Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009457.1 Hibiscus syriacus cultivar Beakdansim tig00113716_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 528656
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:219761 original size:33 final size:33
Alignment explanation
Indices: 219723--219786 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
219713 AAAATAAATT
* *
219723 AACGTATTTTAGTCCTATTAAAACACTAAAACC
1 AACGTATCTGAGTCCTATTAAAACACTAAAACC
*
219756 AACGTATCTGAGTCCTATTAAAATACTAAAA
1 AACGTATCTGAGTCCTATTAAAACACTAAAA
219787 TCGAAGCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.30
Consensus pattern (33 bp):
AACGTATCTGAGTCCTATTAAAACACTAAAACC
Found at i:219801 original size:33 final size:33
Alignment explanation
Indices: 219723--219803 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
219713 AAAATAAATT
* *
219723 AACGTATTTTAGTCCTATTAAAACACTAAAACC
1 AACGCATTTGAGTCCTATTAAAACACTAAAACC
* * * *
219756 AACGTATCTGAGTCCTATTAAAATACTAAAATCG
1 AACGCATTTGAGTCCTATTAAAACACTAAAA-CC
219790 AA-GCATTTGAGTCC
1 AACGCATTTGAGTCC
219804 AAGTAGGACT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 38 0.93
34 3 0.07
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30
Consensus pattern (33 bp):
AACGCATTTGAGTCCTATTAAAACACTAAAACC
Found at i:220115 original size:26 final size:25
Alignment explanation
Indices: 220086--220148 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
220076 TTTTTATTTC
*
220086 ATTTTTTATTTAT-TTACTTTATATAT
1 ATTTTTTATTTATCTTAATTT-TA-AT
* *
220112 ATTTTTCATTTTCTCTTAATTTTAAT
1 ATTTTTTA-TTTATCTTAATTTTAAT
220138 ATTTTTTATTT
1 ATTTTTTATTT
220149 CGTTTTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 3 0.10
26 16 0.52
27 6 0.19
28 6 0.19
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTTTTTATTTATCTTAATTTTAAT
Found at i:220227 original size:39 final size:40
Alignment explanation
Indices: 220142--220220 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
220132 TTTAATATTT
**
220142 TTTATTTCGTTTTACATTGTTTTATATATATATGTATATA
1 TTTATTTATTTTTACATTGTTTTATATATATATGTATATA
*
220182 TTTATTTATTTTTTCATT-TTTTAT-TA-ATAT-TATTATA
1 TTTATTTATTTTTACATTGTTTTATATATATATGTA-TATA
220219 TT
1 TT
220221 AATATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 2 0.06
37 10 0.29
38 2 0.06
39 6 0.17
40 15 0.43
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (40 bp):
TTTATTTATTTTTACATTGTTTTATATATATATGTATATA
Found at i:221005 original size:18 final size:17
Alignment explanation
Indices: 220972--221014 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
220962 GTCTTTTCTC
*
220972 TTTATTTTTCTATTTTT
1 TTTAATTTTCTATTTTT
220989 TTTAATTTTCTATTTTT
1 TTTAATTTTCTATTTTT
221006 TTTAATTTT
1 TTTAATTTT
221015 GACACGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTAATTTTCTATTTTT
Found at i:221030 original size:21 final size:23
Alignment explanation
Indices: 221006--221048 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
220996 TTCTATTTTT
221006 TTTA-ATTT-TGACACGTTTATC
1 TTTATATTTGTGACACGTTTATC
*
221027 TTTATCTTTGTGACACGTTTAT
1 TTTATATTTGTGACACGTTTAT
221049 ATCTATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (23 bp):
TTTATATTTGTGACACGTTTATC
Found at i:221044 original size:23 final size:24
Alignment explanation
Indices: 221014--221082 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
221004 TTTTTAATTT
* *
221014 TGACACGTTTATCTTTATCTTT-G
1 TGACACGTTTATATCTATCTTTCG
221037 TGACACGTTTATATCTATCTTTCG
1 TGACACGTTTATATCTATCTTTCG
* * *
221061 TGACATGTTTTTATCTACCTTT
1 TGACACGTTTATATCTATCTTT
221083 TGGTAGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.51
Consensus pattern (24 bp):
TGACACGTTTATATCTATCTTTCG
Found at i:222250 original size:19 final size:18
Alignment explanation
Indices: 222217--222255 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
222207 TTTTAAAAAA
222217 AAACTTAAATTTAAATTT
1 AAACTTAAATTTAAATTT
*
222235 AAACTTGAATTTTAAATTT
1 AAACTT-AAATTTAAATTT
222254 AA
1 AA
222256 TTTATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
AAACTTAAATTTAAATTT
Found at i:222755 original size:2 final size:2
Alignment explanation
Indices: 222748--222772 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
222738 AACCACTTTC
222748 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
222773 GTGTGATATA
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:222891 original size:160 final size:160
Alignment explanation
Indices: 222627--222922 Score: 565
Period size: 160 Copynumber: 1.9 Consensus size: 160
222617 GATCTAGGTG
*
222627 ACTAATTTTGTATCAATAGTTATAAGACAATGTACTAATTATATTTTAATTTAGGTTTATAATTG
1 ACTAATTTTGTATCAATAGTTATAAGACAATGTACTAATTATATTTTAATTTAAGTTTATAATTG
222692 TAAATCTTCATTATAATTCTAGATATTTTCTAATTTTAATAAAACAAACCACTTTCTATATATAT
66 TAAATCTTCATTATAATTCTAGATATTTTCTAATTTTAATAAAACAAACCACTTTCTATATATAT
222757 ATATATATATATATATGTGTGATATAGATA
131 ATATATATATATATATGTGTGATATAGATA
**
222787 ACTAATTTTGTATCAATAGTTATAAGACAATGTACTAATTATATTTTAATTTAAGTTTATGCTTG
1 ACTAATTTTGTATCAATAGTTATAAGACAATGTACTAATTATATTTTAATTTAAGTTTATAATTG
222852 TAAATCTTCATTATAATTCTAGATATTTTCTAATTTTAATAAAACAAACCACTTTCTATATATAT
66 TAAATCTTCATTATAATTCTAGATATTTTCTAATTTTAATAAAACAAACCACTTTCTATATATAT
222917 ATATAT
131 ATATAT
222923 GCGCCAAATC
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 133 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (160 bp):
ACTAATTTTGTATCAATAGTTATAAGACAATGTACTAATTATATTTTAATTTAAGTTTATAATTG
TAAATCTTCATTATAATTCTAGATATTTTCTAATTTTAATAAAACAAACCACTTTCTATATATAT
ATATATATATATATATGTGTGATATAGATA
Found at i:225725 original size:27 final size:27
Alignment explanation
Indices: 225687--225745 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
225677 CATTGGCGTG
225687 GGAACCATCAAATTGAAGATGTATGAT
1 GGAACCATCAAATTGAAGATGTATGAT
225714 GGAACCATCAAATTGAAGATGTATGAT
1 GGAACCATCAAATTGAAGATGTATGAT
225741 GGAAC
1 GGAAC
225746 AATTAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (27 bp):
GGAACCATCAAATTGAAGATGTATGAT
Found at i:228768 original size:21 final size:20
Alignment explanation
Indices: 228744--228785 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
228734 GTCATACAAC
*
228744 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
228765 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
228785 T
1 T
228786 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:230312 original size:2 final size:2
Alignment explanation
Indices: 230305--230333 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
230295 TGAAGTTAAT
230305 TA TA 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 TA TA T
230334 CAAGACAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:231826 original size:47 final size:46
Alignment explanation
Indices: 231743--231879 Score: 222
Period size: 47 Copynumber: 3.0 Consensus size: 46
231733 GGGCTACTGC
*
231743 TTCAATGATTGGTGGTCGGCCATCTTCCCATATCTACTTGGCTTTG
1 TTCAATGATTGGTGGTAGGCCATCTTCCCATATCTACTTGGCTTTG
* *
231789 TTCAATGATTGGTGGTTGCCCGATCTTCCCATATCTACTTGGCTTTG
1 TTCAATGATTGGTGGTAGGCC-ATCTTCCCATATCTACTTGGCTTTG
*
231836 TTCAATGCTTGGTGGTAGGCCATCTTCCCATATCTACTT-GCTTT
1 TTCAATGATTGGTGGTAGGCCATCTTCCCATATCTACTTGGCTTT
231880 TTTAAGTTGC
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
45 5 0.06
46 37 0.44
47 43 0.51
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.40
Consensus pattern (46 bp):
TTCAATGATTGGTGGTAGGCCATCTTCCCATATCTACTTGGCTTTG
Found at i:242764 original size:7 final size:7
Alignment explanation
Indices: 242749--242781 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
242739 ATCTGGTGGA
*
242749 GTTTTCT
1 GTTTCCT
242756 GTTTCCT
1 GTTTCCT
242763 GTTTCCT
1 GTTTCCT
242770 GTTTCCT
1 GTTTCCT
242777 GTTTC
1 GTTTC
242782 TTGGAGACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.15, T:0.61
Consensus pattern (7 bp):
GTTTCCT
Found at i:261758 original size:13 final size:13
Alignment explanation
Indices: 261740--261765 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
261730 CATTGTTCAT
261740 TGAATACTTGACA
1 TGAATACTTGACA
261753 TGAATACTTGACA
1 TGAATACTTGACA
261766 CAACATGAAT
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):
TGAATACTTGACA
Found at i:267032 original size:20 final size:23
Alignment explanation
Indices: 266984--267030 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
266974 TTCATTATTT
266984 AACATTTCTATAATACTATTAGAAA
1 AACATTTCTATAATACTATT--AAA
267009 AACATTTCTATAATA-TA-TAAA
1 AACATTTCTATAATACTATTAAA
267030 A
1 A
267031 CACTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
23 1 0.05
24 2 0.09
25 15 0.68
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
AACATTTCTATAATACTATTAAA
Found at i:268522 original size:28 final size:28
Alignment explanation
Indices: 268491--268548 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
268481 TCAAAGAAAA
268491 CAACACCAACATTCTACTCATAAAATGG
1 CAACACCAACATTCTACTCATAAAATGG
268519 CAACACCAACATTCTACTCATAAAATGG
1 CAACACCAACATTCTACTCATAAAATGG
268547 CA
1 CA
268549 GACAGATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (28 bp):
CAACACCAACATTCTACTCATAAAATGG
Found at i:283875 original size:4 final size:4
Alignment explanation
Indices: 283848--283913 Score: 105
Period size: 4 Copynumber: 16.5 Consensus size: 4
283838 TATAAATTTC
* * *
283848 ATAT ATAC ATAT ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
283896 ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT AT
283914 TTTTTCGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:293493 original size:19 final size:17
Alignment explanation
Indices: 293459--293498 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
293449 ATGTGAATTG
*
293459 TAAAACATAAAATAAAT
1 TAAAAAATAAAATAAAT
293476 TAAAAAATAATAATTAAAT
1 TAAAAAATAA-AA-TAAAT
293495 TAAA
1 TAAA
293499 CGGGCTACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAAATAAAATAAAT
Found at i:311156 original size:31 final size:31
Alignment explanation
Indices: 311115--311175 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
311105 AATATGGTCT
* *
311115 CTAAAGTTATCGATCCATTCGATTTTAATCG
1 CTAAAATTATCGATCCATTCAATTTTAATCG
**
311146 CTAAAATTATCGATCTGTTCAATTTTAATC
1 CTAAAATTATCGATCCATTCAATTTTAATC
311176 CCTCAACCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (31 bp):
CTAAAATTATCGATCCATTCAATTTTAATCG
Found at i:330966 original size:16 final size:16
Alignment explanation
Indices: 330945--330977 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
330935 TATACATCGA
*
330945 ATAGTATGATGTAATT
1 ATAGTACGATGTAATT
330961 ATAGTACGATGTAATT
1 ATAGTACGATGTAATT
330977 A
1 A
330978 ACAAAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (16 bp):
ATAGTACGATGTAATT
Found at i:331298 original size:15 final size:16
Alignment explanation
Indices: 331280--331313 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
331270 TTTCTAAATA
331280 TTTTAATATT-TTTAT
1 TTTTAATATTATTTAT
331295 TTTTAATATTATTTAT
1 TTTTAATATTATTTAT
331311 TTT
1 TTT
331314 ACTCGTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATATTATTTAT
Found at i:333369 original size:10 final size:10
Alignment explanation
Indices: 333354--333392 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
333344 TATTTAATAA
333354 ATAAACGAAC
1 ATAAACGAAC
333364 ATAAACGAAC
1 ATAAACGAAC
333374 ----ACGAAC
1 ATAAACGAAC
333380 ATAAACGAAC
1 ATAAACGAAC
333390 ATA
1 ATA
333393 TTTTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.24
10 19 0.76
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:333379 original size:16 final size:16
Alignment explanation
Indices: 333358--333390 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
333348 TAATAAATAA
333358 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
333374 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
333390 A
1 A
333391 TATTTTTTTC
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:333483 original size:16 final size:16
Alignment explanation
Indices: 333458--333522 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
333448 TAATAAATAA
*
333458 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
333474 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
333490 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
333506 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
333522 A
1 A
333523 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:333487 original size:10 final size:10
Alignment explanation
Indices: 333454--333528 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
333444 CATTTAATAA
*
333454 ATAAACGAAT
1 ATAAACGAAC
333464 ATAAACGAAC
1 ATAAACGAAC
333474 ----ACGAAC
1 ATAAACGAAC
333480 ATAAACGAAC
1 ATAAACGAAC
** *
333490 ACGAAC-ATAA
1 ATAAACGA-AC
333500 ATGAACACGAAC
1 AT-AA-ACGAAC
333512 ATAAACGAAC
1 ATAAACGAAC
333522 ATAAACG
1 ATAAACG
333529 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:334067 original size:24 final size:24
Alignment explanation
Indices: 334040--334088 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
334030 ATAAATGAAT
*
334040 GAGCATAAGCGAACATAACCGAAC
1 GAGCATAACCGAACATAACCGAAC
334064 GAGCATAACCGAACATAACCGAAC
1 GAGCATAACCGAACATAACCGAAC
334088 G
1 G
334089 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.27, G:0.20, T:0.08
Consensus pattern (24 bp):
GAGCATAACCGAACATAACCGAAC
Found at i:340258 original size:36 final size:34
Alignment explanation
Indices: 340205--340272 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
340195 TTAAACTAGG
*
340205 TTTAAGGTTTATGATTTAGAGGTTATAGAGTTATAT
1 TTTAAGGTTTATAATTTAG-GGTTATA-AGTTATAT
* *
340241 TTTATGGTTTATAATTTAGGGTTTTAAGTTAT
1 TTTAAGGTTTATAATTTAGGGTTATAAGTTAT
340273 GATAGGGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 6 0.21
35 6 0.21
36 17 0.59
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (34 bp):
TTTAAGGTTTATAATTTAGGGTTATAAGTTATAT
Found at i:347140 original size:5 final size:5
Alignment explanation
Indices: 347082--347139 Score: 98
Period size: 5 Copynumber: 11.6 Consensus size: 5
347072 ATCTACACAC
*
347082 ATACG ATACG ATACG ATACG ATACG ATACG ATACG ATACG ATACG ATATG
1 ATACG ATACG ATACG ATACG ATACG ATACG ATACG ATACG ATACG ATACG
*
347132 ATATG ATA
1 ATACG ATA
347140 TAATATAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (5 bp):
ATACG
Found at i:348830 original size:3 final size:3
Alignment explanation
Indices: 348822--348846 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
348812 ATAATTAAGT
348822 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
348847 TTTTTAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:349257 original size:134 final size:131
Alignment explanation
Indices: 349008--349392 Score: 474
Period size: 131 Copynumber: 2.9 Consensus size: 131
348998 ACGACACTGC
* *
349008 TCATACGTGATGAAGA--ATTATGGTTGTCTAAGGGTGACACTG-CTCCTACGTGATGAGGAGAT
1 TCATACGTGATGAAGACGA-T-TGGTTATCTAAGGGTGACAC-GACTCCTACGTGATGAGGAGGT
* * * * *
349070 TTGGTCGGTGGATGACACGATTCCTACGCGATGAGGACGACTGACCATATTTAGGAATGGTGATA
63 TTGGTCGGTGGATGACACGATTCCTACGTGATGAGGATGACTGGCCATCTTTAGG---GATGATA
*
349135 ATACGAT
125 ACACGAT
* *
349142 TCATACGTGATGAAGACGATTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCAT
1 TCATACGTGATGAAGACGATTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGT-TT
* *
349207 -GTTGGTGGATGACACGATTCCTACGTGATGAGGATG-GTAGGCCATCTTTAGGGATGATAACAC
65 GGTCGGTGGATGACACGATTCCTACGTGATGAGGATGACT-GGCCATCTTTAGGGATGATAACAC
349270 GAT
129 GAT
** * * * * *
349273 TTTTACGTGATGAGGACGACTGATTATCTAAGGGTGACACAACTCTTACGTGATGAGGAGGTTTG
1 TCATACGTGATGAAGACGATTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTTTG
* *
349338 GTCGGTGGATGACACGGTTCCTATGTGATGAGGATGACTGGCCATCTTTAGGGAT
66 GTCGGTGGATGACACGATTCCTACGTGATGAGGATGACTGGCCATCTTTAGGGAT
349393 AATATTTCAA
Statistics
Matches: 219, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
130 1 0.00
131 115 0.53
132 1 0.00
133 2 0.01
134 97 0.44
135 2 0.01
136 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.28
Consensus pattern (131 bp):
TCATACGTGATGAAGACGATTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTTTG
GTCGGTGGATGACACGATTCCTACGTGATGAGGATGACTGGCCATCTTTAGGGATGATAACACGA
T
Found at i:349495 original size:20 final size:21
Alignment explanation
Indices: 349470--349510 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
349460 TGTTTCAAGA
349470 GAAAC-TGTCTCAAGAGAAAC
1 GAAACTTGTCTCAAGAGAAAC
* *
349490 GAAACTTGTTTCAAGGGAAAC
1 GAAACTTGTCTCAAGAGAAAC
349511 AGACTCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
GAAACTTGTCTCAAGAGAAAC
Found at i:349501 original size:65 final size:64
Alignment explanation
Indices: 349397--349640 Score: 298
Period size: 65 Copynumber: 3.8 Consensus size: 64
349387 AGGGATAATA
* *
349397 TTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGATGAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGA-CTCAAAGATG-T
349461 G
64 G
* * **
349462 TTTCAAGAGAAACTGTCTCAAGAGAAACGAAACTTGTTTCAAGGGAAACAGACTCAACATTTGTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGACTCAA-AGATGTG
* * * *
349527 TTTCAAGA-AAATCTGTCTCAAGGGAGACAAAATTTGTTTCGAA-GGAACCAGACTCAAAGATTT
1 TTTCAAGAGAAA-CTGTCTCAAGAGAGACAAAACTTGTTTC-AAGGGAAACAGACTCAAAGATGT
349590 G
64 G
* *
349591 TTTTAAGAGAAACTGTCTCAA-AGGAGACGAAACTTGTTTCAAGGGAAACA
1 TTTCAAGAGAAACTGTCTCAAGA-GAGACAAAACTTGTTTCAAGGGAAACA
349641 ATTTTGAAAT
Statistics
Matches: 153, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
63 2 0.01
64 44 0.29
65 100 0.65
66 7 0.05
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (64 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAGACTCAAAGATGTG
Found at i:349634 original size:129 final size:130
Alignment explanation
Indices: 349397--349640 Score: 363
Period size: 129 Copynumber: 1.9 Consensus size: 130
349387 AGGGATAATA
*
349397 TTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATG
349462 TTTCAAGAGAAACTGTCTCAAGAGAAACGAAACTTGTTTCAAGGGAAACAGACTCAACATTTGTG
66 TTTCAAGAGAAACTGTCTCAAGAGAAACGAAACTTGTTTCAAGGGAAACAGACTCAACATTTGTG
* *
349527 TTTCAAGA-AAATCTGTCTCAAGGGAGACAAAATTTGTTTCGAA-GGAACCAGA-CTCAAAGAT-
1 TTTCAAGAGAAA-CTGTCTCAAGAGAGACAAAATTTGTTTC-AAGGGAAAC-GATCTCAAAGATG
* * *
349588 TTGTTTTAAGAGAAACTGTCTCAA-AGGAGACGAAACTTGTTTCAAGGGAAACA
63 ATGTTTCAAGAGAAACTGTCTCAAGA-GAAACGAAACTTGTTTCAAGGGAAACA
349641 ATTTTGAAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
128 1 0.01
129 51 0.49
130 48 0.46
131 4 0.04
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (130 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATG
TTTCAAGAGAAACTGTCTCAAGAGAAACGAAACTTGTTTCAAGGGAAACAGACTCAACATTTGTG
Found at i:349653 original size:129 final size:128
Alignment explanation
Indices: 349397--349692 Score: 361
Period size: 129 Copynumber: 2.3 Consensus size: 128
349387 AGGGATAATA
349397 TTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATG
1 TTTCAAGA-AAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATG
349462 TTTCAAGAGAAACTGTCTCAAGAGAAACGAAACTTGTTTCAAGGGAAACAGACTCAACATTTGT
65 TTTCAAGAGAAACTGTCTCAAGAGAAACGAAACTTGTTTCAAGGGAAACAGACTCAACATTTGT
* * *
349526 GTTTCAAGAAAATCTGTCTCAAGGGAGACAAAATTTGTTTCGAA-GGAACCAGA-CTCAAAGAT-
1 -TTTCAAGAAAA-CTGTCTTAAGAGAGACAAAATTTGTTTC-AAGGGAAAC-GATCTCAAAGATG
* * * * *
349588 TTGTTTTAAGAGAAACTGTCTCAA-AGGAGACGAAACTTGTTTCAAGGGAAACA-ATTTTGAA-A
62 ATGTTTCAAGAGAAACTGTCTCAAGA-GAAACGAAACTTGTTTCAAGGGAAACAGA--CTCAACA
349650 TTTGT
124 TTTGT
* * * * *
349655 CTTAAAGAAAAATGTCTTAAGCGAGACGAAATTTGTTT
1 TTTCAAGAAAACTGTCTTAAGAGAGACAAAATTTGTTT
349693 TGAGAGAAAT
Statistics
Matches: 146, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
127 23 0.16
128 11 0.08
129 57 0.39
130 51 0.35
131 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (128 bp):
TTTCAAGAAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGT
TTCAAGAGAAACTGTCTCAAGAGAAACGAAACTTGTTTCAAGGGAAACAGACTCAACATTTGT
Found at i:349707 original size:36 final size:37
Alignment explanation
Indices: 349659--349753 Score: 131
Period size: 36 Copynumber: 2.6 Consensus size: 37
349649 ATTTGTCTTA
* * *
349659 AAGAAAAATGTCTTAAGCGAGACGAAATTTG-TTTTG
1 AAGAAAAATGTCTCAAGCGAGACAAAACTTGTTTTTG
*
349695 -AGAGAAATTGTCTCAAGCGAGACAAAACTTGTTTTTG
1 AAGA-AAAATGTCTCAAGCGAGACAAAACTTGTTTTTG
349732 AAGAAAAATGTCTCAAGCGAGA
1 AAGAAAAATGTCTCAAGCGAGA
349754 TTAAATGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
35 3 0.06
36 23 0.45
37 22 0.43
38 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (37 bp):
AAGAAAAATGTCTCAAGCGAGACAAAACTTGTTTTTG
Found at i:349767 original size:37 final size:35
Alignment explanation
Indices: 349659--349753 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 35
349649 ATTTGTCTTA
* *
349659 AAGAAAAATGTCTTAAGCGAGACGAAATTTGTTTTG
1 AAGAAAAATGTCTCAAGCGAGACAAAATTT-TTTTG
*
349695 -AGAGAAATTGTCTCAAGCGAGACAAAACTTGTTTTTG
1 AAGA-AAAATGTCTCAAGCGAGACAAAA-TT-TTTTTG
349732 AAGAAAAATGTCTCAAGCGAGA
1 AAGAAAAATGTCTCAAGCGAGA
349754 TTAAATGTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
35 3 0.06
36 20 0.39
37 24 0.47
38 4 0.08
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (35 bp):
AAGAAAAATGTCTCAAGCGAGACAAAATTTTTTTG
Found at i:351033 original size:26 final size:29
Alignment explanation
Indices: 351004--351056 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
350994 GCATGTGTTT
351004 TTTG-TCCTT-TTTTTTCTT-TTTTTTCA
1 TTTGCTCCTTATTTTTTCTTCTTTTTTCA
* *
351030 TTTGCTCTTTATTTTTTTTTCTTTTTT
1 TTTGCTCCTTATTTTTTCTTCTTTTTT
351057 TTCTGTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
27 4 0.18
28 8 0.36
29 6 0.27
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (29 bp):
TTTGCTCCTTATTTTTTCTTCTTTTTTCA
Found at i:351348 original size:13 final size:13
Alignment explanation
Indices: 351330--351356 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
351320 GTATCCCAGG
351330 AGGATAAATTTTT
1 AGGATAAATTTTT
351343 AGGATAAATTTTT
1 AGGATAAATTTTT
351356 A
1 A
351357 TTAACTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AGGATAAATTTTT
Found at i:360084 original size:6 final size:6
Alignment explanation
Indices: 360073--360102 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
360063 AATGGGTGAT
*
360073 CAATGG CAATGG CAATGG CAATGC CAATGG
1 CAATGG CAATGG CAATGG CAATGG CAATGG
360103 GTGATTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (6 bp):
CAATGG
Found at i:382273 original size:2 final size:2
Alignment explanation
Indices: 382255--382304 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
382245 ATATGATGCA
* *
382255 AT AT CAT AT AT AA AT AT AT -T AT AT AT AT AA AT AT -T AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
382296 AT AT AT AT A
1 AT AT AT AT A
382305 GAAACTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:382273 original size:15 final size:15
Alignment explanation
Indices: 382255--382303 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
382245 ATATGATGCA
*
382255 ATATCATATATAAAT
1 ATATTATATATAAAT
382270 ATATTATATATATAA-
1 ATATTATATATA-AAT
*
382285 ATATTATATATATAT
1 ATATTATATATAAAT
382300 ATAT
1 ATAT
382304 AGAAACTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.90
16 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTATATATAAAT
Found at i:382280 original size:17 final size:19
Alignment explanation
Indices: 382255--382302 Score: 73
Period size: 17 Copynumber: 2.6 Consensus size: 19
382245 ATATGATGCA
382255 ATATCATATATAAATA-TAT
1 ATAT-ATATATAAATATTAT
382274 -TATATATATAAATATTAT
1 ATATATATATAAATATTAT
382292 ATATATATATA
1 ATATATATATA
382303 TAGAAACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.41
18 6 0.22
19 10 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATATATAAATATTAT
Found at i:382447 original size:35 final size:33
Alignment explanation
Indices: 382393--382595 Score: 129
Period size: 37 Copynumber: 5.9 Consensus size: 33
382383 TAATATTTTT
*
382393 TTTTGACAAAGTATA-ATATATAATTTTCTTAAAACA
1 TTTTGA-AAA-TATATATATATAA-TTT-TGAAAACA
382429 GTTTTCGAAAATATATATATATAATTTTGAAAACA
1 -TTTT-GAAAATATATATATATAATTTTGAAAACA
*
382464 TTTTTAAAATATATATGATATATAGTTTTGAAAACA
1 TTTTGAAAATATATAT-ATATA-A-TTTTGAAAACA
382500 -TTT----ATAT-TATATAGT--TTTT-AAAACA
1 TTTTGAAAATATATATATA-TAATTTTGAAAACA
* * *
382525 TTTTTGAAAATTATATAATATATAGTTTTTAAAATTA
1 -TTTTGAAAA-TATAT-ATATATAATTTTGAAAA-CA
*
382562 TTTTGAAAACTTATATAATATATAGTTTTGAAAA
1 TTTTGAAAA--TATAT-ATATATAATTTTGAAAA
382596 AAAACCTTTT
Statistics
Matches: 142, Mismatches: 4, Indels: 40
0.76 0.02 0.22
Matches are distributed among these distances:
25 6 0.04
26 4 0.03
27 3 0.02
29 3 0.02
30 4 0.03
31 5 0.04
32 3 0.02
33 13 0.09
34 14 0.10
35 15 0.11
36 31 0.22
37 39 0.27
38 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (33 bp):
TTTTGAAAATATATATATATAATTTTGAAAACA
Found at i:382493 original size:36 final size:36
Alignment explanation
Indices: 382404--382706 Score: 161
Period size: 41 Copynumber: 8.2 Consensus size: 36
382394 TTTGACAAAG
* * *
382404 TATAATATATAATTTTCTTAAAACAGTTTTCGAAAATATA
1 TATAATATAT-AGTTT-TGAAAACA-TTTT-TAAAATATA
382444 TAT-ATATA-A-TTTTGAAAACATTTTTAAAATATA
1 TATAATATATAGTTTTGAAAACATTTTTAAAATATA
*
382477 TATGATATATAGTTTTGAAAACA----T----T-TA
1 TATAATATATAGTTTTGAAAACATTTTTAAAATATA
*
382504 TAT--TATATAGTTTTTAAAACATTTTTGAAAAT-TA
1 TATAATATATAGTTTTGAAAACATTTTT-AAAATATA
* * *
382538 TATAATATATAGTTTTTAAAATTATTTTGAAAACT-TA
1 TATAATATATAGTTTTGAAAA-CATTTTTAAAA-TATA
* *
382575 TATAATATATAGTTTTGAAAAAAAACCTTTTTGAAAAAACTA
1 TATAATATATAGTTTTG----AAAACATTTTT-AAAATA-TA
* *
382617 TATAATATATAGTTTTAAAAAAACATTTTTTTGAAATATTA
1 TATAATATATAGTTTT--GAAAACA--TTTTTAAAATA-TA
** *
382658 TATAATATATAGTTTAAAAAAAACATTTTTGAAAAAACTA
1 TATAATATATAGTTT--TGAAAACATTTTT-AAAATA-TA
382698 TATAATATA
1 TATAATATA
382707 AAAAAACATT
Statistics
Matches: 214, Mismatches: 19, Indels: 60
0.73 0.06 0.20
Matches are distributed among these distances:
25 17 0.08
27 5 0.02
28 1 0.00
29 1 0.00
32 1 0.00
33 11 0.05
34 15 0.07
35 8 0.04
36 34 0.16
37 25 0.12
39 10 0.05
40 27 0.13
41 36 0.17
42 23 0.11
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (36 bp):
TATAATATATAGTTTTGAAAACATTTTTAAAATATA
Found at i:382523 original size:61 final size:62
Alignment explanation
Indices: 382440--382558 Score: 179
Period size: 61 Copynumber: 1.9 Consensus size: 62
382430 TTTTCGAAAA
*
382440 TATATATATATAATTTTGAAAACATTTTT-AAAATATATATGATATATAGTTTTGAAAACATT
1 TATATATATATAATTTTGAAAACATTTTTGAAAAT-TATATAATATATAGTTTTGAAAACATT
* * *
382502 TATAT-TATATAGTTTTTAAAACATTTTTGAAAATTATATAATATATAGTTTTTAAAA
1 TATATATATATAATTTTGAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAA
382559 TTATTTTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 42 0.81
62 10 0.19
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (62 bp):
TATATATATATAATTTTGAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATT
Found at i:382526 original size:25 final size:25
Alignment explanation
Indices: 382464--382527 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
382454 TTTGAAAACA
* *
382464 TTTTTAAAATATATATGATATATAG
1 TTTTTAAAACATTTATGATATATAG
*
382489 TTTTGAAAACATTTAT-ATTATATAG
1 TTTTTAAAACATTTATGA-TATATAG
382514 TTTTTAAAACATTT
1 TTTTTAAAACATTT
382528 TTGAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (25 bp):
TTTTTAAAACATTTATGATATATAG
Found at i:382565 original size:37 final size:38
Alignment explanation
Indices: 382489--382706 Score: 171
Period size: 36 Copynumber: 5.6 Consensus size: 38
382479 TGATATATAG
* * *
382489 TTTTGAAAACATT-TATATTATATAGTTTT-TAAAA-CAT
1 TTTTG-AAA-ATTATATAATATATAGTTTTAAAAAATTAT
*
382526 TTTTGAAAATTATATAATATATAGTTTT-TAAAATTA-
1 TTTTGAAAATTATATAATATATAGTTTTAAAAAATTAT
*
382562 TTTTGAAAACTTATATAATATATAGTTTTGAAAAAA-AACCT
1 TTTTGAAAA-TTATATAATATATAGTTTT-AAAAAATTA--T
*
382603 TTTTGAAAAAACTATATAATATATAGTTTTAAAAAAACATT-T
1 TTTTG--AAAATTATATAATATATAGTTTT--AAAAA-ATTAT
* **
382645 TTTTGAAATATTATATAATATATAGTTTAAAAAAAACAT
1 TTTTGAAA-ATTATATAATATATAGTTTTAAAAAATTAT
*
382684 TTTTGAAAAAACTATATAATATA
1 TTTTG--AAAATTATATAATATA
382707 AAAAAACATT
Statistics
Matches: 152, Mismatches: 12, Indels: 31
0.78 0.06 0.16
Matches are distributed among these distances:
35 3 0.02
36 32 0.21
37 25 0.16
38 2 0.01
39 15 0.10
40 15 0.10
41 26 0.17
42 24 0.16
43 9 0.06
44 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (38 bp):
TTTTGAAAATTATATAATATATAGTTTTAAAAAATTAT
Found at i:382637 original size:41 final size:40
Alignment explanation
Indices: 382519--382706 Score: 210
Period size: 41 Copynumber: 4.7 Consensus size: 40
382509 TATAGTTTTT
* *
382519 AAAACATTTTTG-AAAATTATATAATATATAGTTTT--TA
1 AAAACATTTTTGAAAAACTATATAATATATAGTTTTAAAA
**
382556 AAATTA-TTTTG-AAAACTTATATAATATATAGTTTTGAAAA
1 AAAACATTTTTGAAAAAC-TATATAATATATAGTTTT-AAAA
*
382596 AAAACCTTTTTGAAAAAACTATATAATATATAGTTTT-AAA
1 AAAACATTTTTG-AAAAACTATATAATATATAGTTTTAAAA
* *
382636 AAAACATTTTTTTGAAATATTATATAATATATAG-TTTAAAA
1 AAAACA--TTTTTGAAAAACTATATAATATATAGTTTTAAAA
382677 AAAACATTTTTGAAAAAACTATATAATATA
1 AAAACATTTTTG-AAAAACTATATAATATA
382707 AAAAAACATT
Statistics
Matches: 128, Mismatches: 12, Indels: 19
0.81 0.08 0.12
Matches are distributed among these distances:
36 9 0.07
37 22 0.17
39 6 0.05
40 30 0.23
41 32 0.25
42 24 0.19
43 5 0.04
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.41
Consensus pattern (40 bp):
AAAACATTTTTGAAAAACTATATAATATATAGTTTTAAAA
Found at i:382692 original size:81 final size:79
Alignment explanation
Indices: 382519--382706 Score: 260
Period size: 81 Copynumber: 2.4 Consensus size: 79
382509 TATAGTTTTT
* *
382519 AAAACATTTTTG--AAAATTATATAATATATAGTTTTTAAAATTATTTTGAAAACTTATATAATA
1 AAAACATTTTTGAAAAAACTATATAATATATAGTTTTAAAAATTATTTTGAAAACTTATATAATA
382582 TATAGTTTTGAAAA
66 TATAGTTTTGAAAA
* *
382596 AAAACCTTTTTGAAAAAACTATATAATATATAGTTTTAAAAAAACATTTTTTTGAAATA-TTATA
1 AAAACATTTTTGAAAAAACTATATAATATATAGTTTT---AAAA-ATTATTTTGAAA-ACTTATA
382660 TAATATATAG-TTT-AAAA
61 TAATATATAGTTTTGAAAA
382677 AAAACATTTTTGAAAAAACTATATAATATA
1 AAAACATTTTTGAAAAAACTATATAATATA
382707 AAAAAACATT
Statistics
Matches: 99, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
77 11 0.11
79 22 0.22
81 33 0.33
82 6 0.06
83 26 0.26
84 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.41
Consensus pattern (79 bp):
AAAACATTTTTGAAAAAACTATATAATATATAGTTTTAAAAATTATTTTGAAAACTTATATAATA
TATAGTTTTGAAAA
Found at i:382733 original size:32 final size:31
Alignment explanation
Indices: 382674--382736 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
382664 ATATAGTTTA
382674 AAAAAAACATTTTTGAAAAAACTATATAATAT
1 AAAAAAACATTTTTG-AAAAACTATATAATAT
382706 AAAAAAACATTTTTTG-AAAACTCATATAATA
1 AAAAAAACA-TTTTTGAAAAACT-ATATAATA
382737 CTTTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.21
32 17 0.59
33 6 0.21
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAAAACATTTTTGAAAAACTATATAATAT
Found at i:382844 original size:14 final size:14
Alignment explanation
Indices: 382825--382851 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
382815 TTGAAATATA
382825 TATATTATATTTAG
1 TATATTATATTTAG
382839 TATATTATATTTA
1 TATATTATATTTA
382852 TTATTTTTAT
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:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TATATTATATTTAG
Found at i:382867 original size:23 final size:23
Alignment explanation
Indices: 382821--382896 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
382811 ATTTTTGAAA
* * *
382821 TATATATATTATATTTAGTATAT
1 TATATTTATTATATTTATTTTAT
*
382844 TATATTTATTATTTTTATTTTAT
1 TATATTTATTATATTTATTTTAT
* *
382867 TTTATTCATT-TAATTTATTTTAAT
1 TATATTTATTAT-ATTTATTTT-AT
382891 T-TATTT
1 TATATTT
382897 CATTTTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 1 0.02
23 39 0.91
24 3 0.07
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (23 bp):
TATATTTATTATATTTATTTTAT
Found at i:382882 original size:19 final size:20
Alignment explanation
Indices: 382860--382906 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
382850 TATTATTTTT
382860 ATTTTATTTT-ATTCATTTA
1 ATTTTATTTTAATTCATTTA
* *
382879 A-TTTATTTTAATTTATTTC
1 ATTTTATTTTAATTCATTTA
382898 ATTTT-TTTT
1 ATTTTATTTT
382907 CCAGGTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 8 0.33
19 13 0.54
20 3 0.12
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTATTTTAATTCATTTA
Found at i:384107 original size:3 final size:3
Alignment explanation
Indices: 384084--384141 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
384074 CCTCTAAGTT
* *
384084 TTA TT- TTA TT- TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
384130 TTCA TTA TTA TT
1 TT-A TTA TTA TT
384142 GATTTCAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.88
4 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:384251 original size:16 final size:17
Alignment explanation
Indices: 384230--384271 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
384220 TTAAATCCAA
384230 TTTTTATTTA-TCATTT
1 TTTTTATTTATTCATTT
* *
384246 TTTTTACTTATTCCTTT
1 TTTTTATTTATTCATTT
384263 TTTTTATTT
1 TTTTTATTT
384272 TTTAAACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTATTCATTT
Found at i:384271 original size:26 final size:25
Alignment explanation
Indices: 384242--384302 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
384232 TTTATTTATC
384242 ATTTTTTTTACTTATTCCT-TTTTTTT
1 ATTTTTTTTACTTATT--TATTTTTTT
**
384268 ATTTTTTAAACTTATTTATTTTTTT
1 ATTTTTTTTACTTATTTATTTTTTT
384293 ATTTATTTTT
1 ATTT-TTTTT
384303 TCCTCTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 11 0.38
26 17 0.59
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (25 bp):
ATTTTTTTTACTTATTTATTTTTTT
Found at i:384274 original size:8 final size:8
Alignment explanation
Indices: 384261--384369 Score: 51
Period size: 8 Copynumber: 12.9 Consensus size: 8
384251 ACTTATTCCT
384261 TTTTTTTA
1 TTTTTTTA
*
384269 TTTTTTAAA
1 TTTTTT-TA
* *
384278 CTTATTTA
1 TTTTTTTA
384286 TTTTTTTA
1 TTTTTTTA
384294 TTTATTTT-
1 TTT-TTTTA
384302 TTCCTCTTTT-
1 TT--T-TTTTA
* **
384312 CTTTCGTA
1 TTTTTTTA
384320 TTTTTTTTA
1 TT-TTTTTA
384329 TTTTTTTA
1 TTTTTTTA
*
384337 TTTTGTTGA
1 TTTT-TTTA
*
384346 TTTGTTTA
1 TTTTTTTA
*
384354 TTATTGTTA
1 TT-TTTTTA
384363 TTTTTTT
1 TTTTTTT
384370 TTTCTTTAAC
Statistics
Matches: 74, Mismatches: 19, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
7 2 0.03
8 39 0.53
9 27 0.36
10 6 0.08
ACGTcount: A:0.14, C:0.06, G:0.05, T:0.76
Consensus pattern (8 bp):
TTTTTTTA
Found at i:384296 original size:12 final size:12
Alignment explanation
Indices: 384279--384303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
384269 TTTTTTAAAC
384279 TTATTTATTTTT
1 TTATTTATTTTT
384291 TTATTTATTTTT
1 TTATTTATTTTT
384303 T
1 T
384304 CCTCTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:384340 original size:17 final size:17
Alignment explanation
Indices: 384318--384369 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
384308 TTTTCTTTCG
384318 TATTTTTTTTATTTTTT
1 TATTTTTTTTATTTTTT
* * *
384335 TATTTTGTTGATTTGTT
1 TATTTTTTTTATTTTTT
* *
384352 TATTATTGTTATTTTTT
1 TATTTTTTTTATTTTTT
384369 T
1 T
384370 TTTCTTTAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (17 bp):
TATTTTTTTTATTTTTT
Found at i:391819 original size:2 final size:2
Alignment explanation
Indices: 391814--391847 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
391804 TGTGTGCGTG
391814 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
391848 AAGTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:392344 original size:17 final size:16
Alignment explanation
Indices: 392322--392359 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
392312 TTCTATTAAT
392322 AAAGAAGTAGAGAAAA-A
1 AAAGAAG-A-AGAAAATA
392339 AAAGAAGAAGAAAATA
1 AAAGAAGAAGAAAATA
392355 AAAGA
1 AAAGA
392360 TGGGAGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 7 0.35
17 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (16 bp):
AAAGAAGAAGAAAATA
Found at i:401369 original size:23 final size:23
Alignment explanation
Indices: 401343--401405 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
401333 ATATAACCAC
401343 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
401366 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
401389 TACCTATTACATCATAT
1 TACCTATTACATTATAT
401406 TTTACCTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:401782 original size:430 final size:431
Alignment explanation
Indices: 400994--402047 Score: 1935
Period size: 430 Copynumber: 2.5 Consensus size: 431
400984 TTATAATATG
400994 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
*
401059 TCAA-TTTTTTGAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
401123 CAAAAAATTATTTGATTATTTGATATTTTATAAAATATATTTAGAATTTTTAATTTAA-TA-A-T
131 CAAAAAATTATTTGATT-TTTGATATTTTATAAAATATATTTAGAATTTTTAATTTAACAACATT
401185 --AATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAA
195 AAAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAA
401248 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTAAAAAAAGTATGGACACTTTTATA
260 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTAAAAAAAGTATGGACACTTTTATA
*
401313 AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACAT
325 AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTACAT
* *
401378 TATATAAGCGCTACCTATTACATCATA-TTTTACCTATTATA
390 TATATAAACGCTACATATTACATCATATTTTTACCTATTATA
*
401419 TT-AAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
401483 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
401548 CAAAAAATTATTTGATTTTTGATATTTTATAAAATATATTTAGAATTTTTAATTTAACAACATTA
131 CAAAAAATTATTTGATTTTTGATATTTTATAAAATATATTTAGAATTTTTAATTTAACAACATTA
401613 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAA
196 AA-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAA
* *
401678 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATA
260 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTAAAAAAAGTATGGACACTTTTATA
401743 AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTACAT
325 AAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTACAT
401808 TATATAAACGCTACATATTACATCATATTTTTACCTATTATA
390 TATATAAACGCTACATATTACATCATATTTTTACCTATTATA
*
401850 TTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
401915 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
401980 CAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACAT
131 CAAAAAATTATTTGA-TTTTTGATATTTTATAAAATA-TATTTAGAATTTTTAATTTAACAACAT
402045 TAA
194 TAA
402048 CCAAAGATAA
Statistics
Matches: 608, Mismatches: 10, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
424 105 0.17
425 79 0.13
426 1 0.00
427 1 0.00
429 1 0.00
430 214 0.35
431 16 0.03
432 140 0.23
433 21 0.03
434 30 0.05
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (431 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTTTTGATATTTTATAAAATATATTTAGAATTTTTAATTTAACAACATTA
AAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAAA
CTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTAAAAAAAGTATGGACACTTTTATAA
AAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTACATT
ATATAAACGCTACATATTACATCATATTTTTACCTATTATA
Found at i:401803 original size:23 final size:23
Alignment explanation
Indices: 401777--401835 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
401767 AACCACTACC
401777 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
*
401800 TATTACATTATATAAACGCTACA
1 TATTACATTATATAAACGATACA
*
401823 TATTACATCATAT
1 TATTACATTATAT
401836 TTTTACCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:402312 original size:39 final size:39
Alignment explanation
Indices: 402258--402343 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
402248 CAAGTTGTAG
*
402258 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
402297 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
402336 ATTTTGAT
1 ATTTTGAT
402344 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:402623 original size:18 final size:18
Alignment explanation
Indices: 402600--402636 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
402590 CGAAATATAT
402600 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
402618 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
402636 A
1 A
402637 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:403091 original size:28 final size:26
Alignment explanation
Indices: 403052--403120 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 26
403042 TAAAAAGGAT
403052 CGATA-CT-TTACAATATATTATATAA
1 CGATACCTATTACAATATATTATA-AA
*
403077 GCGCTACCTATTAC-AT-TA-TATAAA
1 -CGATACCTATTACAATATATTATAAA
*
403101 CGATACCTATTACATTATAT
1 CGATACCTATTACAATATAT
403121 ACTTGTAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
23 12 0.34
24 3 0.09
25 6 0.17
26 6 0.17
27 4 0.11
28 4 0.11
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (26 bp):
CGATACCTATTACAATATATTATAAA
Found at i:403098 original size:23 final size:23
Alignment explanation
Indices: 403068--403121 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
403058 TTTACAATAT
* *
403068 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGATACCTATTAC
403091 ATTATATAAACGATACCTATTAC
1 ATTATATAAACGATACCTATTAC
403114 ATTATATA
1 ATTATATA
403122 CTTGTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (23 bp):
ATTATATAAACGATACCTATTAC
Found at i:407235 original size:21 final size:22
Alignment explanation
Indices: 407153--407236 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 22
407143 CAGAACCCCA
*
407153 GGGGGGTATCGATTCCC-C-TGT
1 GGGGGGAATCGATTCCCTCAT-T
* *
407174 GGGGGGAATCGGTTCCCCTTCA-A
1 GGGGGGAATCGATT-CCC-TCATT
* *
407197 AGGGGGAATCGGTTCCCTCATT
1 GGGGGGAATCGATTCCCTCATT
407219 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
407237 TGCACCAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 26 0.51
22 11 0.22
23 13 0.25
24 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCTCATT
Found at i:414549 original size:183 final size:183
Alignment explanation
Indices: 414241--415414 Score: 2107
Period size: 183 Copynumber: 6.4 Consensus size: 183
414231 GACACATTTC
* * * * *
414241 AGGTTGTAGACATATTCGCGCATAAAACCAGTATATTTATACCGGTTATATTACAAAATTATCTA
1 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
414306 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
414371 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
*
414424 AGGTTGTAGACCTATTCGCTCATACTACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
1 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
414489 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
*
414554 TTTCTTCCAATATGGACATAAAGTGCCGACACAATATTAAAAAGTGTCGATAT
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
*
414607 AGGTTGTAGACCTATTCGCTCATACAACTGGTATATTTATACCTGTTATATTACAAAATTATCTA
1 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
414672 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
414737 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
414790 AGGTTGTAGACCTATTCGCTCATACAACCGGTATA-TTATACCTGTTATATTACAAAATTATCTA
1 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
414854 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
414919 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
414972 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
1 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
*
415037 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGATACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
415102 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
* * * * * *
415155 AGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATTTACCTA
1 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
**
415220 TTTTATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
415285 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
* * * * * * *
415338 AGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATTTACCTA
1 AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
**
415403 TTTTATTATAAT
66 TTACATTATAAT
415415 ATGTTGAAAG
Statistics
Matches: 968, Mismatches: 22, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
182 182 0.19
183 786 0.81
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
AGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTA
TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAT
Found at i:415313 original size:548 final size:549
Alignment explanation
Indices: 414241--415414 Score: 2143
Period size: 548 Copynumber: 2.1 Consensus size: 549
414231 GACACATTTC
*
414241 AGGTTGTAGACATATTCGCGCATAAAACCAGTATATTTATACCGGTTATATTACAAAATTATCTA
1 AGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTA
414306 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
414371 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACC
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACC
*
414436 TATTCGCTCATACTACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAAT
196 TATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAAT
414501 TATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
261 TATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
* *
414566 TGGACATAAAGTGCCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
326 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
* * * *
414631 CAACTGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
391 AAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGA
414696 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGT
456 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGT
414761 ACCGACACAATATTAAAAAGTGTCGATAT
521 ACCGACACAATATTAAAAAGTGTCGATAT
* * * *
414790 AGGTTGTAGACCTATTCGCTCATACAACCGGTATA-TTATACCTGTTATATTACAAAATTATCTA
1 AGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTA
414854 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
66 TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
414919 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACC
131 TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACC
414984 TATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAAT
196 TATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAAT
*
415049 TATGGGTTCCGATGTGTAAATGTCGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
261 TATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
415114 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
326 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
* * **
415179 AAACCGGTATATTTATACCGGTTATATTGCAAATTTACCTATTTTATTATAATTATGGGTTCCGA
391 AAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGA
415244 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGT
456 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGT
415309 ACCGACACAATATTAAAAAGTGTCGATAT
521 ACCGACACAATATTAAAAAGTGTCGATAT
* * *
415338 AGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATTTACCTA
1 AGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTA
**
415403 TTTTATTATAAT
66 TTACATTATAAT
415415 ATGTTGAAAG
Statistics
Matches: 598, Mismatches: 26, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
548 532 0.89
549 66 0.11
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (549 bp):
AGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTA
TTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATT
TTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACC
TATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAAT
TATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
AAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGA
TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGT
ACCGACACAATATTAAAAAGTGTCGATAT
Found at i:416668 original size:17 final size:18
Alignment explanation
Indices: 416646--416688 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
416636 ATATATCCGG
416646 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
416663 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
416683 TATCAT
1 TATCAT
416689 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:416706 original size:20 final size:19
Alignment explanation
Indices: 416651--416697 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
416641 TCCGGTATCA
416651 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
416670 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
416691 TTTTACC
1 TTTTACC
416698 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:416845 original size:20 final size:20
Alignment explanation
Indices: 416820--416879 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
416810 ACTTTTAAAT
416820 TTACCGGTTTTATCATTTTG
1 TTACCGGTTTTATCATTTTG
416840 TTACCGGTTTTATCATATTT-
1 TTACCGGTTTTATCAT-TTTG
*
416860 TTACCTGG-TATATCATTTTG
1 TTACC-GGTTTTATCATTTTG
416880 GATCGATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 3 0.08
20 28 0.78
21 5 0.14
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.53
Consensus pattern (20 bp):
TTACCGGTTTTATCATTTTG
Found at i:417930 original size:2 final size:2
Alignment explanation
Indices: 417923--417975 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
417913 TCGGGTCGGG
* * * *
417923 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
417963 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
417976 TTTTTTAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:417994 original size:53 final size:54
Alignment explanation
Indices: 417930--418038 Score: 159
Period size: 53 Copynumber: 2.0 Consensus size: 54
417920 GGGTATATAT
*
417930 ATTTAAATTAAATATATAAATATTATATATATATATAT-ATATATATT-TTTTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATATAAAATA-ATTATTTTTA
* * *
417983 ATTTAATTTAAATTTATTAATATTATATATATATATATAAAATAATTATTTTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATATAAAATAATTATTTTTA
418037 AT
1 AT
418039 ATTTATCGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 38 0.76
54 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (54 bp):
ATTTAAATTAAATATATAAATATTATATATATATATATAAAATAATTATTTTTA
Found at i:418151 original size:35 final size:36
Alignment explanation
Indices: 418100--418167 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
418090 TACTAAACCG
*
418100 GTCCCCGTCCTCGTTTAACATAAACAGTTTTTCTCC
1 GTCCCCATCCTCGTTTAACATAAACAGTTTTTCTCC
* *
418136 GTCCCCATCC-CGTTTAGCATAAACGGTTTTTC
1 GTCCCCATCCTCGTTTAACATAAACAGTTTTTC
418168 CTATCCTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 20 0.69
36 9 0.31
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.35
Consensus pattern (36 bp):
GTCCCCATCCTCGTTTAACATAAACAGTTTTTCTCC
Found at i:424487 original size:18 final size:18
Alignment explanation
Indices: 424464--424501 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
424454 TGCATAAAAG
424464 AAAGGGGACTTTTCATTT
1 AAAGGGGACTTTTCATTT
424482 AAAGGGGACTTTTCATTT
1 AAAGGGGACTTTTCATTT
424500 AA
1 AA
424502 CTAAGGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (18 bp):
AAAGGGGACTTTTCATTT
Found at i:431899 original size:60 final size:60
Alignment explanation
Indices: 431828--431955 Score: 220
Period size: 60 Copynumber: 2.1 Consensus size: 60
431818 GATCTCTATT
*
431828 ATAATTCCCACAAATGAAATAAAGAAAAAAAAAAGAAAGGTTAAATTACAAATTTAGTAA
1 ATAATTTCCACAAATGAAATAAAGAAAAAAAAAAGAAAGGTTAAATTACAAATTTAGTAA
* *
431888 ATAATTTCCACAAATGAAATAAAGAAAAAAAAGAGAAATGTTAAATTACAAATTTAGTAA
1 ATAATTTCCACAAATGAAATAAAGAAAAAAAAAAGAAAGGTTAAATTACAAATTTAGTAA
431948 ATGAATTT
1 AT-AATTT
431956 TATCCTCTCT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
60 59 0.92
61 5 0.08
ACGTcount: A:0.58, C:0.07, G:0.10, T:0.25
Consensus pattern (60 bp):
ATAATTTCCACAAATGAAATAAAGAAAAAAAAAAGAAAGGTTAAATTACAAATTTAGTAA
Found at i:449401 original size:13 final size:13
Alignment explanation
Indices: 449383--449427 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
449373 TCAGAAGAAT
449383 CTCCTTGTTCAAC
1 CTCCTTGTTCAAC
*
449396 CTCCTT-TTCCAAT
1 CTCCTTGTT-CAAC
449409 CTCCTTGTTCAAC
1 CTCCTTGTTCAAC
449422 CTCCTT
1 CTCCTT
449428 TTCCACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.07
13 24 0.86
14 2 0.07
ACGTcount: A:0.13, C:0.40, G:0.04, T:0.42
Consensus pattern (13 bp):
CTCCTTGTTCAAC
Found at i:449409 original size:26 final size:26
Alignment explanation
Indices: 449380--449432 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
449370 ACTTCAGAAG
449380 AATCTCCTTGTTCAACCTCCTTTTCC
1 AATCTCCTTGTTCAACCTCCTTTTCC
449406 AATCTCCTTGTTCAACCTCCTTTTCC
1 AATCTCCTTGTTCAACCTCCTTTTCC
449432 A
1 A
449433 CATATATCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.17, C:0.38, G:0.04, T:0.42
Consensus pattern (26 bp):
AATCTCCTTGTTCAACCTCCTTTTCC
Found at i:454474 original size:36 final size:35
Alignment explanation
Indices: 454429--454506 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 35
454419 TTATAGCAAA
454429 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAG
1 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAG
454464 CAAAAATCGTCTTTATTCGAATTTTGCCAAAAATAG
1 -AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAG
454500 AAAAATC
1 AAAAATC
454507 CCGAAAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (35 bp):
AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAG
Found at i:458996 original size:15 final size:15
Alignment explanation
Indices: 458978--459007 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
458968 CCACGGTGCT
458978 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
458993 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
459008 AATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:459475 original size:36 final size:36
Alignment explanation
Indices: 459430--459505 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
459420 TTATAGCAAA
459430 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
459466 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
459502 AAAA
1 AAAA
459506 TCCCGAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
Found at i:466339 original size:228 final size:227
Alignment explanation
Indices: 465937--466384 Score: 785
Period size: 228 Copynumber: 2.0 Consensus size: 227
465927 GTAAATTATC
* * *
465937 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
466002 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
466067 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAA-TT
466131 GAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
466165 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
466230 TTAATATTGTTAAATTT-AAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-AT
65 TTAATATTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAT
*
466293 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
466358 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
466385 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
227 4 0.02
228 124 0.59
229 83 0.39
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:466473 original size:20 final size:19
Alignment explanation
Indices: 466450--466495 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
466440 CGATATACCA
466450 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
466470 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
466490 GGTAAA
1 GGTAAA
466496 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:466639 original size:20 final size:19
Alignment explanation
Indices: 466616--466662 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
466606 CGATATAACA
*
466616 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
466636 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
466656 GGTAAAA
1 GGTAAAA
466663 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:469017 original size:33 final size:33
Alignment explanation
Indices: 468975--469040 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
468965 AAATAGATGG
*
468975 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
469008 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
469041 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:470869 original size:19 final size:19
Alignment explanation
Indices: 470825--470868 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
470815 AATGTCGAGT
470825 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
470844 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
470863 T-ATTTT
1 TAATTTT
470869 TTATGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:471528 original size:200 final size:200
Alignment explanation
Indices: 470948--472573 Score: 3032
Period size: 200 Copynumber: 8.1 Consensus size: 200
470938 TTAAGGGTCA
* *
470948 TGTCGATACTAATATAGTTTGTGTCGAAATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACG
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT----G
471013 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
62 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
471078 TAATGTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
127 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
471142 TAAATAATG
192 TAAATAATG
*
471151 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
471215 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
471279 GTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
471344 TAATG
196 TAATG
471349 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
471414 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
471479 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGATTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
471544 TAATG
196 TAATG
471549 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
471614 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
471679 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
471744 TAATG
196 TAATG
471749 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
471814 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
471879 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
471944 TAATG
196 TAATG
471949 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
472014 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
472079 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
472144 TAATG
196 TAATG
*
472149 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
472213 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
472277 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
472342 TAATG
196 TAATG
*
472347 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
472412 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
472476 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
472541 TAATG
196 TAATG
*
472546 TGTCGACACTAATATATTTTGTG-CGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
472574 CTAATTTAAA
Statistics
Matches: 1401, Mismatches: 18, Indels: 13
0.98 0.01 0.01
Matches are distributed among these distances:
197 52 0.04
198 255 0.18
199 300 0.21
200 737 0.53
202 30 0.02
203 27 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (200 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATG
Found at i:474056 original size:12 final size:12
Alignment explanation
Indices: 474039--474130 Score: 69
Period size: 12 Copynumber: 7.4 Consensus size: 12
474029 GGTCGCAGAA
*
474039 GATGAAGCTGAC
1 GATGAAGATGAC
474051 GATGAAGATGAC
1 GATGAAGATGAC
474063 GATGATGATGATGAC
1 GATGA--A-GATGAC
* *
474078 GATGAAGCTGGC
1 GATGAAGATGAC
474090 GATGAAGATG-C
1 GATGAAGATGAC
* * *
474101 TGACGATGATGAT
1 -GATGAAGATGAC
* *
474114 GATGATGATGAA
1 GATGAAGATGAC
474126 GATGA
1 GATGA
474131 TGATCCAAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
11 1 0.02
12 52 0.79
13 1 0.02
14 1 0.02
15 11 0.17
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:474075 original size:15 final size:15
Alignment explanation
Indices: 474051--474133 Score: 82
Period size: 15 Copynumber: 5.7 Consensus size: 15
474041 TGAAGCTGAC
*
474051 GATGAAGATGACGAT
1 GATGATGATGACGAT
474066 GATGATGATGACGAT
1 GATGATGATGACGAT
* *
474081 GA--A-GCTGGCGAT
1 GATGATGATGACGAT
* *
474093 GAAGATGCTGACGAT
1 GATGATGATGACGAT
*
474108 GATGATGATGATGAT
1 GATGATGATGACGAT
*
474123 GAAGATGATGA
1 GATGATGATGA
474134 TCCAAACAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 1 0.02
15 46 0.81
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:475911 original size:184 final size:184
Alignment explanation
Indices: 475602--476256 Score: 1229
Period size: 184 Copynumber: 3.6 Consensus size: 184
475592 CTTTCAACAT
** * *
475602 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
475667 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
475732 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
475786 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
475851 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
475916 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
475970 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
476035 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
476100 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
476154 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
476219 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTC
476257 AGAAACGTTT
Statistics
Matches: 462, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 462 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCCAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:483999 original size:19 final size:20
Alignment explanation
Indices: 483975--484018 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
483965 GTCATCCAAT
*
483975 TTTTTAAA-CCCATACCGGA
1 TTTTTAAACCCCAAACCGGA
*
483994 TTTTTAAACCCCAAATCGGA
1 TTTTTAAACCCCAAACCGGA
484014 TTTTT
1 TTTTT
484019 TTCGGGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (20 bp):
TTTTTAAACCCCAAACCGGA
Found at i:487276 original size:16 final size:16
Alignment explanation
Indices: 487255--487289 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
487245 ACACTTTACG
487255 TCATTCACCTATTAAC
1 TCATTCACCTATTAAC
487271 TCATTCACCTATTAAC
1 TCATTCACCTATTAAC
487287 TCA
1 TCA
487290 CTTTAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (16 bp):
TCATTCACCTATTAAC
Found at i:491060 original size:2 final size:2
Alignment explanation
Indices: 491053--491084 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
491043 GATCATGCCC
491053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
491085 AAGAAAGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:498681 original size:11 final size:10
Alignment explanation
Indices: 498665--498710 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
498655 TTGTTATGGT
498665 TTGTTATTAG
1 TTGTTATTAG
498675 CTTGTTATTAG
1 -TTGTTATTAG
*
498686 TTGTTATTATT
1 TTGTTATTA-G
498697 TTGTTA-TAG
1 TTGTTATTAG
498706 TTGTT
1 TTGTT
498711 GGTTACTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 5 0.16
10 11 0.34
11 16 0.50
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (10 bp):
TTGTTATTAG
Found at i:498689 original size:21 final size:20
Alignment explanation
Indices: 498655--498710 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
498645 ATGTTAGAGT
*
498655 TTGTTATGGTTTGTTATTAGC
1 TTGTTATAG-TTGTTATTAGC
**
498676 TTGTTATTAGTTGTTATTATT
1 TTGTTA-TAGTTGTTATTAGC
498697 TTGTTATAGTTGTT
1 TTGTTATAGTTGTT
498711 GGTTACTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.26
21 21 0.68
22 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.62
Consensus pattern (20 bp):
TTGTTATAGTTGTTATTAGC
Found at i:500027 original size:14 final size:14
Alignment explanation
Indices: 500008--500056 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
499998 TTATGTTTGT
500008 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
500022 TTATGTTCG-T---
1 TTATGTTCGTTCGG
500032 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
500046 TTATGTTCGTT
1 TTATGTTCGTT
500057 TATGTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 1 0.03
14 20 0.65
ACGTcount: A:0.08, C:0.12, G:0.24, T:0.55
Consensus pattern (14 bp):
TTATGTTCGTTCGG
Found at i:500076 original size:24 final size:24
Alignment explanation
Indices: 499991--500063 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
499981 CGTTCGTGAA
*
499991 CGTTCGGTTATGTTTGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
500015 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
500039 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
500063 C
1 C
500064 ATTCATTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.55
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:501173 original size:16 final size:15
Alignment explanation
Indices: 501152--501202 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
501142 GTCTCCAACG
501152 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTT-A
*
501168 TTTATGTTCGTGTTTG
1 TTTATGTTCGTG-TTA
501184 TTTATGTTCGT-TTA
1 TTTATGTTCGTGTTA
501198 TTTAT
1 TTTAT
501203 TAAATGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 7 0.22
16 23 0.72
17 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.63
Consensus pattern (15 bp):
TTTATGTTCGTGTTA
Found at i:508277 original size:8 final size:8
Alignment explanation
Indices: 508264--508304 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
508254 CTCATTTTCA
508264 GAGAATTT
1 GAGAATTT
508272 GAGAATTT
1 GAGAATTT
*
508280 -AGAGTTT
1 GAGAATTT
*
508287 GGGAATTT
1 GAGAATTT
508295 GAGAATTT
1 GAGAATTT
508303 GA
1 GA
508305 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:508597 original size:126 final size:126
Alignment explanation
Indices: 508372--508973 Score: 1174
Period size: 126 Copynumber: 4.8 Consensus size: 126
508362 CTATAATCGG
508372 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
508437 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
508498 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
508563 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
508624 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
508689 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
508749 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
508814 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
508875 TTCACTATTCACGTGAA-G-GCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
508938 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
508974 ATAACTTAAA
Statistics
Matches: 474, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
124 80 0.17
125 126 0.27
126 268 0.57
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:508818 original size:251 final size:251
Alignment explanation
Indices: 508372--508971 Score: 1168
Period size: 251 Copynumber: 2.4 Consensus size: 251
508362 CTATAATCGG
508372 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
508437 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTCA
508502 CTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
130 CTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
508567 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
195 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
508624 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
508689 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCAC
508754 TATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCATT
131 TATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCATT
508819 GCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
196 GCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
508875 TTCACTATTCACGTGAA-G-GCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
508938 TCATTGCCCTATTATGTCACTCATGTCCCTCGGG
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGG
508972 GAATAACTTA
Statistics
Matches: 347, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
249 78 0.22
250 1 0.00
251 172 0.50
252 96 0.28
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (251 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCAC
TATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCATT
GCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:509439 original size:32 final size:33
Alignment explanation
Indices: 509354--509457 Score: 140
Period size: 32 Copynumber: 3.2 Consensus size: 33
509344 TAAGTTGAAA
*
509354 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTTATAT
*
509388 TTTAAATTTAAATTT-GAATAATATTATTT-TAT
1 TTT-AATTTAAATTTCGAATAATATAATTTATAT
* *
509420 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
509453 TTTAA
1 TTTAA
509458 AAACATTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
31 10 0.16
32 19 0.31
33 19 0.31
34 11 0.18
35 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (33 bp):
TTTAATTTAAATTTCGAATAATATAATTTATAT
Found at i:510057 original size:21 final size:21
Alignment explanation
Indices: 509969--510062 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
509959 TATGGTATAA
*
509969 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
509990 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
510011 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
510032 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
510053 AACCCTGCGG
1 AACCCTGCGG
510063 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:510092 original size:21 final size:21
Alignment explanation
Indices: 510066--510113 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
510056 CCTGCGGAGA
*
510066 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
510087 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
510108 GGGCAT
1 TGGCAT
510114 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:511891 original size:30 final size:34
Alignment explanation
Indices: 511827--511905 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
511817 TTAATAATTC
* *
511827 TAAATAAATAATAATTATATAAATATTATTTTA-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
511861 TAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
511893 TAAAAAATAATAA
1 TAAAAAATAATAA
511906 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:512752 original size:19 final size:20
Alignment explanation
Indices: 512738--512816 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 20
512728 TTATTTTCGC
*
512738 AACGCGTTGCGATTTTGGAG
1 AACGCGTTGCGATTTTAGAG
512758 AATCGCGTTGCGATTTTAGAG
1 AA-CGCGTTGCGATTTTAGAG
512779 AACTGCGTTGCGATTTTAGAG
1 AAC-GCGTTGCGATTTTAGAG
*
512800 AACCGCGTTACGATTTT
1 AA-CGCGTTGCGATTTT
512817 GCAGAACCGT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
20 3 0.06
21 50 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (20 bp):
AACGCGTTGCGATTTTAGAG
Found at i:512765 original size:21 final size:21
Alignment explanation
Indices: 512740--512875 Score: 106
Period size: 21 Copynumber: 6.8 Consensus size: 21
512730 ATTTTCGCAA
512740 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAT
*
512761 CGCGTTGCGATTTTAGAGAA-
1 CGCGTTGCGATTTTGGAGAAT
* *
512781 CTGCGTTGCGATTTTAGAGAAC
1 C-GCGTTGCGATTTTGGAGAAT
* * *
512803 CGCGTTACGATTTTGCAGAAC
1 CGCGTTGCGATTTTGGAGAAT
** * * *
512824 CGTATTGTGAATTT-GAAAAT
1 CGCGTTGCGATTTTGGAGAAT
512844 --C---GCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAT
*
512860 CGCGTTGTGATTTTGG
1 CGCGTTGCGATTTTGG
512876 GAACTGTATT
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
15 6 0.07
16 5 0.06
18 1 0.01
20 4 0.04
21 73 0.81
22 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.34
Consensus pattern (21 bp):
CGCGTTGCGATTTTGGAGAAT
Found at i:513188 original size:31 final size:31
Alignment explanation
Indices: 513147--513235 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
513137 GTGACAGTCG
*
513147 ATCTGTCATGTTTGAGTTGTCAATTTAATTA
1 ATCTGACATGTTTGAGTTGTCAATTTAATTA
*
513178 ATCTGACATGTTTGAGTTGTCAATTTACTTA
1 ATCTGACATGTTTGAGTTGTCAATTTAATTA
513209 ATCTGACATGTTTGAGTT-TCCAATTTA
1 ATCTGACATGTTTGAGTTGT-CAATTTA
513236 GCCAATATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
30 1 0.02
31 54 0.98
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (31 bp):
ATCTGACATGTTTGAGTTGTCAATTTAATTA
Found at i:513247 original size:31 final size:30
Alignment explanation
Indices: 513147--513250 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 30
513137 GTGACAGTCG
* *
513147 ATCTGTCATGTTTGAGTTGTCAATTTAATTA
1 ATCTGACATGTTTGAGTTGTCAATTT-ACTA
513178 ATCTGACATGTTTGAGTTGTCAATTTACTTA
1 ATCTGACATGTTTGAGTTGTCAATTTAC-TA
*
513209 ATCTGACATGTTTGAGTT-TCCAATTTAGCCA
1 ATCTGACATGTTTGAGTTGT-CAATTTA-CTA
*
513240 ATATGACATGT
1 ATCTGACATGT
513251 CATCCGTCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
30 2 0.03
31 63 0.95
32 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (30 bp):
ATCTGACATGTTTGAGTTGTCAATTTACTA
Done.