Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 30
Found at i:1437098 original size:21 final size:18
Alignment explanation
Indices: 1437047--1437099 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
1437037 GAAACGATGA
1437047 TTTGGGAATTGAACGAGGG
1 TTTGGGAATTGAA-GAGGG
*
1437066 TTAGGG-ATTGAAGAGGGGGG
1 TTTGGGAATTGAAGA---GGG
1437086 TTTGGGAATTGAAG
1 TTTGGGAATTGAAG
1437100 CACGTGAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 6 0.21
19 5 0.18
20 8 0.29
21 7 0.25
ACGTcount: A:0.26, C:0.02, G:0.45, T:0.26
Consensus pattern (18 bp):
TTTGGGAATTGAAGAGGG
Found at i:1442190 original size:21 final size:23
Alignment explanation
Indices: 1442136--1442193 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
1442126 AAACGATGAT
*
1442136 GATTTGGGAATTGAGGAGTGAGG
1 GATTTGGGAATTGAAGAGTGAGG
* *
1442159 G-TTAGGG-ATTGAATAG-G-GG
1 GATTTGGGAATTGAAGAGTGAGG
1442178 GATTTGGGAATTGAAG
1 GATTTGGGAATTGAAG
1442194 CACGTGAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 3 0.11
20 6 0.21
21 13 0.46
22 5 0.18
23 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (23 bp):
GATTTGGGAATTGAAGAGTGAGG
Found at i:1444992 original size:29 final size:29
Alignment explanation
Indices: 1444956--1445022 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
1444946 AAAGTCAGAG
1444956 AGAAAAAAGAAACCAAAACAAAAATATTA
1 AGAAAAAAGAAACCAAAACAAAAATATTA
1444985 AGAAAAAAGAAACCAAAACAAAAATATTA
1 AGAAAAAAGAAACCAAAACAAAAATATTA
1445014 AGAAAAAAG
1 AGAAAAAAG
1445023 GAAAAATCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.73, C:0.09, G:0.09, T:0.09
Consensus pattern (29 bp):
AGAAAAAAGAAACCAAAACAAAAATATTA
Found at i:1448403 original size:32 final size:32
Alignment explanation
Indices: 1448355--1448423 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1448345 GAGCGTTTGG
* *
1448355 AGGACTTGGTGTGACCTATGGAGGTCGCCCGA
1 AGGACTTGGCGCGACCTATGGAGGTCGCCCGA
*
1448387 AGGACTTGGCGCGACCTATGGAGGTCGCCCGG
1 AGGACTTGGCGCGACCTATGGAGGTCGCCCGA
1448419 AGGAC
1 AGGAC
1448424 CTGGTGATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.17
Consensus pattern (32 bp):
AGGACTTGGCGCGACCTATGGAGGTCGCCCGA
Found at i:1448975 original size:20 final size:22
Alignment explanation
Indices: 1448950--1448994 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
1448940 TGGTAAAAAA
*
1448950 TTACCTAAAAC-TTTAT-TTTT
1 TTACCTAAAACATTAATGTTTT
1448970 TTACCTAAAACATTAATGTTTT
1 TTACCTAAAACATTAATGTTTT
1448992 TTA
1 TTA
1448995 ACATTTCCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 4 0.18
22 7 0.32
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (22 bp):
TTACCTAAAACATTAATGTTTT
Found at i:1449122 original size:21 final size:21
Alignment explanation
Indices: 1449096--1449135 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1449086 TAAAACGCCC
1449096 AATAATAATATTTCCGGTAGA
1 AATAATAATATTTCCGGTAGA
*
1449117 AATAATAATGTTTCCGGTA
1 AATAATAATATTTCCGGTA
1449136 ATTTTATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AATAATAATATTTCCGGTAGA
Found at i:1450437 original size:17 final size:17
Alignment explanation
Indices: 1450417--1450475 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
1450407 ATATTGGACT
1450417 TATAATTATTTTATAAG
1 TATAATTATTTTATAAG
*
1450434 TAT-ATT-TTTTATATTCGACT
1 TATAATTATTTTATA----A-G
1450454 TATAATTATTTTATAAG
1 TATAATTATTTTATAAG
1450471 TATAA
1 TATAA
1450476 AATTAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 8 0.24
18 1 0.03
19 1 0.03
20 3 0.09
21 3 0.09
22 7 0.21
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TATAATTATTTTATAAG
Found at i:1450447 original size:37 final size:37
Alignment explanation
Indices: 1450404--1450474 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1450394 AAAAAATATA
*
1450404 TTTATATTGGACTTATAATTATTTTATAAGTATATTT
1 TTTATATTCGACTTATAATTATTTTATAAGTATATTT
1450441 TTTATATTCGACTTATAATTATTTTATAAGTATA
1 TTTATATTCGACTTATAATTATTTTATAAGTATA
1450475 AAATTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (37 bp):
TTTATATTCGACTTATAATTATTTTATAAGTATATTT
Found at i:1450485 original size:37 final size:37
Alignment explanation
Indices: 1450407--1450494 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
1450397 AAATATATTT
* *** *
1450407 ATATTGGACTTATAATTATTTTATAAGTATATTTTTT
1 ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
1450444 ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
1 ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
*
1450481 ATATTCGAATTATA
1 ATATTCGACTTATA
1450495 CTTAAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (37 bp):
ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
Found at i:1450621 original size:22 final size:21
Alignment explanation
Indices: 1450595--1450659 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
1450585 TAAAAATATA
1450595 TTTATATTCGATTTATAATTAT
1 TTTATATTCGA-TTATAATTAT
*
1450617 TTTATA----AGTAT-ATT-T
1 TTTATATTCGATTATAATTAT
1450632 TTTATATTCGACTTATAATTAT
1 TTTATATTCGA-TTATAATTAT
1450654 TTTATA
1 TTTATA
1450660 AGTATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 3 0.09
18 1 0.03
19 1 0.03
20 3 0.09
21 3 0.09
22 13 0.38
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTATATTCGATTATAATTAT
Found at i:1450628 original size:17 final size:17
Alignment explanation
Indices: 1450608--1450666 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
1450598 ATATTCGATT
1450608 TATAATTATTTTATAAG
1 TATAATTATTTTATAAG
*
1450625 TAT-ATT-TTTTATATTCGACT
1 TATAATTATTTTATA----A-G
1450645 TATAATTATTTTATAAG
1 TATAATTATTTTATAAG
1450662 TATAA
1 TATAA
1450667 AATTAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 8 0.24
18 1 0.03
19 1 0.03
20 3 0.09
21 3 0.09
22 7 0.21
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TATAATTATTTTATAAG
Found at i:1450638 original size:37 final size:37
Alignment explanation
Indices: 1450595--1450665 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1450585 TAAAAATATA
*
1450595 TTTATATTCGATTTATAATTATTTTATAAGTATATTT
1 TTTATATTCGACTTATAATTATTTTATAAGTATATTT
1450632 TTTATATTCGACTTATAATTATTTTATAAGTATA
1 TTTATATTCGACTTATAATTATTTTATAAGTATA
1450666 AAATTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (37 bp):
TTTATATTCGACTTATAATTATTTTATAAGTATATTT
Found at i:1450647 original size:191 final size:194
Alignment explanation
Indices: 1450315--1450737 Score: 674
Period size: 191 Copynumber: 2.2 Consensus size: 194
1450305 TATTCAACCT
* * * *
1450315 GACCCACCCAGAAAACATATTGTTTATATTCGACTCGTCCTGACTTGATTCGAATAAATTAATAT
1 GACCCACCCAGAAAATATATTGTTTATATTCGACTTGCCCTGACTTGATTCAAATAAATTAATAT
* *
1450380 TTTAAAATATTTTTAAAAAATATATTTATATTGGACTTATAATTATTTTATAAGTATATTTTTTA
66 TTTAAAATA-TGTTAAAAAATATATTTATATTCGACTTATAATTATTTTATAAGTATATTTTTTA
1450445 TATTCGACTTATAATTATTTTATAAGTATAAAATTAATATTCGAATTATACTT-AAAAAATATTC
130 TATTCGACTTATAATTATTTTATAAGTATAAAATTAATATTCGAATTATACTTAAAAAAATATTC
*
1450509 GACCCACCTAGAAAATATATTGTTTATATTCGACTTGCCCCT-ACTTGATTCAAATAAATTAATA
1 GACCCACCCAGAAAATATATTGTTTATATTCGACTTG-CCCTGACTTGATTCAAATAAATTAATA
*
1450573 TTTTAAAATA-GTT-AAAAATATATTTATATTCGATTTATAATTATTTTATAAGTATATTTTTTA
65 TTTTAAAATATGTTAAAAAATATATTTATATTCGACTTATAATTATTTTATAAGTATATTTTTTA
* * *
1450636 TATTCGACTTATAATTATTTTATAAGTATAAAATTAATATTTGACTTATATTTAAAAAAATATTC
130 TATTCGACTTATAATTATTTTATAAGTATAAAATTAATATTCGAATTATACTTAAAAAAATATTC
* *
1450701 GACCAACCCAGAAATTTATATTGTTTATATTCGACTT
1 GACCCACCCAGAAA-ATATATTGTTTATATTCGACTT
1450738 ATAATTATTT
Statistics
Matches: 212, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
191 98 0.46
192 25 0.12
193 21 0.10
194 65 0.31
195 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (194 bp):
GACCCACCCAGAAAATATATTGTTTATATTCGACTTGCCCTGACTTGATTCAAATAAATTAATAT
TTTAAAATATGTTAAAAAATATATTTATATTCGACTTATAATTATTTTATAAGTATATTTTTTAT
ATTCGACTTATAATTATTTTATAAGTATAAAATTAATATTCGAATTATACTTAAAAAAATATTC
Found at i:1450676 original size:37 final size:37
Alignment explanation
Indices: 1450598--1450685 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
1450588 AAATATATTT
* *** *
1450598 ATATTCGATTTATAATTATTTTATAAGTATATTTTTT
1 ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
1450635 ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
1 ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
*
1450672 ATATTTGACTTATA
1 ATATTCGACTTATA
1450686 TTTAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (37 bp):
ATATTCGACTTATAATTATTTTATAAGTATAAAATTA
Found at i:1452872 original size:23 final size:23
Alignment explanation
Indices: 1452846--1452889 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1452836 TTCTACGCGT
1452846 TCCTTCGAGACAATTCTACGTTA
1 TCCTTCGAGACAATTCTACGTTA
* *
1452869 TCCTTCGAGATATTTCTACGT
1 TCCTTCGAGACAATTCTACGT
1452890 GGTCTTTCGG
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:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (23 bp):
TCCTTCGAGACAATTCTACGTTA
Found at i:1452898 original size:23 final size:23
Alignment explanation
Indices: 1452836--1452890 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1452826 GAGTTGAGGG
* *
1452836 TTCTACGCGTTCCTTCGAGACAA
1 TTCTACGTGATCCTTCGAGACAA
* * *
1452859 TTCTACGTTATCCTTCGAGATAT
1 TTCTACGTGATCCTTCGAGACAA
1452882 TTCTACGTG
1 TTCTACGTG
1452891 GTCTTTCGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.38
Consensus pattern (23 bp):
TTCTACGTGATCCTTCGAGACAA
Found at i:1459118 original size:23 final size:23
Alignment explanation
Indices: 1459084--1459185 Score: 116
Period size: 23 Copynumber: 4.4 Consensus size: 23
1459074 ATGTCGAGGG
* *
1459084 TTCTACGCGGTCTTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
1459107 TCCTACGTGGTCCTTGGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
1459130 TTCTACGTGGTCCTTGGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
1459153 TTCTATGCT-GTCCTTCGGGACAA
1 TTCTACG-TGGTCCTTCGGGACAA
*
1459176 TACTACGTGG
1 TTCTACGTGG
1459186 CACTTCGATG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
22 1 0.02
23 64 0.97
24 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:1459191 original size:23 final size:22
Alignment explanation
Indices: 1459097--1459217 Score: 100
Period size: 23 Copynumber: 5.2 Consensus size: 22
1459087 TACGCGGTCT
*
1459097 TTCGGGACAATCCTACGTGGTCC
1 TTCGGGACAATTCTACGTGG-CC
*
1459120 TTGGGGACAATTCTACGTGGTCC
1 TTCGGGACAATTCTACGTGG-CC
* * * *
1459143 TTGGGGACATTTCTATGCTGTCC
1 TTCGGGACAATTCTACG-TGGCC
*
1459166 TTCGGGACAATACTACGTGGCAC
1 TTCGGGACAATTCTACGTGGC-C
*
1459189 TTCGATG-CAATTTCTACGTGGCAC
1 TTCG-GGACAA-TTCTACGTGGC-C
1459213 TTCGG
1 TTCGG
1459218 TGCAATTTCT
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
22 3 0.04
23 59 0.73
24 19 0.23
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (22 bp):
TTCGGGACAATTCTACGTGGCC
Found at i:1459238 original size:24 final size:24
Alignment explanation
Indices: 1459178--1459254 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
1459168 CGGGACAATA
*
1459178 CTACGTGGCACTTCGATGCAATTT
1 CTACGTGGCACTTCGGTGCAATTT
1459202 CTACGTGGCACTTCGGTGCAATTT
1 CTACGTGGCACTTCGGTGCAATTT
* * * *
1459226 CTATGTTGTACTTCGGTGTAATTT
1 CTACGTGGCACTTCGGTGCAATTT
*
1459250 ATACG
1 CTACG
1459255 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (24 bp):
CTACGTGGCACTTCGGTGCAATTT
Found at i:1462602 original size:22 final size:21
Alignment explanation
Indices: 1462567--1462607 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1462557 AGTTTTATTA
1462567 AAGTTTTCTCTTTTACTTTTTC
1 AAGTTTTCTCTTTT-CTTTTTC
1462589 AAGTTTTCAT-TTTTCTTTT
1 AAGTTTTC-TCTTTTCTTTT
1462608 ATTTTCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 12 0.67
23 1 0.06
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (21 bp):
AAGTTTTCTCTTTTCTTTTTC
Found at i:1462618 original size:25 final size:27
Alignment explanation
Indices: 1462570--1462620 Score: 79
Period size: 25 Copynumber: 1.9 Consensus size: 27
1462560 TTTATTAAAG
1462570 TTTTCTCTTTTACTTTTTCAAGTTTTCA
1 TTTTCTCTTTTAC-TTTTCAAGTTTTCA
1462598 TTTT-TCTTTTA-TTTTCAAGTTTT
1 TTTTCTCTTTTACTTTTCAAGTTTT
1462621 GTTTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.52
27 7 0.30
28 4 0.17
ACGTcount: A:0.14, C:0.14, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTTCTCTTTTACTTTTCAAGTTTTCA
Found at i:1462626 original size:25 final size:26
Alignment explanation
Indices: 1462569--1462626 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1462559 TTTTATTAAA
*
1462569 GTTTTCTCTTTTACTTTTTCAAGTTTT
1 GTTTTTTCTTTTAC-TTTTCAAGTTTT
**
1462596 CATTTTTCTTTTA-TTTTCAAGTTTT
1 GTTTTTTCTTTTACTTTTCAAGTTTT
1462621 GTTTTT
1 GTTTTT
1462627 AATATGCTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 16 0.62
27 10 0.38
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.69
Consensus pattern (26 bp):
GTTTTTTCTTTTACTTTTCAAGTTTT
Found at i:1465214 original size:74 final size:75
Alignment explanation
Indices: 1465093--1465257 Score: 251
Period size: 74 Copynumber: 2.2 Consensus size: 75
1465083 TTAAATGACT
* * *
1465093 AGGGGTATCGGTACCCATAGGGCATTCTATTTTTCTCGGAGCCAAAATTTGCATAGGGGTATCGG
1 AGGGGTATCGGTACCCATAGAGCAATCTATTTTTCTCGGAGCCAAAATTGGCATAGGGGTATCGG
1465158 T-ACCCTATG
66 TAACCCTATG
* * *
1465167 AGGGGTATTGGTACCCATTGAGCAATCTGTTTTTCTCGGAGCCAAAATTGGCATAGGGGTATCGG
1 AGGGGTATCGGTACCCATAGAGCAATCTATTTTTCTCGGAGCCAAAATTGGCATAGGGGTATCGG
1465232 TACACCCTATG
66 TA-ACCCTATG
*
1465243 AGGGGTATCGATACC
1 AGGGGTATCGGTACC
1465258 TCCCTATTTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 60 0.74
76 21 0.26
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (75 bp):
AGGGGTATCGGTACCCATAGAGCAATCTATTTTTCTCGGAGCCAAAATTGGCATAGGGGTATCGG
TAACCCTATG
Found at i:1465883 original size:18 final size:19
Alignment explanation
Indices: 1465852--1465904 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1465842 TCAAATAACT
* * *
1465852 AATAAGCATTCAAACTAA-
1 AATAAACATCCAAACAAAC
1465870 AATAAACATCCAAACAAAC
1 AATAAACATCCAAACAAAC
1465889 AACTTAAACATCCAAA
1 AA--TAAACATCCAAA
1465905 TTCCAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 15 0.52
19 2 0.07
21 12 0.41
ACGTcount: A:0.58, C:0.23, G:0.02, T:0.17
Consensus pattern (19 bp):
AATAAACATCCAAACAAAC
Found at i:1467392 original size:13 final size:13
Alignment explanation
Indices: 1467376--1467414 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1467366 AATGGGTAAT
* *
1467376 TTTGAAATCTATG
1 TTTGAAAACAATG
1467389 TTTGAAAACAATG
1 TTTGAAAACAATG
1467402 TTTGAAAATCAAT
1 TTTGAAAA-CAAT
1467415 ATGTAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:1471299 original size:20 final size:21
Alignment explanation
Indices: 1471260--1471299 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1471250 GAAGCTTTAA
* *
1471260 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
1471281 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
1471300 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:1473442 original size:54 final size:54
Alignment explanation
Indices: 1473356--1473476 Score: 179
Period size: 54 Copynumber: 2.2 Consensus size: 54
1473346 TACCTCTAAG
* *
1473356 GGGGTATCGGAACCCATAGGGCATTCTATTTTTCTTAGAGCCAAAATTCACATA
1 GGGGTATCGGTACCCATAGGGCAATCTATTTTTCTTAGAGCCAAAATTCACATA
* * * **
1473410 GGGTTATCGGTACCCATTGGGCAATCTATTTTTCTTGGAGCCAAAATTGGCATA
1 GGGGTATCGGTACCCATAGGGCAATCTATTTTTCTTAGAGCCAAAATTCACATA
1473464 GGGGTATCGGTAC
1 GGGGTATCGGTAC
1473477 ACCCTATGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (54 bp):
GGGGTATCGGTACCCATAGGGCAATCTATTTTTCTTAGAGCCAAAATTCACATA
Found at i:1478869 original size:18 final size:18
Alignment explanation
Indices: 1478832--1478875 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1478822 TACCCTCTTA
*
1478832 TTTTTACTTTAATTGATT
1 TTTTTACTTTAATAGATT
*
1478850 TTATTTA-TTTAATAGTTT
1 TT-TTTACTTTAATAGATT
1478868 TTTTTACT
1 TTTTTACT
1478876 ATTTAAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTACTTTAATAGATT
Found at i:1481343 original size:81 final size:81
Alignment explanation
Indices: 1481228--1481395 Score: 300
Period size: 81 Copynumber: 2.1 Consensus size: 81
1481218 ATTGAAAACT
* * *
1481228 TTGTAAAAAAATCGAACATACCCATGTCATACATATAACTATATCTGAAGAGATGGAAGAACATA
1 TTGT-AAAAAATCGAACATACCCATGTCAGACATATAACTATATATGAAGAGATGGAAAAACATA
1481293 GTAGCATGCCACTTCCA
65 GTAGCATGCCACTTCCA
1481310 TTGTAAAAAATCGAACATACCCATGTCAGACATATAACTATATATGAAGAGATGGAAAAACATAG
1 TTGTAAAAAATCGAACATACCCATGTCAGACATATAACTATATATGAAGAGATGGAAAAACATAG
1481375 TAGCATGCCACTTCCA
66 TAGCATGCCACTTCCA
1481391 TTGTA
1 TTGTA
1481396 CTTTATTCAA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
81 79 0.95
82 4 0.05
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (81 bp):
TTGTAAAAAATCGAACATACCCATGTCAGACATATAACTATATATGAAGAGATGGAAAAACATAG
TAGCATGCCACTTCCA
Found at i:1488813 original size:18 final size:18
Alignment explanation
Indices: 1488777--1488813 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1488767 CTTACAACAC
*
1488777 TTACCACGACAACATCAT
1 TTACCACGACAACACCAT
*
1488795 TTACCACGACAACGCCAT
1 TTACCACGACAACACCAT
1488813 T
1 T
1488814 AACTTCACCA
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:0.35, C:0.35, G:0.08, T:0.22
Consensus pattern (18 bp):
TTACCACGACAACACCAT
Found at i:1494228 original size:17 final size:17
Alignment explanation
Indices: 1494206--1494241 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1494196 TTAAATCATC
1494206 TAGTTCATTCATTAAAT
1 TAGTTCATTCATTAAAT
* *
1494223 TAGTTCATTTATTAGAT
1 TAGTTCATTCATTAAAT
1494240 TA
1 TA
1494242 AATCTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (17 bp):
TAGTTCATTCATTAAAT
Found at i:1496198 original size:12 final size:12
Alignment explanation
Indices: 1496181--1496206 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1496171 AAATTGATTC
1496181 CTGCAAACAACA
1 CTGCAAACAACA
1496193 CTGCAAACAACA
1 CTGCAAACAACA
1496205 CT
1 CT
1496207 AAATTCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.35, G:0.08, T:0.12
Consensus pattern (12 bp):
CTGCAAACAACA
Found at i:1499165 original size:24 final size:24
Alignment explanation
Indices: 1499137--1499208 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
1499127 AATATGTCTC
1499137 AATAATTGTAGTTTCTTAATTTAT
1 AATAATTGTAGTTTCTTAATTTAT
* *
1499161 AATAATT-CA--ATC-T-ATTTAAAT
1 AATAATTGTAGTTTCTTAATTT--AT
*
1499182 AATAATTGTAGTTTTTTAATTTAT
1 AATAATTGTAGTTTCTTAATTTAT
1499206 AAT
1 AAT
1499209 TACAAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 11 0.31
22 1 0.03
23 1 0.03
24 13 0.36
25 1 0.03
26 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (24 bp):
AATAATTGTAGTTTCTTAATTTAT
Found at i:1501331 original size:30 final size:30
Alignment explanation
Indices: 1501297--1501429 Score: 230
Period size: 30 Copynumber: 4.4 Consensus size: 30
1501287 CCCGAAGGAC
1501297 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1501327 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1501357 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1501387 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1501417 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1501430 CCGAAGAACC
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 98 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1501487 original size:62 final size:63
Alignment explanation
Indices: 1501416--1501539 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
1501406 ATCCTCGATA
* *
1501416 ACTGTCCATAGGTCCCG-AAGAACCTAGGT-AAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAAG-ACATAGGTAAAACTGTCAATATGTTCCTTAGAACATAGGTAT
* *
1501478 ACTGTCCATATGTCTCGAAAGACATAGGTAAAACTGTCAATATGTTCCTTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAAGACATAGGTAAAACTGTCAATATGTTCCTTAGAACATAGGTA
1501540 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 22 0.39
63 34 0.61
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
ACTGTCCATAGGTCCCGAAAGACATAGGTAAAACTGTCAATATGTTCCTTAGAACATAGGTAT
Found at i:1501535 original size:32 final size:31
Alignment explanation
Indices: 1501415--1501542 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
1501405 GATCCTCGAT
* * ** *
1501415 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCTTAGAACATAGGTA
1501446 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCTTAGAACATAGGTA
* ***
1501477 TACTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCTTAGAACATAGGT-A
*
1501509 AACTGTCAATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCTTAGAACATAGGTA
1501540 AAC
1 AAC
1501543 CCTCGACTCT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
31 55 0.69
32 25 0.31
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCTTAGAACATAGGTA
Found at i:1502280 original size:22 final size:22
Alignment explanation
Indices: 1502236--1502277 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1502226 TAAATCAATT
*
1502236 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
1502258 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
1502278 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:1502751 original size:21 final size:21
Alignment explanation
Indices: 1502727--1502771 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1502717 TGTTGTTCGT
* *
1502727 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1502748 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1502769 TTG
1 TTG
1502772 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1506254 original size:30 final size:30
Alignment explanation
Indices: 1506105--1506237 Score: 248
Period size: 30 Copynumber: 4.4 Consensus size: 30
1506095 CCCGAAGGAC
1506105 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1506135 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1506165 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1506195 CTATCAAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1506225 CTGTCCAGAGGTC
1 CTATCCAGAGGTC
1506238 CCAAAGAACC
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 100 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1506277 original size:31 final size:31
Alignment explanation
Indices: 1506242--1506350 Score: 139
Period size: 31 Copynumber: 3.5 Consensus size: 31
1506232 GAGGTCCCAA
*
1506242 AGAACCTAGGTAAACTGTCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCTT
* * ***
1506273 AGAACATATGTATACTGTCCATATGTCTCGAA
1 AGAACATAGGTAAACTGTCCATATGT-TCCTT
1506305 AG-ACATAGGTAAAACTGTCCATATGTTCCTT
1 AGAACATAGGT-AAACTGTCCATATGTTCCTT
1506336 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
1506351 CCTCGACTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
31 38 0.59
32 26 0.41
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCTT
Found at i:1506327 original size:32 final size:31
Alignment explanation
Indices: 1506223--1506350 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
1506213 GATCCTCGGT
* * * *
1506223 AACTGTCCAGAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
** *
1506254 AACTGTCCATATGTTCCTTAGAACATATGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
* *
1506285 TACTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCAAAGAACATAGGT-A
**
1506317 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
1506348 AAC
1 AAC
1506351 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
31 52 0.67
32 26 0.33
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCAAAGAACATAGGTA
Found at i:1507086 original size:22 final size:22
Alignment explanation
Indices: 1507042--1507083 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1507032 TAAATCAATT
*
1507042 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
1507064 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
1507084 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:1507572 original size:21 final size:21
Alignment explanation
Indices: 1507533--1507577 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1507523 TGTTGTTCGT
* *
1507533 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
1507554 TTGAATGGGTACCGATTCCTC
1 TTGAAGGGGTACCGATTCCCC
1507575 TTG
1 TTG
1507578 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1508752 original size:44 final size:45
Alignment explanation
Indices: 1508703--1508994 Score: 195
Period size: 44 Copynumber: 6.5 Consensus size: 45
1508693 AGTAAGGTGT
* * *
1508703 AATGTTCTTTGGATGGCTCCCTTTCATGA-GTTTAAGCCATGTGA
1 AATGTTCTTTGGATGACTCCCCTTCATGAGGTTTAAGCCAAGTGA
* * * *
1508747 AATGTTCTTCGGATGACTTCCCTTCA-CAGGTTTAAGCCAAATGA
1 AATGTTCTTTGGATGACTCCCCTTCATGAGGTTTAAGCCAAGTGA
* * * * **
1508791 AGTATTCTTTGAATGACTCCCCTTCTTG-GGTTTAAATCAAGTGA
1 AATGTTCTTTGGATGACTCCCCTTCATGAGGTTTAAGCCAAGTGA
* * *
1508835 GATGTTTTATTTTGGATGACTCCCCTTCAT-AGGTTTAAGCCAGGTGA
1 AATG--TT-CTTTGGATGACTCCCCTTCATGAGGTTTAAGCCAAGTGA
* ** ** *
1508882 AATGTTCTTTCGGATGACTCCTCTTC--GAGGGTTTAATTCGGGTAA
1 AATGTTCTTT-GGATGACTCCCCTTCATGA-GGTTTAAGCCAAGTGA
* ** **
1508927 AATATTCTTCAGATGACTCCCCTTCGCG-GGTTTAAGCC-AGATGA
1 AATGTTCTTTGGATGACTCCCCTTCATGAGGTTTAAGCCAAG-TGA
* * * *
1508971 AGTATTCTTCGGATGACTACCCTT
1 AATGTTCTTTGGATGACTCCCCTT
1508995 TACGAGCTTA
Statistics
Matches: 192, Mismatches: 44, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
43 2 0.01
44 117 0.61
45 36 0.19
46 3 0.02
47 34 0.18
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (45 bp):
AATGTTCTTTGGATGACTCCCCTTCATGAGGTTTAAGCCAAGTGA
Found at i:1508958 original size:136 final size:135
Alignment explanation
Indices: 1508710--1508961 Score: 305
Period size: 136 Copynumber: 1.9 Consensus size: 135
1508700 TGTAATGTTC
* * *
1508710 TTTGGATGGCTCCCTTTCATGAGTTTAAGCCATGTGAAATGTTCTTCGGATGACTTCCCTTCACA
1 TTTGGATGACTCCCCTTCATGAGTTTAAGCCAGGTGAAATGTTCTTCGGATGACTTCCCTTCACA
* * * **
1508775 GGTTTAAGCCAAATGAAGTATTCTTTGAATGACTCCCCTTCTTGGGTTTAAATCAAGTGAGATGT
66 GGTTTAAGCCAAATAAAATATTCTTAGAATGACTCCCCTTCGCGGGTTTAAATCAAGTGAGATGT
1508840 TTTAT
131 TTTAT
1508845 TTTGGATGACTCCCCTTCAT-AGGTTTAAGCCAGGTGAAATGTTCTTTCGGATGAC-TCCTCTTC
1 TTTGGATGACTCCCCTTCATGA-GTTTAAGCCAGGTGAAATGTTC-TTCGGATGACTTCC-CTTC
* ** ***
1508908 GA-GGGTTTAATTCGGGTAAAATATTCTTCAG-ATGACTCCCCTTCGCGGGTTTAA
63 -ACAGGTTTAAGCCAAATAAAATATTCTT-AGAATGACTCCCCTTCGCGGGTTTAA
1508962 GCCAGATGAA
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
134 1 0.01
135 42 0.43
136 53 0.54
137 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (135 bp):
TTTGGATGACTCCCCTTCATGAGTTTAAGCCAGGTGAAATGTTCTTCGGATGACTTCCCTTCACA
GGTTTAAGCCAAATAAAATATTCTTAGAATGACTCCCCTTCGCGGGTTTAAATCAAGTGAGATGT
TTTAT
Found at i:1513106 original size:18 final size:18
Alignment explanation
Indices: 1513083--1513131 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1513073 GTAGTTTTTA
1513083 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* * *
1513101 AAATAAAAGAAAAATAGTT
1 AAATAAAA-AATAAGAATT
1513120 AAATAAACAAAT
1 AAATAAA-AAAT
1513132 TAAAGCGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 8 0.32
19 16 0.64
20 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:1513768 original size:64 final size:63
Alignment explanation
Indices: 1513697--1513818 Score: 192
Period size: 64 Copynumber: 1.9 Consensus size: 63
1513687 TAAAACATCT
*
1513697 TAAATCCTAATTAAAACACTTAAAA-CTATTTATACTAAAATACCTAAAAGATAATATAATATTC
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAAGA-AATATAATATTC
* *
1513761 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAA
1 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAGAAATATAA
1513819 AATATAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
63 12 0.22
64 42 0.78
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (63 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAGAAATATAATATTC
Found at i:1513788 original size:19 final size:19
Alignment explanation
Indices: 1513732--1513871 Score: 56
Period size: 19 Copynumber: 7.2 Consensus size: 19
1513722 CTATTTATAC
**
1513732 TAAAATACCTAAAAGATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1513752 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1513772 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
*
1513791 TAAACTA--AAATACCTAA-
1 TAAAATACTAAA-ACCTAAT
* **
1513808 AATAAATA-TAAAATATAA-
1 TA-AAATACTAAAACCTAAT
* *
1513826 AAATAATATCCTAAAACTTAAT
1 TAA-AATA--CTAAAACCTAAT
*
1513848 TAAAATACTAAAAACCTATT
1 TAAAATACT-AAAACCTAAT
1513868 TAAA
1 TAAA
1513872 CTAAAATACA
Statistics
Matches: 90, Mismatches: 20, Indels: 19
0.70 0.16 0.15
Matches are distributed among these distances:
17 5 0.06
18 19 0.21
19 26 0.29
20 21 0.23
21 17 0.19
22 2 0.02
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1513841 original size:32 final size:32
Alignment explanation
Indices: 1513799--1513861 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1513789 TTTAAACTAA
1513799 AATACCTAAAA-TAAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
1513830 AATATCCTAAAACTTAATTAAAATACTAAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAAA
1513862 CCTATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 14 0.50
33 10 0.36
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:1513889 original size:76 final size:77
Alignment explanation
Indices: 1513752--1513895 Score: 222
Period size: 77 Copynumber: 1.9 Consensus size: 77
1513742 AAAAGATAAT
* *
1513752 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAT-AAATA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAAATA
1513816 TAAAATATAAAA
66 TAAAATATAAAA
*
1513828 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATA-C-AAAGATAAAA
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACCTAAA-ATAAAA
1513891 TATAA
64 TATAA
1513896 TGTTTAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
75 3 0.05
76 29 0.47
77 30 0.48
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (77 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAAATA
TAAAATATAAAA
Found at i:1513904 original size:77 final size:75
Alignment explanation
Indices: 1513741--1513916 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 75
1513731 CTAAAATACC
* * * *
1513741 TAAAAGATAATATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT
1 TAAAATATAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT
1513806 AAAATAAATA
66 AAAATAAATA
*
1513816 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATA-
1 TAAAATAT-AAAATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATAC
1513880 C-AAAGATAAAATA
64 CTAAA-AT-AAATA
** * *
1513893 TAATGTTTAAAATATTATCCTAAA
1 TAAAATATAAAATAATATCCTAAA
1513917 CTTGAGTTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
75 10 0.11
76 46 0.52
77 32 0.36
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.31
Consensus pattern (75 bp):
TAAAATATAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT
AAAATAAATA
Found at i:1515826 original size:11 final size:11
Alignment explanation
Indices: 1515812--1515858 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1515802 TTAAAAAATA
1515812 AAAATAAAACG
1 AAAATAAAACG
*
1515823 AAAAT-AAATG
1 AAAATAAAACG
*
1515833 AAAATAAAAACA
1 AAAAT-AAAACG
*
1515845 AAAATATAACG
1 AAAATAAAACG
1515856 AAA
1 AAA
1515859 TGGGTTACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 9 0.31
11 12 0.41
12 8 0.28
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (11 bp):
AAAATAAAACG
Found at i:1515836 original size:21 final size:22
Alignment explanation
Indices: 1515807--1515850 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1515797 GTTCGTTAAA
*
1515807 AAATAAAAAT-AAAACGAAAAT
1 AAATAAAAATAAAAACAAAAAT
*
1515828 AAATGAAAATAAAAACAAAAAT
1 AAATAAAAATAAAAACAAAAAT
1515850 A
1 A
1515851 TAACGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (22 bp):
AAATAAAAATAAAAACAAAAAT
Found at i:1521085 original size:5 final size:5
Alignment explanation
Indices: 1521075--1521102 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1521065 AATTAATTAC
1521075 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1521103 GAAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1525725 original size:17 final size:16
Alignment explanation
Indices: 1525703--1525736 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1525693 TAAAAACAGT
1525703 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1525720 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1525736 A
1 A
1525737 TCCTCGCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1532065 original size:25 final size:24
Alignment explanation
Indices: 1532018--1532065 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1532008 AAATCCTAAT
** *
1532018 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
1532042 TAAAATACTTAAAACAAATATAAA
1 TAAAATAC-TAAAACAAATATAAA
1532066 ATATAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:1532069 original size:65 final size:66
Alignment explanation
Indices: 1531931--1532069 Score: 194
Period size: 66 Copynumber: 2.1 Consensus size: 66
1531921 AAAAACAAGC
*
1531931 TAAAACATCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAAATACCTAAAAAAATA
1 TAAAATATCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAAATACCTAAAAAAATA
1531996 A
66 A
* * * *
1531997 TATAATATTTTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACT-AAAATACTTAAAACAAA
1 TAAAATATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAAATACCTAAAA-AAA
1532060 T-A
64 TAA
1532062 TAAAATAT
1 TAAAATAT
1532070 AAAAACAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
65 25 0.38
66 40 0.62
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (66 bp):
TAAAATATCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAAATACCTAAAAAAATA
A
Found at i:1537695 original size:20 final size:20
Alignment explanation
Indices: 1537672--1537709 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1537662 TCTTAAATTC
*
1537672 ATATTGAATATGGT-AAAATG
1 ATATTAAAT-TGGTCAAAATG
1537692 ATATTAAATTGGTCAAAA
1 ATATTAAATTGGTCAAAA
1537710 CTCGAACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (20 bp):
ATATTAAATTGGTCAAAATG
Found at i:1539015 original size:3 final size:3
Alignment explanation
Indices: 1539007--1539044 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1538997 TCATTTTACA
1539007 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1539045 CAAGTATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1539436 original size:23 final size:23
Alignment explanation
Indices: 1539410--1539459 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1539400 CTCGTATAAA
1539410 TGCACCGAAGTACCACGTAGAAT
1 TGCACCGAAGTACCACGTAGAAT
* * *
1539433 TGCATCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTACCACGTAGAAT
1539456 TGCA
1 TGCA
1539460 TCGTAGTGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
TGCACCGAAGTACCACGTAGAAT
Found at i:1539460 original size:23 final size:23
Alignment explanation
Indices: 1539422--1539470 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1539412 CACCGAAGTA
1539422 CCACGTAGAATTGCATCGTAGTG
1 CCACGTAGAATTGCATCGTAGTG
1539445 CCACGTAGAATTGCATCGTAGTG
1 CCACGTAGAATTGCATCGTAGTG
1539468 CCA
1 CCA
1539471 TATAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (23 bp):
CCACGTAGAATTGCATCGTAGTG
Found at i:1543920 original size:3 final size:3
Alignment explanation
Indices: 1543912--1543961 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1543902 CTCCATAGAA
1543912 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1543960 AA
1 AA
1543962 AATGTGTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1548167 original size:20 final size:19
Alignment explanation
Indices: 1548127--1548175 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1548117 TTTATTTGAA
1548127 AAATAAAATAATCAAAGAT
1 AAATAAAATAATCAAAGAT
*
1548146 AAATAAAAATGATCGAAA-AT
1 AAAT-AAAATAATC-AAAGAT
1548166 AAATTAAAAT
1 AAA-TAAAAT
1548176 CCAAATTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 18 0.69
21 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (19 bp):
AAATAAAATAATCAAAGAT
Found at i:1548821 original size:32 final size:31
Alignment explanation
Indices: 1548763--1548822 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
1548753 CACAAACACT
* *
1548763 GCAATAGGTTTATATTTATAGGCGTTTTCCC
1 GCAATAGGTTTATATTTAGAGACGTTTTCCC
* *
1548794 GCAATAGGTTTGTTATTTAGCGACGTTTT
1 GCAATAGGTTT-ATATTTAGAGACGTTTT
1548823 TAGTCATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.46
32 13 0.54
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (31 bp):
GCAATAGGTTTATATTTAGAGACGTTTTCCC
Found at i:1555153 original size:13 final size:13
Alignment explanation
Indices: 1555135--1555180 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1555125 TTCATAAATA
1555135 TATGACGCGCATT
1 TATGACGCGCATT
* *
1555148 TATGACACACATT
1 TATGACGCGCATT
1555161 TATGACGCGCATT
1 TATGACGCGCATT
*
1555174 AATGACG
1 TATGACG
1555181 TTCATTGAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1555272 original size:85 final size:84
Alignment explanation
Indices: 1555158--1555380 Score: 256
Period size: 85 Copynumber: 2.6 Consensus size: 84
1555148 TATGACACAC
* * *
1555158 ATTTATGACGCGCAT-TAATGACGTTCATTGAGTATCATTGAAGCCCCCGTCATAAAT-TAAG-A
1 ATTTATGACACGCATGT-ATGACCTACATTGAGT-TCATTGAAGCCCCCGTCATAAATCT--GCA
1555220 TGAAACACATTTGTGCGTCATAA
62 TGAAACACATTTGTGCGTCATAA
*
1555243 ATTTATGACACGCATGTATGACCTACATTGCACG-TCATTGAAGCCCCCGTCATAAATCTGCTTG
1 ATTTATGACACGCATGTATGACCTACATTG-A-GTTCATTGAAGCCCCCGTCATAAATCTGCATG
* * *
1555307 ACATACATTTGTGTGTCATAA
64 AAACACATTTGTGCGTCATAA
* * * *
1555328 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCAT
1 ATTTATGACACGCATGTATGACCTACATTGAGT-TCATTGAAGCCCCCGTCAT
1555381 TAAAAAAGAC
Statistics
Matches: 120, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
83 1 0.01
84 1 0.01
85 114 0.95
86 3 0.03
87 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACCTACATTGAGTTCATTGAAGCCCCCGTCATAAATCTGCATGAA
ACACATTTGTGCGTCATAA
Found at i:1555435 original size:2 final size:2
Alignment explanation
Indices: 1555428--1555464 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1555418 TTTCGTAAAT
1555428 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1555465 TGTAGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1557280 original size:12 final size:12
Alignment explanation
Indices: 1557263--1557293 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1557253 ATATATTGAT
1557263 AATCAAATGAAA
1 AATCAAATGAAA
1557275 AATCAAATGAAA
1 AATCAAATGAAA
*
1557287 AAACAAA
1 AATCAAA
1557294 CCCGGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:1557878 original size:39 final size:40
Alignment explanation
Indices: 1557812--1557901 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 40
1557802 CTCATCCTTT
* *
1557812 TCTTTCTTTTTTCCCTTTTCGATGTCCCTTCTC-TTTTCTCC
1 TCTTTC-TTTTTCCCTTTTAGATGTCCCTTCTCATTTAC-CC
1557853 TCTTTCTTTTT-CCTTTGTAG-TGTCCCTTCTCATTTACCC
1 TCTTTCTTTTTCCCTTT-TAGATGTCCCTTCTCATTTACCC
*
1557892 TCTTCCTTTT
1 TCTTTCTTTT
1557902 CTTTCTCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
39 27 0.61
40 11 0.25
41 6 0.14
ACGTcount: A:0.04, C:0.32, G:0.06, T:0.58
Consensus pattern (40 bp):
TCTTTCTTTTTCCCTTTTAGATGTCCCTTCTCATTTACCC
Found at i:1557929 original size:51 final size:50
Alignment explanation
Indices: 1557857--1557953 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 50
1557847 TTCTCCTCTT
1557857 TCTTTTTCCTTTGTAGTGTCCCTTCTCATTTAC-CCTCTTCCTTTTCTTTC
1 TCTTTTTCCTTTGTAGTGTCCCTTCTCATTT-CTCCTCTTCCTTTTCTTTC
*
1557907 TCTTTTTCCGTCTT-TAGTGTCCCTTCTCCTTTCTCCTCTTCCTTTTC
1 TCTTTTTCC-T-TTGTAGTGTCCCTTCTCATTTCTCCTCTTCCTTTTC
1557954 AACAAGTTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
50 10 0.23
51 31 0.72
52 2 0.05
ACGTcount: A:0.04, C:0.34, G:0.06, T:0.56
Consensus pattern (50 bp):
TCTTTTTCCTTTGTAGTGTCCCTTCTCATTTCTCCTCTTCCTTTTCTTTC
Found at i:1565666 original size:42 final size:42
Alignment explanation
Indices: 1565604--1565688 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
1565594 TAACACAATC
*
1565604 GCGGTGTTTATAATAAAAACGCCACTAAGGTACATCACTATT
1 GCGGTGTTTATAATAAAAACGCCACTAAAGTACATCACTATT
* * *
1565646 GCGGTGTTTATTAA-ACAAACGCCAGTAAAGTACATGACTATT
1 GCGGTGTTTA-TAATAAAAACGCCACTAAAGTACATCACTATT
1565688 G
1 G
1565689 TGAAATTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (42 bp):
GCGGTGTTTATAATAAAAACGCCACTAAAGTACATCACTATT
Found at i:1568084 original size:13 final size:13
Alignment explanation
Indices: 1568066--1568090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1568056 TTGTCTTCAA
1568066 TAAAAATGAGCAC
1 TAAAAATGAGCAC
1568079 TAAAAATGAGCA
1 TAAAAATGAGCA
1568091 TATCTTGAGT
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:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (13 bp):
TAAAAATGAGCAC
Found at i:1569929 original size:20 final size:18
Alignment explanation
Indices: 1569904--1569951 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
1569894 TAAAACACTC
*
1569904 AAAAGAACAATGTAAAGTAA
1 AAAAGAACAAT-CAAAG-AA
*
1569924 AAAAGAAAAATCAAAGAA
1 AAAAGAACAATCAAAGAA
1569942 AACAAGAACA
1 AA-AAGAACA
1569952 CTCACAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.08
Consensus pattern (18 bp):
AAAAGAACAATCAAAGAA
Found at i:1570769 original size:6 final size:6
Alignment explanation
Indices: 1570753--1570793 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
1570743 CGATTTGTGA
*
1570753 GTTTTT ATTTTT GTTTTT G-TTTT G-TTTT GTTTTTT GTTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT G-TTTTT GTTTTT
1570794 TTCTTTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 10 0.32
6 16 0.52
7 5 0.16
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (6 bp):
GTTTTT
Found at i:1570770 original size:12 final size:11
Alignment explanation
Indices: 1570753--1570795 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
1570743 CGATTTGTGA
1570753 GTTTTTATTTTT
1 GTTTTT-TTTTT
*
1570765 GTTTTTGTTTT
1 GTTTTTTTTTT
1570776 GTTTTGTTTTTT
1 GTTTT-TTTTTT
1570788 GTTTTTTT
1 GTTTTTTT
1570796 CTTTTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:1570780 original size:17 final size:17
Alignment explanation
Indices: 1570755--1570792 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1570745 ATTTGTGAGT
1570755 TTTTATTTT-TGTTTTTG
1 TTTTATTTTGT-TTTTTG
*
1570772 TTTTGTTTTGTTTTTTG
1 TTTTATTTTGTTTTTTG
1570789 TTTT
1 TTTT
1570793 TTTCTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (17 bp):
TTTTATTTTGTTTTTTG
Found at i:1574292 original size:18 final size:18
Alignment explanation
Indices: 1574260--1574303 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1574250 CAGACTTATT
*
1574260 AAAAATAAA-AAAATA-A
1 AAAAAGAAATAAAATATA
1574276 AAAATAGAAATAAAATATA
1 AAAA-AGAAATAAAATATA
1574295 AAAAAGAAA
1 AAAAAGAAA
1574304 AAGACAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 11 0.46
19 5 0.21
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAAGAAATAAAATATA
Found at i:1574297 original size:26 final size:25
Alignment explanation
Indices: 1574261--1574314 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1574251 AGACTTATTA
1574261 AAAATAAAAAAATAAAAAATAGA-AAT
1 AAAATAAAAAAA-AAAAAA-AGACAAT
* *
1574287 AAAATATAAAAAAGAAAAAGACAAT
1 AAAATAAAAAAAAAAAAAAGACAAT
1574312 AAA
1 AAA
1574315 CAATACCGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 11 0.44
26 11 0.44
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.13
Consensus pattern (25 bp):
AAAATAAAAAAAAAAAAAAGACAAT
Found at i:1574647 original size:3 final size:3
Alignment explanation
Indices: 1574639--1574681 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1574629 TTTGGTTTTG
*
1574639 TTA TTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1574682 GTAATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1574655 original size:11 final size:11
Alignment explanation
Indices: 1574640--1574673 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1574630 TTGGTTTTGT
1574640 TATTATTA-TA
1 TATTATTATTA
1574650 TTATTATTATTA
1 -TATTATTATTA
1574662 TATTATTATTA
1 TATTATTATTA
1574673 T
1 T
1574674 TACTATTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.91
12 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:1574658 original size:14 final size:14
Alignment explanation
Indices: 1574639--1574681 Score: 77
Period size: 14 Copynumber: 3.0 Consensus size: 14
1574629 TTTGGTTTTG
1574639 TTATTATTATATTA
1 TTATTATTATATTA
1574653 TTATTATTATATTA
1 TTATTATTATATTA
1574667 TTATTATTACTATTA
1 TTATTATTA-TATTA
1574682 GTAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 23 0.82
15 5 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:1575430 original size:22 final size:22
Alignment explanation
Indices: 1575402--1575448 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1575392 CAGATATGGG
1575402 TTTAGGGGGAAGAATCGAGGGC
1 TTTAGGGGGAAGAATCGAGGGC
1575424 TTTAGGGGGAAGAATCGAGGGC
1 TTTAGGGGGAAGAATCGAGGGC
1575446 TTT
1 TTT
1575449 GGGAGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.43, T:0.23
Consensus pattern (22 bp):
TTTAGGGGGAAGAATCGAGGGC
Found at i:1576427 original size:35 final size:35
Alignment explanation
Indices: 1576385--1576454 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1576375 CAAACTCATT
*
1576385 ATGAATTCCATCGTTGCACACATAGTGCCGATATG
1 ATGAATTCCATCGTTGCACACATAGTACCGATATG
*
1576420 ATGAATTCCATGGTTGCACACATAGTACCGATATG
1 ATGAATTCCATCGTTGCACACATAGTACCGATATG
1576455 GTAATTCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (35 bp):
ATGAATTCCATCGTTGCACACATAGTACCGATATG
Found at i:1576505 original size:54 final size:53
Alignment explanation
Indices: 1576420--1576554 Score: 216
Period size: 54 Copynumber: 2.5 Consensus size: 53
1576410 TGCCGATATG
* * *
1576420 ATGAATTCCATGGTTGCACACATAGTACCGATATGGTAATTCACAAACTCATT
1 ATGAATTCCATGGTTGCACACATAGTGCCGATATGGTAATTCAAAAAATCATT
1576473 ATGAATTCCATGAGTTGCACACATAGTGCCGATATGGTAATTCAAAAAATCATT
1 ATGAATTCCATG-GTTGCACACATAGTGCCGATATGGTAATTCAAAAAATCATT
*
1576527 ATGAATTTCATGGGTTGCACACATAGTG
1 ATGAATTCCAT-GGTTGCACACATAGTG
1576555 TTGATAGTAC
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
53 12 0.16
54 63 0.83
55 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (53 bp):
ATGAATTCCATGGTTGCACACATAGTGCCGATATGGTAATTCAAAAAATCATT
Found at i:1577519 original size:20 final size:21
Alignment explanation
Indices: 1577476--1577519 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1577466 AAACTAAATT
** *
1577476 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
1577497 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
1577517 ACA
1 ACA
1577520 CTCAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:1577666 original size:27 final size:25
Alignment explanation
Indices: 1577640--1577688 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1577630 AACTGACCAT
*
1577640 ATTTAATCAAATCACATAA-AAATCC
1 ATTTTATCAAATCAC-TAATAAATCC
*
1577665 ATTTTATTAAATCACTAATAAATC
1 ATTTTATCAAATCACTAATAAATC
1577689 ACTAATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTTTATCAAATCACTAATAAATCC
Found at i:1583575 original size:53 final size:55
Alignment explanation
Indices: 1583507--1583667 Score: 265
Period size: 54 Copynumber: 3.0 Consensus size: 55
1583497 ACCTAAGTAC
*
1583507 CGATATGGTAATTCACAAACTCATTATGAATTCTAT-GGTTGCACACATAGTGCT
1 CGATATGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCT
* *
1583561 -GATATGGTAGTTCACAAACTCATTATGAATTCCATGGGTTGTACACATAGTG-T
1 CGATATGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCT
*
1583614 CGATATGGTAATTCACAAACTAATTATGAATTCCATGGGTTGCACACATAGTGC
1 CGATATGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCACACATAGTGC
1583668 CAATAGTACA
Statistics
Matches: 98, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
53 34 0.35
54 64 0.65
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (55 bp):
CGATATGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCACACATAGTGCT
Found at i:1586001 original size:13 final size:14
Alignment explanation
Indices: 1585976--1586022 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1585966 TAGATATTAA
1585976 TTTATTAACCTTAT
1 TTTATTAACCTTAT
* *
1585990 TTTATT-ATCTTAA
1 TTTATTAACCTTAT
*
1586003 TTTCTTAACCTTAT
1 TTTATTAACCTTAT
1586017 TTTATT
1 TTTATT
1586023 GTTATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATTAACCTTAT
Found at i:1588666 original size:14 final size:14
Alignment explanation
Indices: 1588643--1588679 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1588633 CATTTTTACC
*
1588643 GTTCACCTTCCACT
1 GTTCATCTTCCACT
1588657 GTTCATCTTCCACT
1 GTTCATCTTCCACT
1588671 GTTCATCTT
1 GTTCATCTT
1588680 TATTAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.35, G:0.08, T:0.43
Consensus pattern (14 bp):
GTTCATCTTCCACT
Found at i:1589097 original size:26 final size:25
Alignment explanation
Indices: 1589061--1589118 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
1589051 ATTTTTCATA
*
1589061 AAAAAATAAAATAAAT-GAAAAATGTC
1 AAAAAATAAAA-AAATCCAAAAAT-TC
1589087 AAAAAATAAAAAAATCCAAAAATTC
1 AAAAAATAAAAAAATCCAAAAATTC
1589112 ACAAAAA
1 A-AAAAA
1589119 GTTCACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.72, C:0.09, G:0.03, T:0.16
Consensus pattern (25 bp):
AAAAAATAAAAAAATCCAAAAATTC
Found at i:1589116 original size:10 final size:10
Alignment explanation
Indices: 1589103--1589132 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1589093 TAAAAAAATC
1589103 CAAAAATTCA
1 CAAAAATTCA
1589113 CAAAAAGTTCA
1 CAAAAA-TTCA
1589124 CAAAAATTC
1 CAAAAATTC
1589133 GAAAATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (10 bp):
CAAAAATTCA
Found at i:1608673 original size:29 final size:29
Alignment explanation
Indices: 1608627--1608682 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1608617 CTATCTCTGC
* *
1608627 CGAATGAGTCTATAAAGCCTGAACAAAGT
1 CGAAGGAGTCTATAAAGCATGAACAAAGT
*
1608656 CGAAGGAGTCTATGAAGCATGAACAAA
1 CGAAGGAGTCTATAAAGCATGAACAAA
1608683 TGAAGATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (29 bp):
CGAAGGAGTCTATAAAGCATGAACAAAGT
Found at i:1610324 original size:20 final size:20
Alignment explanation
Indices: 1610261--1610325 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
1610251 TTTAATGAGG
1610261 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * * **
1610281 CG-TCCTAA-GCGAAAGAAGA
1 AGTTCATAATGAG-AAGAACT
1610300 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1610320 TGTTCA
1 AGTTCA
1610326 ACCCAAGTTC
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1611119 original size:5 final size:5
Alignment explanation
Indices: 1611109--1611177 Score: 57
Period size: 5 Copynumber: 12.2 Consensus size: 5
1611099 ACACACTATT
*
1611109 TTTTA TTTTA TTTTA TTTTCA TGTTTA TTTGTT TTTTA TTTTACA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A T-TTTA TTT-TA TTTTA TTTT--A TTTTA
1611159 TTTGATAA TTTTA TTTTA T
1 TTT--T-A TTTTA TTTTA T
1611178 CACTTCCAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
5 32 0.59
6 9 0.17
7 9 0.17
8 4 0.07
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:1611149 original size:23 final size:23
Alignment explanation
Indices: 1611109--1611176 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 23
1611099 ACACACTATT
1611109 TTTTATTT-TATTTTATTTT-CA
1 TTTTATTTGTATTTTATTTTACA
*
1611130 TGTTTATTTGTTTTTTATTTTACA
1 T-TTTATTTGTATTTTATTTTACA
1611154 TTTTATTTGATAATTTTATTTTA
1 TTTTATTTG-T-ATTTTATTTTA
1611177 TCACTTCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 1 0.03
22 7 0.17
23 18 0.45
24 4 0.10
25 10 0.25
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTATTTGTATTTTATTTTACA
Found at i:1611458 original size:15 final size:14
Alignment explanation
Indices: 1611438--1611471 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
1611428 AAAACAAACT
1611438 AATTTTTGTCTTTAA
1 AATTTTTGTC-TTAA
1611453 AATTTTTTGTCTTAA
1 AA-TTTTTGTCTTAA
1611468 AATT
1 AATT
1611472 ATTTTAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.11
15 8 0.44
16 8 0.44
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (14 bp):
AATTTTTGTCTTAA
Found at i:1611461 original size:16 final size:15
Alignment explanation
Indices: 1611440--1611476 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
1611430 AACAAACTAA
1611440 TTTTTGTCTTTAAAAT
1 TTTTTGTC-TTAAAAT
1611456 TTTTTGTCTTAAAAT
1 TTTTTGTCTTAAAAT
1611471 TATTTT
1 T-TTTT
1611477 AAGGACGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTGTCTTAAAAT
Found at i:1612364 original size:64 final size:65
Alignment explanation
Indices: 1612247--1612432 Score: 243
Period size: 64 Copynumber: 2.9 Consensus size: 65
1612237 CTCTTGGATA
* * * * * * *
1612247 CATCGATACACTACTTGTTTTATTAAAACATCGAATGCATTTTGTGTATCGATGTACAGACAATG
1 CATCAATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACAATG
1612312 CATCAATACAC-CCTGGTTTTATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACAATG
1 CATCAATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACAATG
* * *
1612376 CATCAATACACTCCTGGCTCTT-TTGAAACATCGAATGTA-ATTAGTGTACCGATGCAC
1 CATCAATACACTCCTGG-TTTTATTGAAACATCGAATGCATTTTA-TGTACCGATGCAC
1612433 CCCAAGTGTA
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
64 61 0.56
65 44 0.41
66 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (65 bp):
CATCAATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTATGTACCGATGCACAGACAATG
Found at i:1618512 original size:12 final size:13
Alignment explanation
Indices: 1618483--1618515 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1618473 GTATTATGAT
*
1618483 TTTTCAAACATTG
1 TTTTCAAACATAG
1618496 TTTTCAAA-ATAG
1 TTTTCAAACATAG
1618508 TTTTCAAA
1 TTTTCAAA
1618516 GTTTGCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:1620253 original size:13 final size:13
Alignment explanation
Indices: 1620231--1620264 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1620221 AGGGGGAGTA
*
1620231 ATTTTCAAAATTG
1 ATTTTCAAAAATG
1620244 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1620256 ATTTTCAAA
1 ATTTTCAAA
1620265 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1620769 original size:65 final size:65
Alignment explanation
Indices: 1620583--1620772 Score: 274
Period size: 65 Copynumber: 2.9 Consensus size: 65
1620573 ACACTCTTGG
* * * * *
1620583 ATGCATCGATACACTCATTGTTTTATTAAAACATCGAATGCATTTTGTGTATCGATACACAGACA
1 ATGCATCGATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCACAGACA
*
1620648 ATGCATCGATACACTCCTGGTTTTATTGAAACGTCGAATGCATTTTGTGTACCGATGCACAGACA
1 ATGCATCGATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCACAGACA
* * * *
1620713 ATGCATCGATACACTCCTGGCTCTT-TTGAAACATCGAATGTAATTAGTGTACCGATGCAC
1 ATGCATCGATACACTCCTGG-TTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCAC
1620773 CCCAAGTGTA
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
65 110 0.97
66 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (65 bp):
ATGCATCGATACACTCCTGGTTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCACAGACA
Found at i:1623814 original size:31 final size:31
Alignment explanation
Indices: 1623761--1623825 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1623751 TTAATTTTGA
* *
1623761 CCCTAATTTTATATGGTTAATTATACTTTAC
1 CCCTAATTTTATATGATCAATTATACTTTAC
* *
1623792 CCCTCATTTTCTATGATCAATTATACTTTAC
1 CCCTAATTTTATATGATCAATTATACTTTAC
1623823 CCC
1 CCC
1623826 CTTTCAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.05, T:0.45
Consensus pattern (31 bp):
CCCTAATTTTATATGATCAATTATACTTTAC
Found at i:1632095 original size:19 final size:19
Alignment explanation
Indices: 1632063--1632099 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1632053 ATGACCAACA
* *
1632063 AAATCGCAATGCGATCTCT
1 AAATCACAACGCGATCTCT
1632082 AAATCACAACGCGATCTC
1 AAATCACAACGCGATCTC
1632100 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:1632213 original size:20 final size:20
Alignment explanation
Indices: 1632125--1632211 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
1632115 GTTTCCATAT
*
1632125 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * *
1632145 TCGCAACGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
*
1632165 TCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1632185 TCGCAACACGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1632205 TCGCAAC
1 TCGCAAC
1632212 ACTGAATTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.02
20 54 0.96
21 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1632380 original size:17 final size:17
Alignment explanation
Indices: 1632358--1632412 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
1632348 CGACATCCGT
*
1632358 TCCTATATCCAACGACA
1 TCCTATATCTAACGACA
1632375 TCCTATATCTAACGACA
1 TCCTATATCTAACGACA
1632392 TCCTATATCTAACGACA
1 TCCTATATCTAACGACA
1632409 TCCT
1 TCCT
1632413 TCCCCATCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (17 bp):
TCCTATATCTAACGACA
Found at i:1635402 original size:18 final size:18
Alignment explanation
Indices: 1635379--1635413 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1635369 AGCAAAAGGC
*
1635379 AATCAAATTCACAATCAA
1 AATCAAAATCACAATCAA
*
1635397 AATCAAAATCCCAATCA
1 AATCAAAATCACAATCA
1635414 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (18 bp):
AATCAAAATCACAATCAA
Found at i:1635609 original size:20 final size:20
Alignment explanation
Indices: 1635584--1635750 Score: 170
Period size: 20 Copynumber: 8.7 Consensus size: 20
1635574 TTACACATTC
*
1635584 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1635604 ATTTGACTATCACAAAGCGA
1 ATTTGACTATCGCAACGCGA
1635624 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1635644 ATTTGACTGTCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
1635664 ATTTGATTATCGCAACTG-GA
1 ATTTGACTATCGCAAC-GCGA
*
1635684 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1635704 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
1635718 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1635738 A-TTGACTTTCGCA
1 ATTTGACTATCGCA
1635751 TTGCGATTTT
Statistics
Matches: 122, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
19 11 0.09
20 98 0.80
21 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1635768 original size:20 final size:20
Alignment explanation
Indices: 1635743--1635781 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1635733 CGCGAATTGA
1635743 CTTTCGCATTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
1635763 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
1635782 AGTTTAGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:1635794 original size:20 final size:20
Alignment explanation
Indices: 1635743--1635796 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1635733 CGCGAATTGA
*
1635743 CTTTCGCATTGCGATTTTGG
1 CTTTAGCATTGCGATTTTGG
*
1635763 CTTTCGCATTGCGATTTTGAG
1 CTTTAGCATTGCGATTTTG-G
*
1635784 -TTTAGCGTTGCGA
1 CTTTAGCATTGCGA
1635797 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.43
Consensus pattern (20 bp):
CTTTAGCATTGCGATTTTGG
Found at i:1635937 original size:14 final size:14
Alignment explanation
Indices: 1635916--1635954 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1635906 CATCAATTAA
1635916 ACAAATCAATTTTT
1 ACAAATCAATTTTT
* *
1635930 ATAAATCAACTTTT
1 ACAAATCAATTTTT
1635944 ACAAATCAATT
1 ACAAATCAATT
1635955 AAACAAGCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:1637397 original size:21 final size:20
Alignment explanation
Indices: 1637331--1637400 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1637321 GTGAATCGGG
*
1637331 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
1637351 CCTCTTCAACGATGACAGGGGC
1 -CTCTTGAACGGTGGGA-GGGA
1637373 CTCTTGAACGGTGGGAGAGGA
1 CTCTTGAACGGTGGGAG-GGA
1637394 CTCTTGA
1 CTCTTGA
1637401 GGGATGATAG
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.89
22 3 0.08
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:1637398 original size:42 final size:42
Alignment explanation
Indices: 1637331--1637453 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
1637321 GTGAATCGGG
* *
1637331 CTCTTGAATGGTGGGAG-GGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGAGGA-CTCTTGAACGATGACAGGGGC
** *
1637373 CTCTTGAACGGTGGGAGAGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGAGGACTCTTGAACGATGACAGGGGC
* ** * *
1637415 CTCTTGAACGATAAGAGAGGCCTTTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGAGGACTCTTGAACGATGACAGG
1637454 TGAGTCGGGA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 64 0.96
43 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGGACTCTTGAACGATGACAGGGGC
Found at i:1637436 original size:21 final size:21
Alignment explanation
Indices: 1637351--1637449 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 21
1637341 GTGGGAGGGA
* * *
1637351 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGAGG
* *
1637372 CCTCTTGAACGGTGGGAGAGG
1 CCTCTTGAACGATGAGAGAGG
* ** * *
1637393 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGAGAGAGG
*
1637414 CCTCTTGAACGATAAGAGAGG
1 CCTCTTGAACGATGAGAGAGG
*
1637435 CCTTTTGAACGATGA
1 CCTCTTGAACGATGA
1637450 CAGGTGAGTC
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGAGG
Found at i:1638132 original size:33 final size:34
Alignment explanation
Indices: 1638074--1638145 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
1638064 ACTAAATCCG
* *
1638074 CGTTGCGATTTTCATTTTCGTATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
1638108 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
1638141 CGTTG
1 CGTTG
1638146 TGATAGTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:1638170 original size:20 final size:20
Alignment explanation
Indices: 1638141--1638209 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1638131 GCGATTATCC
*
1638141 CGTTGTGATAGTCAAATTT-G
1 CGTTGCGATAGTC-AATTTCG
1638161 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
1638181 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
1638201 CGTTGCGAT
1 CGTTGCGAT
1638210 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.09
20 37 0.84
21 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:1640117 original size:20 final size:20
Alignment explanation
Indices: 1640094--1640147 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1640084 GAAACTTAAA
*
1640094 ATCGCAACACGAAAATAACT
1 ATCGCAACGCGAAAATAACT
** *
1640114 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATAACT
1640134 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1640148 CTAAAATCGC
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:0.26, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:1640546 original size:22 final size:22
Alignment explanation
Indices: 1640519--1640565 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1640509 GAGATAGACA
1640519 GATTTCGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
1640541 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
1640563 GAT
1 GAT
1640566 GTCACCGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.45, T:0.21
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACG
Found at i:1640735 original size:21 final size:21
Alignment explanation
Indices: 1640711--1640785 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
1640701 CGCTTTGAAA
*
1640711 ATCGCATTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* * **
1640732 ATCGCGTTGAGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
1640752 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
1640773 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
1640786 AGTCAGAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 24 0.57
22 3 0.07
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:1640757 original size:20 final size:20
Alignment explanation
Indices: 1640732--1640805 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1640722 ATTTTGTATT
*
1640732 ATCGCGTTGAGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
1640752 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
1640773 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
1640793 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1640806 TTACATATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 24 0.56
21 13 0.30
22 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:1640767 original size:41 final size:41
Alignment explanation
Indices: 1640710--1640807 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
1640700 GCGCTTTGAA
1640710 AATCGCATTGCGATTTTGTATTATCGCGTTGAGATAGTCAG
1 AATCGCATTGCGATTTTGTATTATCGCGTTGAGATAGTCAG
* *
1640751 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATTTTGTATTATCGCGTTGAGATAGTCAG
1640792 AATCGCATTGCGATTT
1 AATCGCATTGCGATTT
1640808 ACATATTCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.37
Consensus pattern (41 bp):
AATCGCATTGCGATTTTGTATTATCGCGTTGAGATAGTCAG
Done.