATGTTTTGATCCCTTAGACTATGACAAAGATTATGTCTTGACGC
* * * *
1327237 CTAAAATTATGTCTATTGATGCCTTAGATTATGATAAAGATTATGTCTTGACGAT
1 C-AAAATTATGT-T-TTGATCCCTTAGACTATGACAAAGATTATGTCTTGACG-C
1327292 CAAAATT
1 CAAAATT
1327299 GCTTTAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
51 1 0.02
52 10 0.20
53 1 0.02
54 37 0.74
55 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (51 bp):
CAAAATTATGTTTTGATCCCTTAGACTATGACAAAGATTATGTCTTGACGC
Found at i:1331191 original size:15 final size:17
Alignment explanation
Indices: 1331161--1331194 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1331151 TATTGTTTAA
1331161 TTTAATTATTTAATATT
1 TTTAATTATTTAATATT
1331178 TTTAATT-TTT-ATATT
1 TTTAATTATTTAATATT
1331193 TT
1 TT
1331195 GATTTACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATTATTTAATATT
Found at i:1331919 original size:7 final size:7
Alignment explanation
Indices: 1331909--1331992 Score: 57
Period size: 7 Copynumber: 11.6 Consensus size: 7
1331899 ATAAAGTCTG
1331909 TTTAAAA
1 TTTAAAA
1331916 TTTAAAA
1 TTTAAAA
1331923 TTTTAAAA
1 -TTTAAAA
1331931 TTT-AAA
1 TTTAAAA
*
1331937 TTT-AGA
1 TTTAAAA
1331943 TTCTAAAAA
1 TT-T-AAAA
1331952 TTTGAATAA
1 TTT-AA-AA
* *
1331961 TATCATAA
1 T-TTAAAA
1331969 TTT-AAA
1 TTTAAAA
1331975 TTTAAAA
1 TTTAAAA
*
1331982 TTTAAAT
1 TTTAAAA
1331989 TTTA
1 TTTA
1331993 GATAATAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
6 15 0.24
7 25 0.40
8 13 0.21
9 8 0.13
10 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:1331985 original size:13 final size:13
Alignment explanation
Indices: 1331913--1332016 Score: 57
Period size: 13 Copynumber: 7.4 Consensus size: 13
1331903 AGTCTGTTTA
1331913 AAATTTAAAATTTT
1 AAATTTAAAA-TTT
1331927 AAAATTT-AAATTT
1 -AAATTTAAAATTT
*
1331940 AGATTCTAAAAATTT
1 AAATT-T-AAAATTT
* *
1331955 GAATAATATCATAATTT
1 --A-AAT-TTAAAATTT
1331972 AAATTTAAAATTT
1 AAATTTAAAATTT
* * *
1331985 AAATTTTAGATAAT
1 AAATTTAAAAT-TT
*
1331999 AATTTTAAAATTT
1 AAATTTAAAATTT
1332012 AAATT
1 AAATT
1332017 GGATAATTAA
Statistics
Matches: 67, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
12 4 0.06
13 25 0.37
14 15 0.22
15 13 0.19
17 7 0.10
18 2 0.03
19 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:1332008 original size:27 final size:27
Alignment explanation
Indices: 1331965--1332041 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
1331955 GAATAATATC
*
1331965 ATAATTTAAATTTAAAATTTAAATTTTAG
1 ATAA-TTAATTTTAAAATTTAAA-TTTAG
*
1331994 ATAA-TAATTTTAAAATTTAAA-TTGG
1 ATAATTAATTTTAAAATTTAAATTTAG
* *
1332019 ATAATTAATTTTTAAATCTAAAT
1 ATAATTAATTTTAAAATTTAAAT
1332042 AGAATATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 7 0.17
26 15 0.36
27 16 0.38
29 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (27 bp):
ATAATTAATTTTAAAATTTAAATTTAG
Found at i:1332027 original size:26 final size:26
Alignment explanation
Indices: 1331965--1332041 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
1331955 GAATAATATC
*
1331965 ATAATTTAAATTTAAAATTTAAATTTTAG
1 ATAA-TTAATTTTAAAATTTAAA--TTAG
*
1331994 ATAA-TAATTTTAAAATTTAAATTGG
1 ATAATTAATTTTAAAATTTAAATTAG
* *
1332019 ATAATTAATTTTTAAATCTAAAT
1 ATAATTAATTTTAAAATTTAAAT
1332042 AGAATATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 7 0.16
26 16 0.37
27 16 0.37
29 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (26 bp):
ATAATTAATTTTAAAATTTAAATTAG
Found at i:1332420 original size:24 final size:24
Alignment explanation
Indices: 1332393--1332444 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
1332383 AATCTTACTC
1332393 TAATTAA-TCAACTATTCATTCAAA
1 TAATTAACTCAA-TATTCATTCAAA
*
1332417 TAATTAATCTCAATGTTCATTCAAA
1 TAATTAA-CTCAATATTCATTCAAA
1332442 TAA
1 TAA
1332445 GTTCAGCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATTAACTCAATATTCATTCAAA
Found at i:1335478 original size:6 final size:6
Alignment explanation
Indices: 1335464--1335495 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1335454 CCTTGATTGC
1335464 AAAAA- AAAAAG AAAAA- AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1335496 GGAATTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1335480 original size:11 final size:11
Alignment explanation
Indices: 1335464--1335496 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1335454 CCTTGATTGC
1335464 AAAAAAAAAAG
1 AAAAAAAAAAG
1335475 AAAAAAAAAAG
1 AAAAAAAAAAG
*
1335486 AAAAAGAAAAG
1 AAAAAAAAAAG
1335497 GAATTGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1335489 original size:17 final size:16
Alignment explanation
Indices: 1335464--1335495 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1335454 CCTTGATTGC
1335464 AAAAAAAAAAGAAAAA
1 AAAAAAAAAAGAAAAA
1335480 AAAAAGAAAAAGAAAA
1 AAAAA-AAAAAGAAAA
1335496 GGAATTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAA
Found at i:1338180 original size:21 final size:21
Alignment explanation
Indices: 1338156--1338214 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
1338146 ATTATTGACT
1338156 ACAAGTATCGATACATTCTTA
1 ACAAGTATCGATACATTCTTA
1338177 ACAAGTATCGATACATTCTTA
1 ACAAGTATCGATACATTCTTA
1338198 ACAAGTATCGATACATT
1 ACAAGTATCGATACATT
1338215 TGGTCATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (21 bp):
ACAAGTATCGATACATTCTTA
Found at i:1338827 original size:22 final size:22
Alignment explanation
Indices: 1338800--1338844 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1338790 TTTTCTTTTC
1338800 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
1338822 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
1338844 T
1 T
1338845 AACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:1340258 original size:20 final size:22
Alignment explanation
Indices: 1340219--1340263 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
1340209 GCTGCTAGTG
*
1340219 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
1340241 TGGGGG-TG-CCGGTCGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
1340261 TGG
1 TGG
1340264 TGAGTGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.04, C:0.29, G:0.49, T:0.18
Consensus pattern (22 bp):
TGGGGGCTGCCCGGTCGCGACC
Found at i:1340913 original size:8 final size:8
Alignment explanation
Indices: 1340900--1340925 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1340890 AACATCATTC
1340900 ATCACAAA
1 ATCACAAA
1340908 ATCACAAA
1 ATCACAAA
1340916 ATCACAAA
1 ATCACAAA
1340924 AT
1 AT
1340926 AAATCATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:1346628 original size:20 final size:20
Alignment explanation
Indices: 1346605--1346677 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1346595 ACAATTCAAA
1346605 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1346625 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1346646 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1346666 GTATCGATACAT
1 GTATCGATACAT
1346678 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1346649 original size:21 final size:21
Alignment explanation
Indices: 1346623--1346698 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1346613 ACATGTTGCA
1346623 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1346644 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1346664 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1346685 ATGTATCGATACAT
1 ATGTATCGATACAT
1346699 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1346656 original size:41 final size:41
Alignment explanation
Indices: 1346605--1346698 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1346595 ACAATTCAAA
*
1346605 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1346646 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1346687 GTATCGATACAT
1 GTATCGATACAT
1346699 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1346755 original size:13 final size:13
Alignment explanation
Indices: 1346737--1346762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1346727 TACAGCAAGT
1346737 ATGTATCGATACA
1 ATGTATCGATACA
1346750 ATGTATCGATACA
1 ATGTATCGATACA
1346763 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1350844 original size:15 final size:15
Alignment explanation
Indices: 1350824--1350854 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1350814 TAAAAATGTC
*
1350824 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1350839 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1350854 C
1 C
1350855 TAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1352951 original size:13 final size:13
Alignment explanation
Indices: 1352933--1352971 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1352923 ACATTTTTCC
1352933 TTGTATCGATACA
1 TTGTATCGATACA
1352946 TTGTATCGATACA
1 TTGTATCGATACA
*
1352959 CTGTATCGATACA
1 TTGTATCGATACA
1352972 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1354786 original size:24 final size:24
Alignment explanation
Indices: 1354754--1354803 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1354744 AGTGCAAATA
1354754 AATTTTGATATGAATTACTTGATT
1 AATTTTGATATGAATTACTTGATT
1354778 AATTTTGATATGAATTACTTGATT
1 AATTTTGATATGAATTACTTGATT
1354802 AA
1 AA
1354804 GGGGGAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (24 bp):
AATTTTGATATGAATTACTTGATT
Found at i:1355461 original size:20 final size:20
Alignment explanation
Indices: 1355438--1355510 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1355428 ACAATTCAAA
1355438 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1355458 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1355479 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1355499 GTATCGATACAT
1 GTATCGATACAT
1355511 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1355482 original size:21 final size:21
Alignment explanation
Indices: 1355456--1355531 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1355446 ACATGTTGCA
1355456 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1355477 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1355497 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1355518 ATGTATCGATACAT
1 ATGTATCGATACAT
1355532 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1355489 original size:41 final size:41
Alignment explanation
Indices: 1355438--1355531 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1355428 ACAATTCAAA
*
1355438 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1355479 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1355520 GTATCGATACAT
1 GTATCGATACAT
1355532 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1355588 original size:13 final size:13
Alignment explanation
Indices: 1355570--1355595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1355560 TACAGCAAGT
1355570 ATGTATCGATACA
1 ATGTATCGATACA
1355583 ATGTATCGATACA
1 ATGTATCGATACA
1355596 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1356893 original size:20 final size:20
Alignment explanation
Indices: 1356868--1356919 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1356858 TTACAAGCCA
*
1356868 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
* *
1356888 ATGTATCGACACATATTGTG
1 ATGTATCGATACATATTGGG
1356908 -TGTATCGATACA
1 ATGTATCGATACA
1356920 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:1359485 original size:20 final size:20
Alignment explanation
Indices: 1359462--1359504 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1359452 TAATGTCTCA
1359462 ATACATAAGTAAATGTATCG
1 ATACATAAGTAAATGTATCG
*
1359482 ATACATAAGTGAATGTATCG
1 ATACATAAGTAAATGTATCG
1359502 ATA
1 ATA
1359505 TTGGACCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (20 bp):
ATACATAAGTAAATGTATCG
Found at i:1359638 original size:52 final size:52
Alignment explanation
Indices: 1359558--1359665 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
1359548 ATCTATATAG
* *
1359558 TTTTCATTGTATAGACATATTCTAGGTTTTTGACCCAAATGTATCGATACAT
1 TTTTCATTGTATAGACACATTCTAGGTTTTTGACCCAAATGTATCAATACAT
* * * * *
1359610 TTTTCATTGTATCGATACATTTTGGGTTTTTGACGCAAATGTATCAATACAT
1 TTTTCATTGTATAGACACATTCTAGGTTTTTGACCCAAATGTATCAATACAT
1359662 TTTT
1 TTTT
1359666 TGATGTATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (52 bp):
TTTTCATTGTATAGACACATTCTAGGTTTTTGACCCAAATGTATCAATACAT
Found at i:1359673 original size:52 final size:52
Alignment explanation
Indices: 1359582--1359681 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
1359572 ACATATTCTA
* *
1359582 GGTTTTTGACCCAAATGTATCGATACATTTTTCATTGTATCGATACATTTTG
1 GGTTTTTGACCCAAATGTATCAATACATTTTTCATTGTATCAATACATTTTG
* *
1359634 GGTTTTTGACGCAAATGTATCAATACATTTTTTGA-TGTATCAATACAT
1 GGTTTTTGACCCAAATGTATCAATACA-TTTTTCATTGTATCAATACAT
1359682 CTAGTTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 37 0.86
53 6 0.14
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (52 bp):
GGTTTTTGACCCAAATGTATCAATACATTTTTCATTGTATCAATACATTTTG
Found at i:1362185 original size:21 final size:21
Alignment explanation
Indices: 1362161--1362200 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1362151 GGTTATCTTA
1362161 AGATA-ATCGATGACAATTATG
1 AGATACATCG-TGACAATTATG
*
1362182 AGATACATCGTGACTATTA
1 AGATACATCGTGACAATTA
1362201 CGCTTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
AGATACATCGTGACAATTATG
Found at i:1363918 original size:21 final size:20
Alignment explanation
Indices: 1363851--1363921 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1363841 AACATAGTCT
**
1363851 TGTATCGATGCATTTCAGATA
1 TGTATCGATGCA-TTCACTTA
* *
1363872 TGTATTGATACATTCACTTA
1 TGTATCGATGCATTCACTTA
1363892 TGTATCGATGCATTCACTTA
1 TGTATCGATGCATTCACTTA
1363912 TTGTATCGAT
1 -TGTATCGAT
1363922 AAAAATTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 24 0.56
21 19 0.44
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATGCATTCACTTA
Found at i:1367662 original size:21 final size:21
Alignment explanation
Indices: 1367638--1367680 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1367628 ATATACTTAG
*
1367638 CTTTAGCTA-AGAATTGAGCTA
1 CTTTAGCTAGA-AATTAAGCTA
1367659 CTTTAGCTAGAAATTAAGCTA
1 CTTTAGCTAGAAATTAAGCTA
1367680 C
1 C
1367681 AACTTCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CTTTAGCTAGAAATTAAGCTA
Found at i:1369555 original size:13 final size:13
Alignment explanation
Indices: 1369537--1369561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1369527 ATAATGAACA
1369537 TGTATCGATACAT
1 TGTATCGATACAT
1369550 TGTATCGATACA
1 TGTATCGATACA
1369562 AAACAGCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1377665 original size:32 final size:33
Alignment explanation
Indices: 1377608--1377669 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1377598 CAGGCCAATG
1377608 TATCGATACAACTTTATGTGTATCGATACATTA
1 TATCGATACAACTTTATGTGTATCGATACATTA
1377641 TATCGATACATAC-TT-TGTGTATCGATACA
1 TATCGATACA-ACTTTATGTGTATCGATACA
1377670 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
32 14 0.50
33 12 0.43
34 2 0.07
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (33 bp):
TATCGATACAACTTTATGTGTATCGATACATTA
Found at i:1382316 original size:15 final size:15
Alignment explanation
Indices: 1382296--1382326 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1382286 ATTTCGTTTG
*
1382296 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1382311 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1382326 G
1 G
1382327 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1386413 original size:13 final size:13
Alignment explanation
Indices: 1386395--1386420 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1386385 CAACTTTATG
1386395 TGTATCGATACAT
1 TGTATCGATACAT
1386408 TGTATCGATACAT
1 TGTATCGATACAT
1386421 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1386434 original size:32 final size:33
Alignment explanation
Indices: 1386375--1386438 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1386365 TACAGGCCAA
1386375 TGTATCGATACAACTTTATGTGTATCGATACAT
1 TGTATCGATACAACTTTATGTGTATCGATACAT
1386408 TGTATCGATACATAC-TT-TGTGTATCGATACA
1 TGTATCGATACA-ACTTTATGTGTATCGATACA
1386439 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAACTTTATGTGTATCGATACAT
Found at i:1387333 original size:25 final size:25
Alignment explanation
Indices: 1387305--1387356 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1387295 AATTTCACTG
1387305 TAACTAATCTCATCGT-TCATTCAAA
1 TAACTAATCTCA-CGTATCATTCAAA
*
1387330 TAACTAATCTCACTTATCATTCAAA
1 TAACTAATCTCACGTATCATTCAAA
1387355 TA
1 TA
1387357 GTGTCTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (25 bp):
TAACTAATCTCACGTATCATTCAAA
Found at i:1396925 original size:23 final size:23
Alignment explanation
Indices: 1396895--1396938 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1396885 TTATTATACT
*
1396895 TTATTTTTTTTAGAAAATTGAGA
1 TTATTTTTGTTAGAAAATTGAGA
*
1396918 TTATTTTTGTTAGATAATTGA
1 TTATTTTTGTTAGAAAATTGA
1396939 AATTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (23 bp):
TTATTTTTGTTAGAAAATTGAGA
Found at i:1400145 original size:16 final size:17
Alignment explanation
Indices: 1400126--1400202 Score: 67
Period size: 16 Copynumber: 4.8 Consensus size: 17
1400116 TGATAGAGAA
1400126 ATTTTAGA-TTTAAATT
1 ATTTTAGAGTTTAAATT
1400142 ATTTT-GAGTTTAAATT
1 ATTTTAGAGTTTAAATT
*
1400158 ATTTTCA-AGTTTAAATA
1 ATTTT-AGAGTTTAAATT
* * *
1400175 ATTATGGA-TTTGAATT
1 ATTTTAGAGTTTAAATT
1400191 A-TTTA-AGTTTAA
1 ATTTTAGAGTTTAA
1400203 CACTCAAGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 1 0.02
15 8 0.17
16 25 0.52
17 14 0.29
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.52
Consensus pattern (17 bp):
ATTTTAGAGTTTAAATT
Found at i:1401241 original size:20 final size:20
Alignment explanation
Indices: 1401196--1401249 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1401186 TTTTTAGACC
***
1401196 TAAATGTATTGATACATGGC
1 TAAATGTATTGATACATAAA
*
1401216 TTAATGTATTGATACATAAA
1 TAAATGTATTGATACATAAA
1401236 TAAATGTATTGATA
1 TAAATGTATTGATA
1401250 AATTTGCTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.39
Consensus pattern (20 bp):
TAAATGTATTGATACATAAA
Found at i:1402448 original size:20 final size:21
Alignment explanation
Indices: 1402401--1402453 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1402391 GCCAATCACC
*
1402401 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
1402422 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
1402442 TGTATCGATACA
1 TGTATCGATACA
1402454 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:1402498 original size:20 final size:19
Alignment explanation
Indices: 1402475--1402513 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1402465 CTGTGTATTC
1402475 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
1402495 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
1402514 GTTTTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:1404949 original size:13 final size:13
Alignment explanation
Indices: 1404931--1404955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1404921 ATAAACCCTT
1404931 TGTATCGATACAA
1 TGTATCGATACAA
1404944 TGTATCGATACA
1 TGTATCGATACA
1404956 GAGAATGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1411079 original size:52 final size:52
Alignment explanation
Indices: 1411001--1411150 Score: 207
Period size: 52 Copynumber: 2.9 Consensus size: 52
1410991 TGAAATATGG
*
1411001 AAATTTGCCTGTATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
1411053 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
* * *
1411105 AAATTTACCTGCATGTATTGATACA--AAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTTA-AT-AGTGTATCGATACAT
1411151 TTAAGTAATG
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
49 1 0.01
50 1 0.01
52 81 0.92
53 5 0.06
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:1414748 original size:13 final size:13
Alignment explanation
Indices: 1414730--1414755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1414720 CAATTTGGGA
1414730 TGTATCGATACAT
1 TGTATCGATACAT
1414743 TGTATCGATACAT
1 TGTATCGATACAT
1414756 CTTATGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1421852 original size:79 final size:80
Alignment explanation
Indices: 1421708--1422123 Score: 388
Period size: 79 Copynumber: 5.2 Consensus size: 80
1421698 GATGAAAACT
* * * * * ** **
1421708 TTGATATTTTGGAGATAAAATCGGAGTTGGAGTATCCCCTT-GAAAATAGTGGGGTCAGAGTATC
1 TTGATATTTTGAAAATAAAATCGGGGTTAGAGTATCCCTTTAGAAAATAACGGGGTTGGAGTATC
*
1421772 CCCAAGA-T-AAAATT
66 CCCAAGAGTGAAAA-A
* * *
1421786 TTAATATTTTGAAAATAAAAACGGGGTTTA-AGTATCCTTTTAGAAAATAACGGGGTTGGAGTAT
1 TTGATATTTTGAAAATAAAATCGGGG-TTAGAGTATCCCTTTAGAAAATAACGGGGTTGGAGTAT
1421850 CCCCAAGAGTGAAAAA
65 CCCCAAGAGTGAAAAA
* * *
1421866 TTGATATTTTGGAGATAAAATCGGGGTTAGAGTATCCCTTT-GAAAATAACGAGGTTGGAGTATC
1 TTGATATTTTGAAAATAAAATCGGGGTTAGAGTATCCCTTTAGAAAATAACGGGGTTGGAGTATC
*
1421930 CCCAATAGT-AAAAA
66 CCCAAGAGTGAAAAA
*** * * * * *
1421944 TTTGATATTTTGAAAATAAAATTAAGGTTGGAGTATCCCCTCA-AAAATAACAGGGTTGGAGAAT
1 -TTGATATTTTGAAAATAAAATCGGGGTTAGAGTATCCCTTTAGAAAATAACGGGGTTGGAGTAT
**
1422008 CCTTAATG-GTGAAAAA
65 CCCCAA-GAGTGAAAAA
* * * *
1422024 TTGATATTTTGAAAATAAAACCCGGGTTAGAGTATTTCC--TCGAAAATAACGGGGTTGGAGTAT
1 TTGATATTTTGAAAATAAAATCGGGGTTAGAGTA-TCCCTTTAGAAAATAACGGGGTTGGAGTAT
1422087 CCCCAATG-GTGAAAAAAA
65 CCCCAA-GAGTG--AAAAA
*
1422105 TCGATATTTTG-AAATAAAA
1 TTGATATTTTGAAAATAAAA
1422124 ACAGAGTTTT
Statistics
Matches: 278, Mismatches: 47, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
78 35 0.13
79 175 0.63
80 49 0.18
81 19 0.07
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (80 bp):
TTGATATTTTGAAAATAAAATCGGGGTTAGAGTATCCCTTTAGAAAATAACGGGGTTGGAGTATC
CCCAAGAGTGAAAAA
Found at i:1421991 original size:158 final size:158
Alignment explanation
Indices: 1421708--1422143 Score: 468
Period size: 158 Copynumber: 2.7 Consensus size: 158
1421698 GATGAAAACT
* * ** **
1421708 TTGATATTTTGGAGATAAAATCGGAGTTGGAGTATCCCCTTGAAAATAGTGGGGTCAGAGTATCC
1 TTGATATTTTGGAGATAAAATCGGGGTTAGAGTAT-CCCTTGAAAATAACGGGGTTGGAGTATCC
* * * ** * ** *
1421773 CCAAGA-TAAAATTTTAATATTTTGAAAATAAAAACGGGGTTTAAGTATCCTTTTAGAAAATAAC
65 CCAATAGTAAAAATTTGATATTTTGAAAATAAAAACAAGGTTGAAGTATCCCCTCAGAAAATAAC
* *
1421837 GGGGTTGGAGTATCCCCAA-GAGTGAAAAA
130 AGGGTTGGAGAATCCCCAATG-GTGAAAAA
*
1421866 TTGATATTTTGGAGATAAAATCGGGGTTAGAGTATCCCTTTGAAAATAACGAGGTTGGAGTATCC
1 TTGATATTTTGGAGATAAAATCGGGGTTAGAGTATCCC-TTGAAAATAACGGGGTTGGAGTATCC
** *
1421931 CCAATAGTAAAAATTTGATATTTTGAAAATAAAATTAAGGTTGGAGTATCCCCTCA-AAAATAAC
65 CCAATAGTAAAAATTTGATATTTTGAAAATAAAAACAAGGTTGAAGTATCCCCTCAGAAAATAAC
**
1421995 AGGGTTGGAGAATCCTTAATGGTGAAAAA
130 AGGGTTGGAGAATCCCCAATGGTGAAAAA
* * * * * *
1422024 TTGATATTTTGAAAATAAAACCCGGGTTAGAGTATTTCCTCGAAAATAACGGGGTTGGAGTATCC
1 TTGATATTTTGGAGATAAAATCGGGGTTAGAGTA-TCCCTTGAAAATAACGGGGTTGGAGTATCC
* * * * *
1422089 CCAATGGTGAAAAAAATCGATATTTTG-AAATAAAAACAGAGTTTTAA-TATCCCCT
65 CCAATAGT--AAAAATTTGATATTTTGAAAATAAAAACA-AGGTTGAAGTATCCCCT
1422144 TTTGATGTTT
Statistics
Matches: 233, Mismatches: 38, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
157 3 0.01
158 151 0.65
159 59 0.25
160 20 0.09
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (158 bp):
TTGATATTTTGGAGATAAAATCGGGGTTAGAGTATCCCTTGAAAATAACGGGGTTGGAGTATCCC
CAATAGTAAAAATTTGATATTTTGAAAATAAAAACAAGGTTGAAGTATCCCCTCAGAAAATAACA
GGGTTGGAGAATCCCCAATGGTGAAAAA
Found at i:1423002 original size:33 final size:33
Alignment explanation
Indices: 1422965--1423029 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1422955 TACCACTGTT
** *
1422965 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATAACAAATTGTATCGATACAA
1422998 TGTATCGATACATAACAAATTGTATCGATACA
1 TGTATCGATACATAACAAATTGTATCGATACA
1423030 TTGTCCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATAACAAATTGTATCGATACAA
Found at i:1423003 original size:13 final size:13
Alignment explanation
Indices: 1422985--1423009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1422975 CATGGCACAT
1422985 TGTATCGATACAA
1 TGTATCGATACAA
1422998 TGTATCGATACA
1 TGTATCGATACA
1423010 TAACAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1424630 original size:15 final size:15
Alignment explanation
Indices: 1424610--1424644 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1424600 AACCATCAAA
1424610 GATGATGAAGATAAT
1 GATGATGAAGATAAT
**
1424625 GATGATGGTGATAAT
1 GATGATGAAGATAAT
1424640 GATGA
1 GATGA
1424645 AGTTGACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:1431806 original size:13 final size:13
Alignment explanation
Indices: 1431788--1431843 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
1431778 TGGCATATTA
1431788 TATCGATACAATG
1 TATCGATACAATG
1431801 TATCGATAC-ATG
1 TATCGATACAATG
* *
1431813 --GC-AT--ATTG
1 TATCGATACAATG
1431821 TATCGATACAATG
1 TATCGATACAATG
1431834 TATCGATACA
1 TATCGATACA
1431844 TAACAAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 22 0.67
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1431824 original size:20 final size:20
Alignment explanation
Indices: 1431765--1431830 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1431755 CTACCACTAT
1431765 TTGTATCGATACATGGCATA
1 TTGTATCGATACATGGCATA
*
1431785 TTATATCGAT--A---CA-A
1 TTGTATCGATACATGGCATA
1431799 -TGTATCGATACATGGCATA
1 TTGTATCGATACATGGCATA
1431818 TTGTATCGATACA
1 TTGTATCGATACA
1431831 ATGTATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 3 0.08
18 3 0.08
19 1 0.03
20 21 0.57
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGCATA
Found at i:1431854 original size:33 final size:33
Alignment explanation
Indices: 1431766--1431861 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
1431756 TACCACTATT
*
1431766 TGTATCGATACATGGCATATTATATCGATACAA
1 TGTATCGATACATGGCATATTGTATCGATACAA
1431799 TGTATCGATACATGGCATATTGTATCGATACAA
1 TGTATCGATACATGGCATATTGTATCGATACAA
** *
1431832 TGTATCGATACATAACAAATTGTATCGATA
1 TGTATCGATACATGGCATATTGTATCGATA
1431862 AATTGTCCTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGGCATATTGTATCGATACAA
Found at i:1434739 original size:20 final size:21
Alignment explanation
Indices: 1434705--1434758 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1434695 CATTTTAGGC
*
1434705 ATGTATCGAAACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
1434725 ATGTATCGATGCATTTACTAT
1 ATGTATCGATACATTCACTAT
*
1434746 TTGTATCGATACA
1 ATGTATCGATACA
1434759 AATTGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:1441036 original size:10 final size:10
Alignment explanation
Indices: 1440991--1441019 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1440981 CTAAGATCCC
1440991 TTCATCAAAA
1 TTCATCAAAA
1441001 TTCATCAAAA
1 TTCATCAAAA
1441011 TTCATCAAA
1 TTCATCAAA
1441020 TCTTCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (10 bp):
TTCATCAAAA
Found at i:1442802 original size:31 final size:31
Alignment explanation
Indices: 1442767--1442825 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1442757 AATAAATTTT
1442767 TTATCAAGGGGGAGAAAATCTTTTTAACCGA
1 TTATCAAGGGGGAGAAAATCTTTTTAACCGA
* *
1442798 TTATCAAGGGGGAGAAATTTTTTTTAAC
1 TTATCAAGGGGGAGAAAATCTTTTTAAC
1442826 GAGAGCCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (31 bp):
TTATCAAGGGGGAGAAAATCTTTTTAACCGA
Found at i:1443427 original size:20 final size:20
Alignment explanation
Indices: 1443388--1443437 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1443378 TATGCTTTGC
* *
1443388 ATCGATACAT-GTTCATTGT
1 ATCGATACATGGATAATTGT
1443407 ATCGATACATGGATAATTGT
1 ATCGATACATGGATAATTGT
1443427 ATCGATACATG
1 ATCGATACATG
1443438 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
ATCGATACATGGATAATTGT
Found at i:1443501 original size:13 final size:13
Alignment explanation
Indices: 1443483--1443534 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
1443473 GATACATGGC
*
1443483 ACATTGTATTGAT
1 ACATTGTATCGAT
1443496 ACATTGTATCGAT
1 ACATTGTATCGAT
1443509 ACA-TG-AT-G--
1 ACATTGTATCGAT
1443517 A-ATTGTATCGAT
1 ACATTGTATCGAT
1443529 ACATTG
1 ACATTG
1443535 CTTCAAACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 19 0.59
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1443503 original size:33 final size:32
Alignment explanation
Indices: 1443466--1443534 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
1443456 CTACCACTGT
*
1443466 TTGTATCGATACATG-GCACATTGTATTGATACA
1 TTGTATCGATACATGAG-A-ATTGTATCGATACA
1443499 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGA-GAATTGTATCGATACA
1443532 TTG
1 TTG
1443535 CTTCAAACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACATGAGAATTGTATCGATACA
Found at i:1447818 original size:16 final size:16
Alignment explanation
Indices: 1447793--1447836 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1447783 GCCTGAACCA
*
1447793 AGATAACCCAAACCCG
1 AGATAGCCCAAACCCG
*
1447809 AGATAGCCCAAACTCG
1 AGATAGCCCAAACCCG
1447825 AGATAGCCCAAA
1 AGATAGCCCAAA
1447837 TATGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.43, C:0.32, G:0.16, T:0.09
Consensus pattern (16 bp):
AGATAGCCCAAACCCG
Found at i:1449277 original size:20 final size:20
Alignment explanation
Indices: 1449254--1449326 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1449244 ACAATTCAAA
1449254 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1449274 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1449295 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1449315 GTATCGATACAT
1 GTATCGATACAT
1449327 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1449298 original size:21 final size:21
Alignment explanation
Indices: 1449272--1449347 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1449262 ACATGTTGCA
1449272 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1449293 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1449313 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1449334 TTGTATCGATACAT
1 ATGTATCGATACAT
1449348 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1449305 original size:41 final size:41
Alignment explanation
Indices: 1449254--1449347 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1449244 ACAATTCAAA
*
1449254 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1449295 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1449336 GTATCGATACAT
1 GTATCGATACAT
1449348 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1449404 original size:13 final size:13
Alignment explanation
Indices: 1449386--1449411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1449376 TACAGCAAGT
1449386 ATGTATCGATACA
1 ATGTATCGATACA
1449399 ATGTATCGATACA
1 ATGTATCGATACA
1449412 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1453492 original size:15 final size:15
Alignment explanation
Indices: 1453472--1453502 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1453462 TAAAAATGTC
*
1453472 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1453487 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1453502 C
1 C
1453503 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1455536 original size:20 final size:20
Alignment explanation
Indices: 1455510--1455587 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
1455500 AATGTCCAAA
1455510 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
1455530 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
1455555 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
1455575 TTGTATCGATACA
1 ATGTATCGATACA
1455588 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:1455594 original size:13 final size:13
Alignment explanation
Indices: 1455576--1455613 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1455566 CATTTTTCTT
1455576 TGTATCGATACAA
1 TGTATCGATACAA
*
1455589 TGTATCGATACAC
1 TGTATCGATACAA
1455602 TGTATCGATACA
1 TGTATCGATACA
1455614 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1457426 original size:21 final size:21
Alignment explanation
Indices: 1457401--1457442 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1457391 AAATAAATTT
1457401 TTGTTGTGAATTACTTGATTA
1 TTGTTGTGAATTACTTGATTA
1457422 TTGTTGTGAATTACTTGATTA
1 TTGTTGTGAATTACTTGATTA
1457443 AGGGGGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (21 bp):
TTGTTGTGAATTACTTGATTA
Found at i:1458100 original size:20 final size:20
Alignment explanation
Indices: 1458077--1458149 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1458067 ACAATTCAAA
1458077 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1458097 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1458118 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1458138 GTATCGATACAT
1 GTATCGATACAT
1458150 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1458121 original size:21 final size:21
Alignment explanation
Indices: 1458095--1458170 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1458085 ACATGTTGCA
1458095 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1458116 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1458136 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1458157 TTGTATCGATACAT
1 ATGTATCGATACAT
1458171 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1458128 original size:41 final size:41
Alignment explanation
Indices: 1458077--1458170 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1458067 ACAATTCAAA
*
1458077 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1458118 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1458159 GTATCGATACAT
1 GTATCGATACAT
1458171 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1458227 original size:13 final size:13
Alignment explanation
Indices: 1458209--1458234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1458199 TACAGCAAGT
1458209 ATGTATCGATACA
1 ATGTATCGATACA
1458222 ATGTATCGATACA
1 ATGTATCGATACA
1458235 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1460983 original size:14 final size:14
Alignment explanation
Indices: 1460964--1460994 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1460954 TTATCAATTG
1460964 TGAGAAGTGAGAAC
1 TGAGAAGTGAGAAC
*
1460978 TGAGAATTGAGAAC
1 TGAGAAGTGAGAAC
1460992 TGA
1 TGA
1460995 AGATTTGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.19
Consensus pattern (14 bp):
TGAGAAGTGAGAAC
Found at i:1461487 original size:24 final size:24
Alignment explanation
Indices: 1461435--1461496 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
1461425 TTTAAGGATA
*
1461435 AATATTAAAT-TATATAAAAACGAT
1 AATATTAAATATAAATAAAAAC-AT
*
1461459 TATATTAAATATAAAATAAAAA-AT
1 AATATTAAATAT-AAATAAAAACAT
1461483 AATA-TAAA-ATAAAT
1 AATATTAAATATAAAT
1461497 TTAAATCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 4 0.12
22 2 0.06
23 4 0.12
24 14 0.42
25 1 0.03
26 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
AATATTAAATATAAATAAAAACAT
Found at i:1462102 original size:26 final size:26
Alignment explanation
Indices: 1462049--1462100 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1462039 ATTTAGATAT
* *
1462049 ATTTATAAATTAAGTTATTTATTTAA
1 ATTTAAAAATTAAGTTATATATTTAA
*
1462075 ATTTAAAAATTAATTTA-ATATTTAA
1 ATTTAAAAATTAAGTTATATATTTAA
1462100 A
1 A
1462101 ATATTGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTAAAAATTAAGTTATATATTTAA
Found at i:1462491 original size:22 final size:20
Alignment explanation
Indices: 1462457--1462520 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 20
1462447 AAATTATTAC
*
1462457 TATAATTATATAAAATATAA
1 TATAATTAAATAAAATATAA
1462477 TATGAATTGAAATAAAATA-AA
1 TAT-AATT-AAATAAAATATAA
1462498 -A-AATTAAA-AAAATATAA
1 TATAATTAAATAAAATATAA
1462515 TATAAT
1 TATAAT
1462521 ATAATAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 6 0.16
17 5 0.13
18 5 0.13
19 3 0.08
20 4 0.11
21 6 0.16
22 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TATAATTAAATAAAATATAA
Found at i:1471040 original size:42 final size:42
Alignment explanation
Indices: 1470984--1471102 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1470974 TTCTTCTCTC
* * *
1470984 CTCCTTCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1471026 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1471068 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1471103 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1471043 original size:12 final size:11
Alignment explanation
Indices: 1471017--1471092 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1471007 TCTATTATCT
*
1471017 CTCCTGTCTCTC
1 CTCCTATCTC-C
1471029 CTCCTATCATCC
1 CTCCTATC-TCC
1471041 CTCCTATCT--
1 CTCCTATCTCC
*
1471050 CTACTATCT--
1 CTCCTATCTCC
*
1471059 CTCCTGTCTCTC
1 CTCCTATCTC-C
1471071 CTCCTATCATCC
1 CTCCTATC-TCC
*
1471083 CTCCTCTCTC
1 CTCCTATCTC
1471093 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1471044 original size:24 final size:24
Alignment explanation
Indices: 1471008--1471093 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1470998 CCTCCTCTCT
* *
1471008 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1471032 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1471053 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1471074 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1471094 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1471068 original size:18 final size:18
Alignment explanation
Indices: 1470999--1471069 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1470989 TCTGTCATCC
* *
1470999 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1471017 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1471039 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1471059 CTCCTGTCTCT
1 CTCCTGTCTCT
1471070 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1473111 original size:16 final size:16
Alignment explanation
Indices: 1473087--1473120 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1473077 AAAGCTGAAG
1473087 CTTGAGTGCTAGCTTT
1 CTTGAGTGCTAGCTTT
*
1473103 CTTGGGTGCTAGCTTT
1 CTTGAGTGCTAGCTTT
1473119 CT
1 CT
1473121 GAATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44
Consensus pattern (16 bp):
CTTGAGTGCTAGCTTT
Found at i:1474561 original size:2 final size:2
Alignment explanation
Indices: 1474554--1474591 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1474544 TTCAATTAAC
1474554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1474592 CCATAAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1475393 original size:22 final size:21
Alignment explanation
Indices: 1475355--1475401 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1475345 AAAATTTATT
1475355 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1475376 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
1475396 -AAATTT
1 TAAATTT
1475402 TATTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 4 0.16
20 3 0.12
21 12 0.48
22 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1476918 original size:2 final size:2
Alignment explanation
Indices: 1476911--1476957 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1476901 AACGAGATAA
*
1476911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1476953 AT AT A
1 AT AT A
1476958 ACGCTTAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1477025 original size:2 final size:2
Alignment explanation
Indices: 1477018--1477042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1477008 ACTAACATAG
1477018 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1477043 GAATACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1480273 original size:19 final size:19
Alignment explanation
Indices: 1480249--1480307 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1480239 AAAATATGGC
1480249 TTTTCTATCACCATGCATT
1 TTTTCTATCACCATGCATT
* *
1480268 TTTTCTCTTA--ATG-ATAT
1 TTTTCTATCACCATGCAT-T
1480285 TTTGTC-ATCACCATGCATT
1 TTT-TCTATCACCATGCATT
1480304 TTTT
1 TTTT
1480308 TCTTTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 11
0.67 0.09 0.24
Matches are distributed among these distances:
16 2 0.06
17 9 0.29
18 3 0.10
19 15 0.48
20 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (19 bp):
TTTTCTATCACCATGCATT
Done.