Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 24 of 150
Found at i:6208351 original size:13 final size:13
Alignment explanation
Indices: 6208335--6208359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6208325 TATAACCCCA
6208335 AAAAATAAAAAAT
1 AAAAATAAAAAAT
6208348 AAAAATAAAAAA
1 AAAAATAAAAAA
6208360 GAGAGAAAAT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:6209992 original size:9 final size:9
Alignment explanation
Indices: 6209978--6210005 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6209968 GGAACAGAAT
6209978 AATAATAAA
1 AATAATAAA
6209987 AATAATAAA
1 AATAATAAA
6209996 AATAATAAA
1 AATAATAAA
6210005 A
1 A
6210006 TAGTAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAATAAA
Found at i:6225445 original size:31 final size:31
Alignment explanation
Indices: 6225410--6225470 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
6225400 CTTACACTCT
**
6225410 AATTTGATTCGTTTTAGTCCCTTTACTTTTC
1 AATTTGATTAATTTTAGTCCCTTTACTTTTC
* * *
6225441 AATTTGGTTAATTTTAGTCCTTTTATTTTT
1 AATTTGATTAATTTTAGTCCCTTTACTTTT
6225471 TTTAATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (31 bp):
AATTTGATTAATTTTAGTCCCTTTACTTTTC
Found at i:6226771 original size:2 final size:2
Alignment explanation
Indices: 6226764--6226792 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6226754 AATCAAGGGG
6226764 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
6226793 TTGGTGATGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6228065 original size:21 final size:21
Alignment explanation
Indices: 6228036--6228075 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6228026 ATAAGAAAAC
*
6228036 AAAACTATAACATTTTTATGA
1 AAAAATATAACATTTTTATGA
**
6228057 AAAAATATATTATTTTTAT
1 AAAAATATAACATTTTTAT
6228076 AATATATAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
AAAAATATAACATTTTTATGA
Found at i:6228278 original size:29 final size:27
Alignment explanation
Indices: 6228234--6228287 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
6228224 CCATTTGAAA
*
6228234 TTTTTTTTAGAATTTACATAATATACT
1 TTTTTTTTAGAATTTACAAAATATACT
* *
6228261 TTTTTTGTTATAACTTTATAAAATATA
1 TTTTTT-TTAGAA-TTTACAAAATATA
6228288 TAAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 5 0.23
29 11 0.50
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (27 bp):
TTTTTTTTAGAATTTACAAAATATACT
Found at i:6228868 original size:34 final size:33
Alignment explanation
Indices: 6228825--6228918 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 33
6228815 GAATTTTTTT
6228825 TAAATTTAATTAAATTAAGTTTTAGGGGTTTTAAG
1 TAAA-TTAATTAAATTAAG-TTTAGGGGTTTTAAG
* *
6228860 TAAATTAATTAAAATAAAGTTTAGGGTTTTTAAG
1 TAAATTAATT-AAATTAAGTTTAGGGGTTTTAAG
* *
6228894 AAAATTAATTAAATTAGGGTTTAGG
1 TAAATTAATTAAATTA-AGTTTAGG
6228919 TTTTAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.10
34 36 0.69
35 11 0.21
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (33 bp):
TAAATTAATTAAATTAAGTTTAGGGGTTTTAAG
Found at i:6229372 original size:127 final size:126
Alignment explanation
Indices: 6229018--6229544 Score: 696
Period size: 126 Copynumber: 4.2 Consensus size: 126
6229008 GATTTTGTTT
* * * * * * *
6229018 TCTTTTTCTACAGTAGTTTCTGAAAAATTAATTTTGAGAAGATACTTCTGAAAAGATAATGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAA
* * * *
6229083 ACACGCTTCAAGCAGGATGTACTGTCAGCAAAAGTACTAAAAAAAGCTCCCACGTGGACGC
66 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
* * * *
6229144 TCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAA
* * *
6229209 AAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCACGTGGATGC
66 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
*
6229270 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTCTGAAAAAAATAGTGTCA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACAGTTCTG-AAAAAATAGTGTCA
* * * * * * *
6229335 AAAACGCTTCAAACAGGATACACTGTCAACAAAATTACTGAAAAAAGC-TCATACATGAACGC
65 AAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTTC-CACGTGGACGC
* * ** * * *
6229397 TATTTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGATGGTTATGAAGAAATAGTGTTAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAA
* *
6229462 AAACGCTTCAAGCAGGATGCACTGTTAGCAAAATTACTAAAAAAAGCTTCCAGGTGGACGC
66 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
* *
6229523 ACTTTTTCTAAAGTAGTTCCTG
1 TCTTTTTCTACAGTAGTTCCTG
6229545 CTTGGCCTTA
Statistics
Matches: 350, Mismatches: 48, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
126 237 0.68
127 113 0.32
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (126 bp):
TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAA
AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
Found at i:6229466 original size:253 final size:252
Alignment explanation
Indices: 6229018--6229544 Score: 721
Period size: 253 Copynumber: 2.1 Consensus size: 252
6229008 GATTTTGTTT
* * * * *
6229018 TCTTTTTCTACAGTAGTTTCTGAAAAATTAATTTTGAGAAGATACTTCTGAAAAGATAATGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACACTTCTGAAAAAATAATGTCAA
* * ** * * * * *
6229083 ACACGCTTCAAGCAGGATGTACTGTCAGCAAAAGTACTAAAAAAAGCTCCCACGTGGACGCTCTT
66 AAACGCTTCAAACAGGATACACTGTCAACAAAAGTACTAAAAAAAGCTCACACATGAACGCTATT
* * * *
6229148 TTTCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTCAAAAAC
131 TTTCTACAATAGATCCTGAAAAAATAATTTAGAGAAGACAGTTATGAAAAAATAGTGTCAAAAAC
* *
6229213 GCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCACGTGGATGC
196 GCTTCAAGCAGGATGCACTATCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
** *
6229270 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTCTGAAAAAAATAGTGTCA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACACTTCTG-AAAAAATAATGTCA
* * *
6229335 AAAACGCTTCAAACAGGATACACTGTCAACAAAATTACTGAAAAAAGCTCATACATGAACGCTAT
65 AAAACGCTTCAAACAGGATACACTGTCAACAAAAGTACTAAAAAAAGCTCACACATGAACGCTAT
* ** * *
6229400 TTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGATGGTTATGAAGAAATAGTGTTAAAAA
130 TTTTCTACAATAGATCCTGAAAAAATAATTTAGAGAAGACAGTTATGAAAAAATAGTGTCAAAAA
* * *
6229465 CGCTTCAAGCAGGATGCACTGTTAGCAAAATTACTAAAAAAAGCTTCCAGGTGGACGC
195 CGCTTCAAGCAGGATGCACTATCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
* *
6229523 ACTTTTTCTAAAGTAGTTCCTG
1 TCTTTTTCTACAGTAGTTCCTG
6229545 CTTGGCCTTA
Statistics
Matches: 238, Mismatches: 36, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
252 44 0.18
253 194 0.82
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (252 bp):
TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACACTTCTGAAAAAATAATGTCAA
AAACGCTTCAAACAGGATACACTGTCAACAAAAGTACTAAAAAAAGCTCACACATGAACGCTATT
TTTCTACAATAGATCCTGAAAAAATAATTTAGAGAAGACAGTTATGAAAAAATAGTGTCAAAAAC
GCTTCAAGCAGGATGCACTATCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
Found at i:6231496 original size:42 final size:42
Alignment explanation
Indices: 6231439--6231572 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 42
6231429 TTCCATTTAG
* * *
6231439 CTCTCATGAGCTTCAGTTTAACCC-TATTGGGTTTTTGTTCAG
1 CTCTTATGAGCTTCAGTTTAACCCTTA-TGGGTTTCTGTTCAA
* *
6231481 CTCTTTTGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAA
1 CTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTCAA
* * * * * *
6231523 CTCTTATGAGCTTCCGTTCAACTCTTATGAGCTTCCGTTCAA
1 CTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTCAA
*
6231565 CCCTTATG
1 CTCTTATG
6231573 GGTTTCTGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 75 0.97
43 2 0.03
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.42
Consensus pattern (42 bp):
CTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTCAA
Found at i:6231528 original size:21 final size:21
Alignment explanation
Indices: 6231475--6231572 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
6231465 TTGGGTTTTT
* * *
6231475 GTTCAGCTCTTTTGAGCTTCA
1 GTTCAACTCTTATGAGCTTCC
* * * *
6231496 GTTTC-ACCCTTATGGGTTTCT
1 G-TTCAACTCTTATGAGCTTCC
6231517 GTTCAACTCTTATGAGCTTCC
1 GTTCAACTCTTATGAGCTTCC
6231538 GTTCAACTCTTATGAGCTTCC
1 GTTCAACTCTTATGAGCTTCC
*
6231559 GTTCAACCCTTATG
1 GTTCAACTCTTATG
6231573 GGTTTCTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTCAACTCTTATGAGCTTCC
Found at i:6231592 original size:63 final size:63
Alignment explanation
Indices: 6231475--6231593 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
6231465 TTGGGTTTTT
* * *
6231475 GTTCAGCTCTTTTGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAACTCTTATGAGCTTCC
1 GTTCAACTCTTATGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAACACTTATGAGCTTCC
* * *
6231538 GTTCAACTCTTATGAGCTTCCG-TTCAACCCTTATGGGTTTCTGTTTAGCACTTATG
1 GTTCAACTCTTATGAGCTTCAGTTTC-ACCCTTATGGGTTTCTGTTCAACACTTATG
6231594 TTCTTCTGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
62 3 0.06
63 46 0.94
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (63 bp):
GTTCAACTCTTATGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAACACTTATGAGCTTCC
Found at i:6235940 original size:18 final size:18
Alignment explanation
Indices: 6235919--6235953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6235909 AAGGAAACAC
*
6235919 ATAAATGTTAGGATACAT
1 ATAAAGGTTAGGATACAT
*
6235937 ATAAGGGTTAGGATACA
1 ATAAAGGTTAGGATACA
6235954 CACTGGTATA
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:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (18 bp):
ATAAAGGTTAGGATACAT
Found at i:6236632 original size:5 final size:5
Alignment explanation
Indices: 6236624--6236649 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6236614 GAGATGGAAT
6236624 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
6236650 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:6236649 original size:26 final size:26
Alignment explanation
Indices: 6236598--6236649 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
6236588 TGAAGTTTTC
* * *
6236598 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
6236624 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
6236650 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:6237605 original size:21 final size:21
Alignment explanation
Indices: 6237571--6237611 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6237561 GGGGTAAAGT
*
6237571 GGGAAGAAGTAAAAGTTTTGA
1 GGGAAGAAGTAAAAGGTTTGA
6237592 GGGAA-AAGTAAAAAGGTTTG
1 GGGAAGAAGT-AAAAGGTTTG
6237612 GGAGTTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAGAAGTAAAAGGTTTGA
Found at i:6237666 original size:9 final size:9
Alignment explanation
Indices: 6237649--6237685 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6237639 TATAGTTTGA
6237649 TATTCGAAT
1 TATTCGAAT
*
6237658 TATTTGAAT
1 TATTCGAAT
*
6237667 TATTCGAGT
1 TATTCGAAT
6237676 TATTCGAAT
1 TATTCGAAT
6237685 T
1 T
6237686 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6255827 original size:6 final size:6
Alignment explanation
Indices: 6255816--6255840 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6255806 TGTGGGTGAT
6255816 TGATGG TGATGG TGATGG TGATGG T
1 TGATGG TGATGG TGATGG TGATGG T
6255841 CTTCTTGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TGATGG
Found at i:6261174 original size:12 final size:12
Alignment explanation
Indices: 6261157--6261181 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6261147 AACTCTGTAG
6261157 CTAGTTTAAATT
1 CTAGTTTAAATT
6261169 CTAGTTTAAATT
1 CTAGTTTAAATT
6261181 C
1 C
6261182 GATTTTAAAA
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:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (12 bp):
CTAGTTTAAATT
Found at i:6269583 original size:13 final size:13
Alignment explanation
Indices: 6269565--6269589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6269555 TTTCTCTCTT
6269565 AAGCTGGATGTTC
1 AAGCTGGATGTTC
6269578 AAGCTGGATGTT
1 AAGCTGGATGTT
6269590 AATTTGCCTA
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:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (13 bp):
AAGCTGGATGTTC
Found at i:6282514 original size:25 final size:25
Alignment explanation
Indices: 6282455--6282515 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
6282445 AGCTCATATA
* *
6282455 AGCTTACCGATACTCAGCTCGCATG
1 AGCTTACCGTTACTCAGCTCGCAGG
* * *
6282480 AGCTTGCCGTTATTCAGCTCGGAGG
1 AGCTTACCGTTACTCAGCTCGCAGG
6282505 AGCTTACCGTT
1 AGCTTACCGTT
6282516 TATAGCTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (25 bp):
AGCTTACCGTTACTCAGCTCGCAGG
Found at i:6304189 original size:31 final size:31
Alignment explanation
Indices: 6304153--6304211 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
6304143 AACTTTAATT
* *
6304153 CTTATACTTTTCGAATTGGTCAATTTTAGGC
1 CTTATACTTTTCAAATTGGTAAATTTTAGGC
*
6304184 CTTATACTTTTCAAATTTGTAAATTTTA
1 CTTATACTTTTCAAATTGGTAAATTTTA
6304212 ATGCTGACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (31 bp):
CTTATACTTTTCAAATTGGTAAATTTTAGGC
Found at i:6312750 original size:2 final size:2
Alignment explanation
Indices: 6312745--6312775 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6312735 GCATATATGA
6312745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6312776 GTAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6312800 original size:17 final size:17
Alignment explanation
Indices: 6312778--6312813 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
6312768 TATATATAGT
6312778 AAATAAA-AATAAAACTA
1 AAATAAATAA-AAAACTA
6312795 AAATAAATAAAAAACTA
1 AAATAAATAAAAAACTA
6312812 AA
1 AA
6312814 TTAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAATAAAAAACTA
Found at i:6312814 original size:16 final size:17
Alignment explanation
Indices: 6312777--6312819 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
6312767 ATATATATAG
6312777 TAAATAAA-AATAAAAC
1 TAAATAAATAATAAAAC
6312793 TAAAATAAATAA-AAAAC
1 T-AAATAAATAATAAAAC
*
6312810 TAAATTAATA
1 TAAATAAATA
6312820 TATTATCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
17 13 0.54
18 2 0.08
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAATAAATAATAAAAC
Found at i:6312932 original size:3 final size:3
Alignment explanation
Indices: 6312829--6312913 Score: 68
Period size: 3 Copynumber: 27.7 Consensus size: 3
6312819 ATATTATCAC
* * *
6312829 AAT AAT AAT GAAT AAAT AA- AAG AAA AAT AA- AACT AAT AAT GAT CAAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT
*
6312876 AAT AAT AGT AAT AAT AAT AAT AAT GAA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
6312914 AGTAATTAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.09
3 50 0.74
4 12 0.18
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:6314395 original size:2 final size:2
Alignment explanation
Indices: 6314388--6314439 Score: 72
Period size: 2 Copynumber: 26.0 Consensus size: 2
6314378 TCATTGTACA
6314388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
6314429 AT GAT AT AT AT
1 AT -AT AT AT AT
6314440 CTATTTGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.04
2 41 0.89
3 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6315292 original size:58 final size:58
Alignment explanation
Indices: 6315202--6315318 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
6315192 AATCAATGAA
* *
6315202 CACCTCTAGTTAGAAGGCTATGGGCTTGATTTGTCGGGTTTTAATATAGAGGATTAGT
1 CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
6315260 CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
1 CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
6315318 C
1 C
6315319 TTGATTGGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (58 bp):
CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
Found at i:6316910 original size:6 final size:6
Alignment explanation
Indices: 6316899--6316926 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6316889 AACTCTAATT
6316899 TCCCAA TCCCAA TCCCAA TCCCAA TCCC
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCC
6316927 GATTCATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.18
Consensus pattern (6 bp):
TCCCAA
Found at i:6330744 original size:2 final size:2
Alignment explanation
Indices: 6330737--6330763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6330727 AATAGAGAAC
6330737 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6330764 GCTGGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6331947 original size:2 final size:2
Alignment explanation
Indices: 6331940--6331979 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
6331930 TCCATGGTGA
*
6331940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6331980 GATTTGTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6342762 original size:21 final size:21
Alignment explanation
Indices: 6342706--6342787 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
6342696 TGATCAGTAA
*
6342706 ACGACACAT-AAGTGCCTGAA
1 ACGACACATAAAGTGCCTGAT
** *
6342726 ACGACACACGAGGTGCCTGAT
1 ACGACACATAAAGTGCCTGAT
*
6342747 ACGACACATAAAGTGCTTGATGT
1 ACGACACATAAAGTGCCTGA--T
*
6342770 ATGACACATAAAGTGCCT
1 ACGACACATAAAGTGCCT
6342788 AATCGGTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
20 8 0.16
21 25 0.50
23 17 0.34
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
ACGACACATAAAGTGCCTGAT
Found at i:6343153 original size:16 final size:16
Alignment explanation
Indices: 6343127--6343166 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
6343117 TTAATAATAA
*
6343127 TACTTATCTTA-TATT
1 TACTTACCTTATTATT
6343142 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
6343159 TACTTACC
1 TACTTACC
6343167 ATACACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:6343459 original size:13 final size:13
Alignment explanation
Indices: 6343441--6343466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6343431 TTGCTTTTTC
6343441 TAATAATATAATA
1 TAATAATATAATA
6343454 TAATAATATAATA
1 TAATAATATAATA
6343467 GTTTTACTTA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:6343597 original size:5 final size:5
Alignment explanation
Indices: 6343587--6343684 Score: 196
Period size: 5 Copynumber: 19.6 Consensus size: 5
6343577 TTTTTACATA
6343587 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6343637 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
6343685 TTTAAAACAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 93 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:6348539 original size:32 final size:33
Alignment explanation
Indices: 6348496--6348568 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
6348486 TATTTATCAT
* *
6348496 ATAAAAAATC-TTTTACTAATTA-ATAATAAATA
1 ATAAAATATCTTTTTACTAAATATAT-ATAAATA
6348528 ATAAAATATCTTTTTACTAAATATATATAAATA
1 ATAAAATATCTTTTTACTAAATATATATAAATA
6348561 ATACAAAT
1 ATA-AAAT
6348569 GTACTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 9 0.25
33 21 0.58
34 6 0.17
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (33 bp):
ATAAAATATCTTTTTACTAAATATATATAAATA
Found at i:6355559 original size:98 final size:98
Alignment explanation
Indices: 6355385--6355579 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
6355375 ATAATGAAAA
*
6355385 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACAATT
*
6355450 CCTTTAGAATCCCAAACTCGGAATATTTCCTTC
66 CCTTTAGAATCCCAAACTCGGAAAATTTCCTTC
* * *
6355483 ACTTTAAATGAACATCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACAATT
*
6355548 CCTTTATAATCCCAAACTCGGAAAATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAAAATTTCCTT
6355580 TATGATTCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACAATT
CCTTTAGAATCCCAAACTCGGAAAATTTCCTTC
Found at i:6357580 original size:40 final size:41
Alignment explanation
Indices: 6357513--6357591 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
6357503 GAGTTTTAGT
* * **
6357513 TTAACCCTATTGGATTTCCGTTTAGCTCTTTTGAGCTTCAG
1 TTAACCCTATTGGATTTCCATTCAGCTCTTACGAGCTTCAG
6357554 TTAACCCT-TATGG-TTTCCATTCAGCTCTTACGAGCTTC
1 TTAACCCTAT-TGGATTTCCATTCAGCTCTTACGAGCTTC
6357592 TTTCAACCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (41 bp):
TTAACCCTATTGGATTTCCATTCAGCTCTTACGAGCTTCAG
Found at i:6357982 original size:15 final size:15
Alignment explanation
Indices: 6357958--6357993 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6357948 ATCAATACGG
*
6357958 CCCAACTAGCCTAAA
1 CCCAATTAGCCTAAA
*
6357973 CCCAATTAGCCTAAG
1 CCCAATTAGCCTAAA
6357988 CCCAAT
1 CCCAAT
6357994 ACCCTAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.17
Consensus pattern (15 bp):
CCCAATTAGCCTAAA
Found at i:6361035 original size:2 final size:2
Alignment explanation
Indices: 6361028--6361069 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6361018 AAATGTTAGA
6361028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6361070 GATAATATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6374754 original size:16 final size:17
Alignment explanation
Indices: 6374723--6374755 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6374713 TGCCATTTCA
*
6374723 TAACTAAACAACATTTT
1 TAACCAAACAACATTTT
6374740 TAACCAAAC-ACATTTT
1 TAACCAAACAACATTTT
6374756 ACTTGCTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TAACCAAACAACATTTT
Found at i:6375646 original size:40 final size:40
Alignment explanation
Indices: 6375541--6375676 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
6375531 TATTATAATC
** * * * **
6375541 TCGCACACTAAGTGCTTTACATACCCAAAGCTATCTCAGTC
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTC-GAA
* * * * *
6375582 TCGCACACTAAGTGTCGTATATAGCTGAAGCTAT-TCCTAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCT-CGAA
*
6375622 TCGCACACTAAGTGCCATAAATAGCCGAAGTTATCTCGAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
6375662 TCGCACACTAAGTGC
1 TCGCACACTAAGTGC
6375677 TAAACATAGT
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
40 48 0.62
41 29 0.38
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
Found at i:6378489 original size:9 final size:9
Alignment explanation
Indices: 6378475--6378505 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6378465 GTTAAACGAA
6378475 TCGAGTTAT
1 TCGAGTTAT
*
6378484 TCGAGTTAA
1 TCGAGTTAT
6378493 TCGAGTTAT
1 TCGAGTTAT
6378502 TCGA
1 TCGA
6378506 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:6378577 original size:9 final size:9
Alignment explanation
Indices: 6378558--6378594 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6378548 TGAGTTTTCA
*
6378558 AATTTGAAT
1 AATTCGAAT
*
6378567 AACTCGAAT
1 AATTCGAAT
6378576 AATTCGAAT
1 AATTCGAAT
6378585 AATTCGAAT
1 AATTCGAAT
6378594 A
1 A
6378595 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6378656 original size:21 final size:21
Alignment explanation
Indices: 6378630--6378672 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6378620 ACCCCAAACT
*
6378630 CTCAAACCGTTTTACTT-TTCC
1 CTCAAAAC-TTTTACTTCTTCC
6378651 CTCAAAACTTTTACTTCTTCC
1 CTCAAAACTTTTACTTCTTCC
6378672 C
1 C
6378673 ACTTTCCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTACTTCTTCC
Found at i:6380253 original size:23 final size:22
Alignment explanation
Indices: 6380219--6380266 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
6380209 TCTAAATTTT
6380219 AAAATTTTAAAAATAAAAA-AC
1 AAAATTTTAAAAATAAAAATAC
6380240 AAAATTCTTAAAAATAAAAATAC
1 AAAATT-TTAAAAATAAAAATAC
6380263 AAAA
1 AAAA
6380267 CTAAATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 6 0.24
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAATTTTAAAAATAAAAATAC
Found at i:6382591 original size:21 final size:22
Alignment explanation
Indices: 6382565--6382612 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
6382555 GAGCAAGTAT
6382565 AAAAAAA-TTGAGAAAATACAA
1 AAAAAAATTTGAGAAAATACAA
* *
6382586 AAAAAAATTTGAGAAGATACCA
1 AAAAAAATTTGAGAAAATACAA
6382608 AAAAA
1 AAAAA
6382613 TGTGAGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAAAATTTGAGAAAATACAA
Found at i:6382728 original size:20 final size:21
Alignment explanation
Indices: 6382705--6382754 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
6382695 AAGTGAATAT
6382705 ACCAAAAAAAC-TGAGGACAA
1 ACCAAAAAAACATGAGGACAA
* *
6382725 ACC-AATAAACATGAGGAGAA
1 ACCAAAAAAACATGAGGACAA
6382745 ACCAAAAAAA
1 ACCAAAAAAA
6382755 TAGGAGGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 14 0.56
21 5 0.20
ACGTcount: A:0.62, C:0.18, G:0.14, T:0.06
Consensus pattern (21 bp):
ACCAAAAAAACATGAGGACAA
Found at i:6383165 original size:23 final size:22
Alignment explanation
Indices: 6383139--6383185 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
6383129 TACTGAATTC
*
6383139 TAATTTTGAAACTATACCAATAA
1 TAATTATGAAACTATACCAA-AA
**
6383162 TAATTATGAAGGTATACCAAAA
1 TAATTATGAAACTATACCAAAA
6383184 TA
1 TA
6383186 TATGAAGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (22 bp):
TAATTATGAAACTATACCAAAA
Found at i:6383191 original size:20 final size:23
Alignment explanation
Indices: 6383151--6383193 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
6383141 ATTTTGAAAC
6383151 TATACCAATAATAATTATGAAGG
1 TATACCAATAATAATTATGAAGG
6383174 TATACCAA-AAT-A-TATGAAGG
1 TATACCAATAATAATTATGAAGG
6383194 AATATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 3 0.15
23 8 0.40
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (23 bp):
TATACCAATAATAATTATGAAGG
Found at i:6383745 original size:17 final size:17
Alignment explanation
Indices: 6383702--6383747 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
6383692 GCTTTTAAAG
*
6383702 ATATC-AAAATTATAAA
1 ATATCAAAAATTAAAAA
*
6383718 AT-TACATAAATTAAAAA
1 ATAT-CAAAAATTAAAAA
6383735 ATATCAAAAATTA
1 ATATCAAAAATTA
6383748 TGAGAGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 19 0.79
18 1 0.04
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATCAAAAATTAAAAA
Found at i:6384285 original size:15 final size:15
Alignment explanation
Indices: 6384265--6384308 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
6384255 GGTCAAAGTA
**
6384265 TAATTTTATCTTTTT
1 TAATTTTATAATTTT
6384280 TAATTTT-TAATTTT
1 TAATTTTATAATTTT
*
6384294 TAATTTTAAAATTTT
1 TAATTTTATAATTTT
6384309 ATCCTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTATAATTTT
Found at i:6384302 original size:6 final size:7
Alignment explanation
Indices: 6384276--6384300 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6384266 AATTTTATCT
6384276 TTTTTAA
1 TTTTTAA
6384283 TTTTTAA
1 TTTTTAA
6384290 TTTTTAA
1 TTTTTAA
6384297 TTTT
1 TTTT
6384301 AAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:6386025 original size:114 final size:114
Alignment explanation
Indices: 6385906--6386527 Score: 887
Period size: 114 Copynumber: 5.4 Consensus size: 114
6385896 GTTTACTTGT
* * *
6385906 AAGCGCCACAAAATATCTTAACCAAAATGCGGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
6385971 GCTTATGAAAAAACGCCGCTAAAGCACATAATTAGCGACACTTTTATAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCACTTTTATAA
* * * *
6386020 AAGCGCCACAAAATATCTTAACCAAAATGCAGTGCTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
*** * *
6386085 GCTTATGAAAAAACGCCGCTAAAGCACGGAATTAGCGGCGC-ATTATAAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCACTTTTAT-AA
6386134 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * * * *
6386199 GCTTATGAAAAAATGCAGCTAAAGCACAGCATTAGCGGCGC-ATTATAAA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCACTTTTAT-AA
*
6386248 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCTTTTGGTCTTGAGGTATATTTAGAATTAGTGG
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA-TTAGAATTAGTGG
* * * *
6386313 TGCTTATGAGAAAACGTCGCTAAAGCACATCATTAGCGG-AGC-ATTATAAA
65 CGCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCA-CTTTTAT-AA
* *
6386363 AAGCGCCGTAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
6386428 GCTTATGAGAAAACGCCGCTAAAGCACATCATTAGCGGTGCA-TTATA-AA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGC-G-GCACTTTTATAA
6386477 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
6386528 GAGCTAATAG
Statistics
Matches: 468, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
113 4 0.01
114 356 0.76
115 104 0.22
116 3 0.01
117 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (114 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCACTTTTATAA
Found at i:6386425 original size:229 final size:228
Alignment explanation
Indices: 6385906--6386527 Score: 978
Period size: 229 Copynumber: 2.7 Consensus size: 228
6385896 GTTTACTTGT
* * *
6385906 AAGCGCCACAAAATATCTTAACCAAAATGCGGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * * * *
6385971 GCTTATGAAAAAACGCCGCTAAAGCACATAATTAGCGACAC-TTTTATAAAAGCGCCACAAAATA
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATA-AAAAGCGCCGCAAAATA
* *
6386035 TCTTAACCAAAATGCAG-TGCTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAAC
130 TCTTAACCAAAACGCAGCT-TTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAAC
* *
6386099 GCCGCTAAAGCACGGAATTAGCGGCGCATTATAAA
194 GCCGCTAAAGCACAGAATTAGCGGAGCATTATAAA
6386134 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* * *
6386199 GCTTATGAAAAAATGCAGCTAAAGCACAGCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
* *
6386264 CTTAACCAAAACGCAGCTTTTGGTCTTGAGGTATATTTAGAATTAGTGGTGCTTATGAGAAAACG
131 CTTAACCAAAACGCAGCTTTTGGTCTTGAGGTATA-TTAGAATTAGTGGCGCTTATGAAAAAACG
* **
6386329 TCGCTAAAGCACATCATTAGCGGAGCATTATAAA
195 CCGCTAAAGCACAGAATTAGCGGAGCATTATAAA
* *
6386363 AAGCGCCGTAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
* *
6386428 GCTTATGAGAAAACGCCGCTAAAGCACATCATTAGCGGTGCATTATAAAAAGCGCCGCAAAATAT
66 GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
*
6386493 CTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA
131 CTTAACCAAAACGCAGCTTTTGGTCTTGAGGTATA
6386528 GAGCTAATAG
Statistics
Matches: 363, Mismatches: 28, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
228 145 0.40
229 218 0.60
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (228 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAAACGCCGCTAAAGCACATCATTAGCGGCGCATTATAAAAAGCGCCGCAAAATAT
CTTAACCAAAACGCAGCTTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGC
CGCTAAAGCACAGAATTAGCGGAGCATTATAAA
Found at i:6386512 original size:343 final size:342
Alignment explanation
Indices: 6385906--6386527 Score: 1023
Period size: 343 Copynumber: 1.8 Consensus size: 342
6385896 GTTTACTTGT
* *
6385906 AAGCGCCACAAAATATCTTAACCAAAATGCGGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCACAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
*
6385971 GCTTATGAAAAAACGCCGCTAAAGCACATAATTAGCGACACTTTTATAAAAGCGCCACAAAATAT
66 GCTTATGAAAAAACGCCGCTAAAGCACATAATTAGCGACACTTATATAAAAGCGCCACAAAATAT
* *
6386036 CTTAACCAAAATGCAGTGCTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGC
131 CTTAACCAAAACGCAGCGCTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGC
*
6386101 CGCTAAAGCACGGAATTAGCGGCGCATTATAAAAAGCGCCGCAAAATATCTTAACCAAAACGCAG
196 CGCTAAAGCACAGAATTAGCGGCGCATTATAAAAAGCGCCGCAAAATATCTTAACCAAAACGCAG
6386166 CGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAATGCAGCTAAAGCACAGCAT
261 CGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAATGCAGCTAAAGCACAGCAT
6386231 TAGCGGCGCATTATAAA
326 TAGCGGCGCATTATAAA
* *
6386248 AAGCGCCGCAAAATATCTTAACCAAAACGCAGCTTTTGGTCTTGAGGTATATTTAGAATTAGTGG
1 AAGCGCCACAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATA-TTAGAATTAGTGG
* * * * **
6386313 TGCTTATGAGAAAACGTCGCTAAAGCACATCATTAGCGGAGCA-TTATA-AAAAGCGCCGTAAAA
65 CGCTTATGAAAAAACGCCGCTAAAGCACATAATTAGC-GA-CACTTATATAAAAGCGCCACAAAA
* * *
6386376 TATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAGAAAA
128 TATCTTAACCAAAACGCAGCGCTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAA
** *
6386441 CGCCGCTAAAGCACATCATTAGCGGTGCATTATAAAAAGCGCCGCAAAATATCTTAACCAAAACG
193 CGCCGCTAAAGCACAGAATTAGCGGCGCATTATAAAAAGCGCCGCAAAATATCTTAACCAAAACG
6386506 CAGCGTTTGGTCTTGAGGTATA
258 CAGCGTTTGGTCTTGAGGTATA
6386528 GAGCTAATAG
Statistics
Matches: 257, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
342 47 0.18
343 202 0.79
344 6 0.02
345 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (342 bp):
AAGCGCCACAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGC
GCTTATGAAAAAACGCCGCTAAAGCACATAATTAGCGACACTTATATAAAAGCGCCACAAAATAT
CTTAACCAAAACGCAGCGCTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAACGC
CGCTAAAGCACAGAATTAGCGGCGCATTATAAAAAGCGCCGCAAAATATCTTAACCAAAACGCAG
CGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGAAAAAATGCAGCTAAAGCACAGCAT
TAGCGGCGCATTATAAA
Found at i:6388337 original size:24 final size:24
Alignment explanation
Indices: 6388310--6388368 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
6388300 ATCCCTCAGT
6388310 TTTCCCCTCAAATTTTTCCCCAAA
1 TTTCCCCTCAAATTTTTCCCCAAA
* *
6388334 TTTCCCCTCCAA-TTTTCCCTAAA
1 TTTCCCCTCAAATTTTTCCCCAAA
*
6388357 ATTCCCC-CAAAT
1 TTTCCCCTCAAAT
6388369 CTAGAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 16 0.53
24 11 0.37
ACGTcount: A:0.25, C:0.39, G:0.00, T:0.36
Consensus pattern (24 bp):
TTTCCCCTCAAATTTTTCCCCAAA
Found at i:6388347 original size:12 final size:12
Alignment explanation
Indices: 6388310--6388368 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 12
6388300 ATCCCTCAGT
6388310 TTTCCCCTCAAA
1 TTTCCCCTCAAA
*
6388322 TTTTTCCC-CAAA
1 -TTTCCCCTCAAA
*
6388334 TTTCCCCTCCAA
1 TTTCCCCTCAAA
*
6388346 TTTTCCCT-AAA
1 TTTCCCCTCAAA
*
6388357 ATTCCCC-CAAA
1 TTTCCCCTCAAA
6388368 T
1 T
6388369 CTAGAACCCT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
11 16 0.44
12 14 0.39
13 6 0.17
ACGTcount: A:0.25, C:0.39, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTCCCCTCAAA
Found at i:6389591 original size:26 final size:26
Alignment explanation
Indices: 6389562--6389620 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
6389552 CTCGTTGCAT
*
6389562 AATAATTCTTACTCTATAGCTTATCA
1 AATAATTCTTACTCTATAGCTTATAA
6389588 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTTACTCTATAGCTTATAA
6389614 AATAATT
1 AATAATT
6389621 AAATTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.42
Consensus pattern (26 bp):
AATAATTCTTACTCTATAGCTTATAA
Found at i:6390448 original size:43 final size:44
Alignment explanation
Indices: 6390297--6390587 Score: 210
Period size: 42 Copynumber: 6.8 Consensus size: 44
6390287 TTTTTTTATA
* ** * *
6390297 AAAGCGCCGCTAAA-AGTCATGTTCTATAGCGGCGTTTGT-GGA-
1 AAAGCGCCGCTAAAGA-ACATGACCTTTAGCGGCGTTTGTCGAAG
* * * * * *
6390339 AAATCGCCGCTAAAGAGCACGACCTTTAGTGGCGTTTGTGGAAA
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTCGAAG
* * *
6390383 AAAACGCCGCTAAAGAACATTACTTTTAGCGGCGTTTGT-GAAG
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTCGAAG
* * * * *
6390426 AAAGGGCGGCTAAAGAACATTACCTTTAGCTGTGTTT-TCG-AG
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTCGAAG
* ***
6390468 GAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTGTT-T-TTTG
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGT-TTGTCGAAG
* * ***
6390511 -AAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-T--TTT
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTCGAAG
* *
6390551 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGTTT
1 AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
6390588 ATTTCTGTAA
Statistics
Matches: 207, Mismatches: 35, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
40 2 0.01
41 36 0.17
42 94 0.45
43 42 0.20
44 33 0.16
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
AAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTCGAAG
Found at i:6390560 original size:41 final size:41
Alignment explanation
Indices: 6390387--6390587 Score: 213
Period size: 42 Copynumber: 4.8 Consensus size: 41
6390377 TGGAAAAAAA
* * ***
6390387 CGCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGAAGAAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTT-TTTTG-AAG
* * * * * ***
6390430 GGCGGCTAAAGAACATTACCTTTAGCTGTGTTTTCGAGGAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT-TTTGAAG
6390472 CGCCGCTAAAGAACATGACCTTTAGCGGCGTGTTTTTTGAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGT-TTTTTTGAAG
* * *
6390514 TGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAG
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTGAAG
*
6390555 CGCCGCTAAAGAACATGACCTTTAGCGGTGTTT
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
6390588 ATTTCTGTAA
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.29
42 63 0.46
43 34 0.25
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTGAAG
Found at i:6392339 original size:16 final size:15
Alignment explanation
Indices: 6392304--6392339 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6392294 CAAAGCTAAG
6392304 ATTTTTAAAACATTT
1 ATTTTTAAAACATTT
* *
6392319 ATTTTTACAATATTT
1 ATTTTTAAAACATTT
6392334 ATTTTT
1 ATTTTT
6392340 GCTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTTAAAACATTT
Found at i:6395751 original size:19 final size:18
Alignment explanation
Indices: 6395711--6395751 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
6395701 AATATTACAC
*
6395711 ATTTCAATTTCACATTAA
1 ATTTCAATTTCACACTAA
*
6395729 ATTTCAATTTTCACACTAT
1 ATTTCAA-TTTCACACTAA
6395748 ATTT
1 ATTT
6395752 TGCTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTCAATTTCACACTAA
Found at i:6396190 original size:9 final size:9
Alignment explanation
Indices: 6396173--6396216 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
6396163 TCCTTCCTCC
6396173 CTTTCTTTT
1 CTTTCTTTT
*
6396182 CTTTTTTTT
1 CTTTCTTTT
*
6396191 CATTCTTTTT
1 CTTTC-TTTT
6396201 CTTTCTTTT
1 CTTTCTTTT
6396210 CTTTCTT
1 CTTTCTT
6396217 AATTTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:6396202 original size:19 final size:19
Alignment explanation
Indices: 6396178--6396216 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6396168 CCTCCCTTTC
*
6396178 TTTTCTTTTTTTTCATTCT
1 TTTTCTTTCTTTTCATTCT
*
6396197 TTTTCTTTCTTTTCTTTCT
1 TTTTCTTTCTTTTCATTCT
6396216 T
1 T
6396217 AATTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTCTTTCTTTTCATTCT
Found at i:6402518 original size:14 final size:14
Alignment explanation
Indices: 6402494--6402526 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6402484 AAATCTCACC
6402494 AAAATAATATTTTA
1 AAAATAATATTTTA
6402508 TAAAA-AATATTTTA
1 -AAAATAATATTTTA
6402522 AAAAT
1 AAAAT
6402527 TAAAAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATAATATTTTA
Found at i:6414717 original size:23 final size:23
Alignment explanation
Indices: 6414686--6414745 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
6414676 AGCCAAATAT
*
6414686 ATAAA-TTTTAAAAAAGTTT-TAA
1 ATAAATTTTTAAAAAA-TTTCAAA
6414708 ATAAATTTTTAAAAAATTTCAAA
1 ATAAATTTTTAAAAAATTTCAAA
* *
6414731 ATATATATTTAAAAA
1 ATAAATTTTTAAAAA
6414746 TTTTATGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAAATTTTTAAAAAATTTCAAA
Found at i:6414724 original size:11 final size:11
Alignment explanation
Indices: 6414691--6414726 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
6414681 AATATATAAA
*
6414691 TTTTAAAAAAG
1 TTTTAAAAAAT
6414702 TTTTAAATAAAT
1 TTTTAAA-AAAT
6414714 TTTTAAAAAAT
1 TTTTAAAAAAT
6414725 TT
1 TT
6414727 CAAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TTTTAAAAAAT
Found at i:6425603 original size:44 final size:42
Alignment explanation
Indices: 6425460--6425618 Score: 133
Period size: 42 Copynumber: 3.7 Consensus size: 42
6425450 AACTCGTACA
* ** * *
6425460 ATGCCAACGTCCCAGATGTGGTCTTACATGTAATC-AATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATA-CG
** * * *
6425502 ATATCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATACG
* * *
6425544 ATGCCGATGTCCCAGACATGGTCTTATACATAAATCTCAAAT-CG
1 ATGCCAATGTCCCAGACATGGTCTTACAC-GAAA--TCAAATACG
* *
6425588 ATGCCAATGTCCCAGACGTGGTCCTACACGA
1 ATGCCAATGTCCCAGACATGGTCTTACACGA
6425619 TAACACATAT
Statistics
Matches: 90, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
42 50 0.56
43 8 0.09
44 26 0.29
45 6 0.07
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATACG
Found at i:6425981 original size:11 final size:12
Alignment explanation
Indices: 6425957--6425985 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
6425947 TAACTTAATT
6425957 ATTCAATATTTC
1 ATTCAATATTTC
6425969 ATTCAAT-TTTC
1 ATTCAATATTTC
6425980 ATTCAA
1 ATTCAA
6425986 GAACATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTCAATATTTC
Found at i:6431425 original size:21 final size:21
Alignment explanation
Indices: 6431384--6431425 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6431374 TAACACTGTT
**
6431384 AAACAATAAATGGTATTTTTA
1 AAACAATAAATGGTAACTTTA
*
6431405 AAACAATAAATGTTAACTTTA
1 AAACAATAAATGGTAACTTTA
6431426 TTCTAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (21 bp):
AAACAATAAATGGTAACTTTA
Found at i:6433646 original size:3 final size:3
Alignment explanation
Indices: 6433638--6433666 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6433628 ATTGATGGTT
6433638 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
6433667 GAATAAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6437710 original size:16 final size:16
Alignment explanation
Indices: 6437674--6437704 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6437664 TGATGAATCT
6437674 ATATATATACATGTAC
1 ATATATATACATGTAC
*
6437690 ATATATATATATGTA
1 ATATATATACATGTA
6437705 ATTATAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
ATATATATACATGTAC
Found at i:6439371 original size:32 final size:31
Alignment explanation
Indices: 6439300--6439396 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
6439290 CAATCTGATT
*
6439300 ACTAAACTATTCAAAAGTTTTCATTTAAGTC
1 ACTAAACTATTCAAAAGTTTTTATTTAAGTC
6439331 ACTAAACTATTCAAAAGTTTTTATTTTAAGTC
1 ACTAAACTATTCAAAAGTTTTTA-TTTAAGTC
* * *
6439363 ATTGAACTATTCAAAAGTTTTTACTTAAGTC
1 ACTAAACTATTCAAAAGTTTTTATTTAAGTC
6439394 ACT
1 ACT
6439397 GGGCTGTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.41
Consensus pattern (31 bp):
ACTAAACTATTCAAAAGTTTTTATTTAAGTC
Found at i:6440263 original size:24 final size:24
Alignment explanation
Indices: 6440236--6440281 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6440226 CTAATTAAAT
* *
6440236 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
6440260 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
6440282 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:6446371 original size:13 final size:14
Alignment explanation
Indices: 6446353--6446389 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
6446343 ACTATTAATC
*
6446353 AATAAATAAAT-AG
1 AATAAATAAATGAA
6446366 AATAAATAAATGAA
1 AATAAATAAATGAA
6446380 AATAAATAAA
1 AATAAATAAA
6446390 AATTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (14 bp):
AATAAATAAATGAA
Found at i:6447811 original size:44 final size:43
Alignment explanation
Indices: 6447775--6447858 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 43
6447765 AGGAATTAGT
*
6447775 GCTTCAATCTATTCCACTGCAACTTCAGGGAAATAGGATTATC
1 GCTTCAATCTACTCCACTGCAACTTCAGGGAAATAGGATTATC
* * *
6447818 GGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
1 -GCTTCAATCTACTCCACTGCAACTTCAGGGAAATAGGATT
6447859 TGCCATCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (43 bp):
GCTTCAATCTACTCCACTGCAACTTCAGGGAAATAGGATTATC
Found at i:6447943 original size:44 final size:44
Alignment explanation
Indices: 6447821--6448726 Score: 391
Period size: 44 Copynumber: 20.9 Consensus size: 44
6447811 GATTATCGGC
* * * *
6447821 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGC-CA
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
*
6447864 TCTTCAGTCTG-TCTTACTGCAACTTCA-GGAGGATAAGACTTGCTTA
1 T-TT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTA
*
6447910 TTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAG---A
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTTA
** * * * ** *
6447951 -TGCGATCTACT-CTCTGTAACTTCAGAAAGATAAGA--T-CTGA
1 TTTAG-TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
* * * * *
6447991 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TT-ATCA
1 -TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
* * * * *
6448034 GCTTTAATCTGCTCCACTGCCACTTCAGGGAGGTAAGATTTGC-CA
1 --TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
* *
6448079 TCTTCAGTCTGC-CTCACTGCAGCTTCA-AGAGGATAAGACTTGCTTA
1 T-TT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTA
* * *
6448125 CTTAGTCTGCGCCACTGCAACTTCAGGGAGATAAGACTAG---A
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
** * * ** *
6448166 -TGCGATCTGCT-CTCTGCAACTTCATAGAGAGATAAGATCCAAGGTT-
1 TTTAG-TCTGCTCCACTGCAACTTC--AGGGAGATAAGA--CTTGCTTA
*
6448212 TTTA-TCCT-CTCCACTGCAACTTCAGGGAGATAAGATTTGC-TA
1 TTTAGT-CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
*
6448254 TCTTCAGTCTGC-CTCACTGCAACTTCA-GAAGGATAAGACTTGCTTA
1 T-TT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTA
* * *
6448300 CTTAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACTAG---A
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
** * * * *
6448341 -TGCGATATGCT-CTCTGCAACTTCAGGGAGATAAGATTTG-TGA
1 TTTAG-TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
* * * * * **
6448383 TTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGA-TTATCGGA
1 -TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTTA
* * * *
6448428 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGC-CA
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
* *
6448471 TCTTCAGTCTGC-CTCACTGCAACTTCA--G-GATAAGACTAG-ATA
1 T-TT-AGTCTGCTC-CACTGCAACTTCAGGGAGATAAGACTTGCTTA
* * * * ** *
6448513 -TGA-TCTGCT-CTCTGTAACTTCATAGAGAGATAAGATCCAAG-GT-
1 TTTAGTCTGCTCCACTGCAACTTC--AGGGAGATAAGA--CTTGCTTA
* * * * * *
6448556 TTTAATCCGCTCCACTGCAACTTCAGGGAGGTAGGA-TT-ATTGGC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTT--A
* * * *
6448600 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGC-CA
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
* * *
6448643 TCTTCAGTCTGCTTCACTGCAACTTTA-AGAGGATAAGACTTGCTTA
1 T-TT-AGTCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCTTA
*
6448689 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
6448727 AGATGCGATC
Statistics
Matches: 659, Mismatches: 122, Indels: 163
0.70 0.13 0.17
Matches are distributed among these distances:
37 10 0.02
38 5 0.01
39 3 0.00
40 64 0.10
41 24 0.04
42 51 0.08
43 19 0.03
44 285 0.43
45 168 0.25
46 29 0.04
47 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA
Found at i:6448134 original size:89 final size:88
Alignment explanation
Indices: 6448041--6448335 Score: 329
Period size: 89 Copynumber: 3.4 Consensus size: 88
6448031 TCAGCTTTAA
* * *
6448041 TCTGCTCCACTGCCACTTCAGGGAGGTAAGATTTGCCATCTTCAGTCTGCCTCACTGCAGCTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-CATCTTCAGTCTGCCTCACTGCAACTTCA
6448106 AGAGGATAAGACTTGCTTACTTAG
65 AGAGGATAAGACTTGCTTACTTAG
* * * * *
6448130 TCTGCGCCACTGCAACTTCAGGGAGATAAGACTAG-A--TGC-GATCTG-CTCTCTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCATCTTCAG-TCTGCCTCACTGCAACTTCA
** * *
6448190 TAGAGAGATAAGATCCAAGGTT-TTTA-
65 -AGAG-GATAAGA--CTTGCTTACTTAG
6448216 TCCT-CTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCCTCACTGCAACTTC
1 T-CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGC-ATCTTCAGTCTGCCTCACTGCAACTTC
6448280 -AGAAGGATAAGACTTGCTTACTTAG
64 AAG-AGGATAAGACTTGCTTACTTAG
*
6448305 TCTGCTCCGCTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
6448336 CTAGATGCGA
Statistics
Matches: 168, Mismatches: 22, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
84 14 0.08
85 10 0.06
86 36 0.21
87 10 0.06
88 10 0.06
89 66 0.39
90 8 0.05
91 14 0.08
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (88 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCATCTTCAGTCTGCCTCACTGCAACTTCAA
GAGGATAAGACTTGCTTACTTAG
Found at i:6448158 original size:215 final size:218
Alignment explanation
Indices: 6447787--6448248 Score: 705
Period size: 215 Copynumber: 2.1 Consensus size: 218
6447777 TTCAATCTAT
* *
6447787 TCCACTGCAACTTCAGGGAAATAGGATTATCGGCTTTAATCTACTCCACTGCAACTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTACTCCACTGCAACTTCAGGGAGA
* * * *
6447852 TAAGATTTGCCATCTTCAGTCTGTCTTACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGCC
66 TAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTAGCC
* * *
6447917 TGCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTACTCTCTGTAACTTC-AGAAAGA
131 TGCGCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAGAAAGA
*
6447981 TAAGAT-C-TGATTTTAATCCGC
196 TAAGATCCAAGATTTTAATCCGC
* * *
6448002 TCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCCACTTCAGGGAGG
1 TCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTACTCCACTGCAACTTCAGGGAGA
* *
6448067 TAAGATTTGCCATCTTCAGTCTGCCTCACTGCAGCTTCAAGAGGATAAGACTTGCTTACTTAGTC
66 TAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTAGCC
* *
6448132 TGCGCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCATAGAGAG
131 TGCGCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCA-AGAAAG
* * *
6448197 ATAAGATCCAAGGTTTTTATCCTC
195 ATAAGATCCAAGATTTTAATCCGC
*
6448221 TCCACTGCAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAGGATT
6448249 TGCTATCTTC
Statistics
Matches: 222, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
215 172 0.77
217 12 0.05
218 1 0.00
219 37 0.17
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (218 bp):
TCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTACTCCACTGCAACTTCAGGGAGA
TAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAAGAGGATAAGACTTGCTTACTTAGCC
TGCGCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAGAAAGA
TAAGATCCAAGATTTTAATCCGC
Found at i:6448226 original size:175 final size:173
Alignment explanation
Indices: 6448036--6448585 Score: 697
Period size: 175 Copynumber: 3.2 Consensus size: 173
6448026 GATTATCAGC
* * * *
6448036 TTTAATCTGCTCCACTGCCACTTCAGGGAGGTAAGATTTGCCATCTTCAGTCTGCCTCACTGCAG
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAA
6448101 CTTCAAGAGGATAAGACTTGCTTACTTAGTCTGCGCCACTGCAACTTCAGGGAGATAAGACTAGA
66 CTTC-AGAGGATAAGACTTGCTTACTTAGTCTGC-CCACTGCAACTTCAGGGAGATAAGACTAGA
6448166 TGCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
129 TGCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
* * *
6448211 TTTTATCCTCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCCTCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAA
*
6448276 CTTCAGAAGGATAAGACTTGCTTACTTAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACTAGA
66 CTTCAG-AGGATAAGACTTGCTTACTTAGTCTGC-CCACTGCAACTTCAGGGAGATAAGACTAGA
* * **** *
6448341 TGCGATATGCTCTCTGCAACTTC--AGGGAGATAAGATTTGTGAT
129 TGCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
* * * *
6448384 TTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTAT-CGGAT-TT-AATCTG-CTCCACTG
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATT-TGC-CATCTTCAGTCTGCCT-CACTG
* * * *
6448445 TAACTTCAGGGAGATAAGATTTGC-CATCTTCAGTCTGCCTCACTGCAACTTCA--G-GATAAGA
63 CAACTTCAGAG-GATAAGACTTGCTTA-CTT-AGTCTGCC-CACTGCAACTTCAGGGAGATAAGA
** *
6448506 CTAGATATGATCTGCTCTCTGTAACTTCATAGAGAGATAAGATCCAAGGT
124 CTAGATGCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
6448556 TTTAATCCGCTCCACTGCAACTTCAGGGAG
1 TTTAATCCGCTCCACTGCAACTTCAGGGAG
6448586 GTAGGATTAT
Statistics
Matches: 327, Mismatches: 38, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
170 31 0.09
171 5 0.02
172 76 0.23
173 70 0.21
174 5 0.02
175 140 0.43
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (173 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAA
CTTCAGAGGATAAGACTTGCTTACTTAGTCTGCCCACTGCAACTTCAGGGAGATAAGACTAGATG
CGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
Found at i:6448572 original size:172 final size:173
Alignment explanation
Indices: 6448036--6448682 Score: 678
Period size: 172 Copynumber: 3.7 Consensus size: 173
6448026 GATTATCAGC
* * * * * *
6448036 TTTAATCTGCTCCACTGCCACTTCAGGGAGGTAAGATT-TGCCATCTTCAGTCTGC-CTCACTGC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATG-GAT-TT-AATCTGCTC-CACTGC
* * * *
6448099 AGCTTCA-AGAGGATAAGACTTG-CTTACTT-AGTCTGCGC-CACTGCAACTTCAGGGAGATAAG
62 AACTTCAGGGA-GATAAGATTTGCCAT-CTTCAGTCTGC-CTCACTGCAACTTCA-GGAGATAAG
6448160 ACTAGATGCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
123 ACTAGATGCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
* * * * *
6448211 TTTTATCCTCTCCACTGCAACTTCAGGGAGATAAGATT-TGCTATCTTCAGTCTGC-CTCACTGC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATG-GAT-TT-AATCTGCTC-CACTGC
* * * *
6448274 AACTTCA-GAAGGATAAGACTTG-CTTACTT-AGTCTG-CTCCGCTGCAACTTCAGGGAGATAAG
62 AACTTCAGGGA-GATAAGATTTGCCAT-CTTCAGTCTGCCT-CACTGCAACTTCA-GGAGATAAG
* * **** *
6448335 ACTAGATGCGATATGCTCTCTGCAACTTC--AGGGAGATAAGATTTGTGAT
123 ACTAGATGCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
* *
6448384 TTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTATCGGATTTAATCTGCTCCACTGTAAC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT-GGATTTAATCTGCTCCACTGCAAC
6448449 TTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA-G-GATAAGACTAGAT
65 TTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGATAAGACTAGAT
** *
6448512 ATGATCTGCTCTCTGTAACTTCATAGAGAGATAAGATCCAAGGT
130 GCGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
* *
6448556 TTTAATCCGCTCCACTGCAACTTCAGGGAGGTAGGATTATTGGCTTTAATCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTA-TGGATTTAATCTGCTCCACTGCAAC
* * * *
6448621 TTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCTTCACTGCAACTTTAAGAGGATAAGACT
65 TTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGA-GATAAGACT
6448683 TGCTTACTTA
Statistics
Matches: 412, Mismatches: 45, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
170 31 0.08
171 1 0.00
172 150 0.36
173 76 0.18
174 5 0.01
175 149 0.36
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (173 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATGGATTTAATCTGCTCCACTGCAACT
TCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGATAAGACTAGATG
CGATCTGCTCTCTGCAACTTCATAGAGAGATAAGATCCAAGGT
Found at i:6448680 original size:217 final size:215
Alignment explanation
Indices: 6448354--6448816 Score: 609
Period size: 217 Copynumber: 2.1 Consensus size: 215
6448344 GATATGCTCT
* ** *
6448354 CTGCAACTTCAGGGAGATAAGATT-TGTGATTTTAATCCGCTCCACTGCAACTTCAAGGAGATAG
1 CTGCAACTTCAGGGAGATAGGATTAT-TGGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAA
* * * * *
6448418 GATTATCGGATTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCCAT-CTTCAGTCTG
65 GATTATCGCATTTAATCTGCTCCACTGCAACTTAAGAGAGATAAGACTTG-CATACTT-AGTCTG
*
6448482 C-CTCACTGCAACTTCA-G-GATAAGACTAGATATGATCTGCTCTCTGTAACTTCATAGAGAGAT
128 CTC-CACTGCAACTTCAGGAGATAAGACTAGATACGATCTGCTCTCTGTAACTTC--AGAGAGAT
6448544 AAGATCCAAGGTTTTAATCCGCTCCA
190 AAGATCCAAGGTTTTAATCCGCTCCA
* * * *
6448570 CTGCAACTTCAGGGAGGTAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAG
1 CTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAG
* * *
6448635 ATT-T-GCCATCTTCAGTCTGCTTCACTGCAACTTTAAGAG-GATAAGACTTGCTTACTTAGTCT
66 ATTATCG-CAT-TT-AATCTGCTCCACTGCAAC-TTAAGAGAGATAAGACTTGCATACTTAGTCT
*
6448697 GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATA
127 GCTCCACTGCAACTTCA-GGAGATAAGACTAGATACGATCTGCTCTCTGTAACTTCAGAGAGATA
6448762 AGATCCAAGGTTTTAATCCGCTCCA
191 AGATCCAAGGTTTTAATCCGCTCCA
6448787 CTGCAACTTCAGGGAGATAGGATTATTGGC
1 CTGCAACTTCAGGGAGATAGGATTATTGGC
6448817 CACCGATCTG
Statistics
Matches: 218, Mismatches: 19, Indels: 19
0.85 0.07 0.07
Matches are distributed among these distances:
214 1 0.00
215 3 0.01
216 82 0.38
217 93 0.43
218 6 0.03
219 33 0.15
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (215 bp):
CTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAG
ATTATCGCATTTAATCTGCTCCACTGCAACTTAAGAGAGATAAGACTTGCATACTTAGTCTGCTC
CACTGCAACTTCAGGAGATAAGACTAGATACGATCTGCTCTCTGTAACTTCAGAGAGATAAGATC
CAAGGTTTTAATCCGCTCCA
Found at i:6448710 original size:389 final size:387
Alignment explanation
Indices: 6447787--6448812 Score: 1379
Period size: 389 Copynumber: 2.6 Consensus size: 387
6447777 TTCAATCTAT
* *
6447787 TCCACTGCAACTTCAGGGAAATAGGATTATCGGCTTTAATCTACTCCACTGCAACTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAGGATTATAGGCTTTAATCT-CTCCACTGCAACTTCAGGGAGA
* * * *
6447852 TAAGATTTGCCATCTTCAGTCTGTCTT-ACTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGC
65 TAAGATTTGCCATCTTCAGTCTG-CTTCACTGCAACTTTAAGAGGATAAGACTTGCTTACTTAGT
* * *
6447916 CTGCTCCACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTACTCTCTGTAACTTCAGAAAGA
129 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGA
* *
6447981 TAAGA-TCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTG
194 TAAGATTATGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAGATTTAATCTG
* * *
6448045 CTCCACTGCCACTTCAGGGAGGTAAGATTTGCCATCTTCAGTCTGCCTCACTGCAGCTTCAAGAG
259 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC-A-AG
* * * * * * *
6448110 GATAAGACTTGCTTACTTAGTCTGCGCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTG
322 GATAAGACTAGCATACTGAGTCTGCGCCACTGCAACTTCAGAGAGATAAGACAAGATGCAATCCG
6448175 C
387 C
* * * * * *
6448176 T-CTCTGCAACTTCATAGAGAGATAAGATCCA-AGGTTTTTATCCTCTCCACTGCAACTTCAGGG
1 TCCACTGCAACTTC--AGGGAGATAGGAT-TATAGGCTTTAAT-CTCTCCACTGCAACTTCAGGG
* * *
6448239 AGATAAGATTTGCTATCTTCAGTCTGCCTCACTGCAAC-TTCAGAAGGATAAGACTTGCTTACTT
62 AGATAAGATTTGCCATCTTCAGTCTGCTTCACTGCAACTTTAAG-AGGATAAGACTTGCTTACTT
* * * *
6448303 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTCTGCAACTTCAGGG
126 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAG
* * *
6448368 AGATAAGATTTGTGATTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTATCGGATTTAA
191 AGATAAGA-TTATGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAGATTTAA
*
6448433 TCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC-
255 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
* * * * *
6448497 AGGATAAGACTAG-ATA-TGA-TCTGC-TCTCTGTAACTTCATAGAGAGATAAGATCCAAGGTTT
320 AGGATAAGACTAGCATACTGAGTCTGCGCCACTGCAACTTC--AGAGAGATAAGA--CAA-GATG
*
6448558 TAATCCGC
380 CAATCCGC
* * *
6448566 TCCACTGCAACTTCAGGGAGGTAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAGGATTATAGGCTTTAATCT-CTCCACTGCAACTTCAGGGAGA
6448631 TAAGATTTGCCATCTTCAGTCTGCTTCACTGCAACTTTAAGAGGATAAGACTTGCTTACTTAGTC
65 TAAGATTTGCCATCTTCAGTCTGCTTCACTGCAACTTTAAGAGGATAAGACTTGCTTACTTAGTC
6448696 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGAT
130 TGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGAT
* * *
6448761 AAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT
195 AAGAT-TATGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT
6448813 TGGCCACCGA
Statistics
Matches: 555, Mismatches: 64, Indels: 36
0.85 0.10 0.05
Matches are distributed among these distances:
385 10 0.02
386 5 0.01
387 13 0.02
388 17 0.03
389 220 0.40
390 165 0.30
391 14 0.03
392 111 0.20
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (387 bp):
TCCACTGCAACTTCAGGGAGATAGGATTATAGGCTTTAATCTCTCCACTGCAACTTCAGGGAGAT
AAGATTTGCCATCTTCAGTCTGCTTCACTGCAACTTTAAGAGGATAAGACTTGCTTACTTAGTCT
GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATA
AGATTATGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCAGATTTAATCTGCT
CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAAGGATA
AGACTAGCATACTGAGTCTGCGCCACTGCAACTTCAGAGAGATAAGACAAGATGCAATCCGC
Found at i:6462647 original size:18 final size:17
Alignment explanation
Indices: 6462617--6462650 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6462607 AAATTACTAT
6462617 ATAAAAAATTTAAATAA
1 ATAAAAAATTTAAATAA
*
6462634 ATAAAAATTATTAAATA
1 ATAAAAAAT-TTAAATA
6462651 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATTTAAATAA
Found at i:6467986 original size:26 final size:28
Alignment explanation
Indices: 6467918--6467978 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
6467908 TACAATGTAA
*
6467918 AAAAATAA-AAAAATACATATGCTGTTAT
1 AAAAATAATATAAATACATAT-CTGTTAT
*
6467946 AAAATTAATATAAATACATAT-T-TTAT
1 AAAAATAATATAAATACATATCTGTTAT
6467972 AAAAATA
1 AAAAATA
6467979 CTGTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.34
27 1 0.03
28 7 0.24
29 11 0.38
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAAATAATATAAATACATATCTGTTAT
Found at i:6470042 original size:59 final size:60
Alignment explanation
Indices: 6469955--6470068 Score: 212
Period size: 59 Copynumber: 1.9 Consensus size: 60
6469945 TATTTAAGTT
*
6469955 AAAAAATCTAAAAACAATCATTTTAATAGCCT-AAAAAAACTCATTTCCTTTCTTTTTAA
1 AAAAAATCTAAAAAAAATCATTTTAATAGCCTAAAAAAAACTCATTTCCTTTCTTTTTAA
6470014 AAAAAATCTAAAAAAAATCATTTTAATAGCCTAAAAAAAACTCATTTCCTTTCTT
1 AAAAAATCTAAAAAAAATCATTTTAATAGCCTAAAAAAAACTCATTTCCTTTCTT
6470069 ATTTTTCTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
59 31 0.58
60 22 0.42
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (60 bp):
AAAAAATCTAAAAAAAATCATTTTAATAGCCTAAAAAAAACTCATTTCCTTTCTTTTTAA
Found at i:6475100 original size:57 final size:57
Alignment explanation
Indices: 6475026--6475181 Score: 182
Period size: 51 Copynumber: 2.8 Consensus size: 57
6475016 GGAGAAATGG
6475026 GAAAT-ATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAATAAAAATAAAGAAAT
1 GAAATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAATAAAAATAAAGAAAT
* * **
6475082 GAAATCATTTGGAAATGATTATAGTTTTCTCCAAAATG-AAAT-----TGGAGAAAT
1 GAAATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAATAAAAATAAAGAAAT
* * * *
6475133 GGAATCATTTAAAAATGAATGTGGTTTTCTCCAAAATGAAAATGAAAAA
1 GAAATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAAT-AAAAA
6475182 GATTTGGAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
51 39 0.48
52 4 0.05
56 9 0.11
57 30 0.37
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (57 bp):
GAAATCATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAATAAAAATAAAGAAAT
Found at i:6484001 original size:2 final size:2
Alignment explanation
Indices: 6483994--6484019 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6483984 CACATACATG
6483994 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
6484020 CCTTCCCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6484991 original size:18 final size:18
Alignment explanation
Indices: 6484968--6485003 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6484958 AGTTGAACTA
6484968 GAATTTTTAAAAATTTTT
1 GAATTTTTAAAAATTTTT
*
6484986 GAATTTTTAATAATTTTT
1 GAATTTTTAAAAATTTTT
6485004 TAATCGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
GAATTTTTAAAAATTTTT
Found at i:6487972 original size:45 final size:45
Alignment explanation
Indices: 6487905--6488156 Score: 371
Period size: 45 Copynumber: 5.6 Consensus size: 45
6487895 AAGCTTTATA
*
6487905 GTCTTCCTGTATTGGCAACGAAGTAGATCAAAGATAGCAGATCTT
1 GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTT
* * * *
6487950 GTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTT
1 GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTT
*
6487995 GTCTTCCTGTACTGGCAGCGAAGTAGATCAAAGATAGCAGATCTT
1 GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTT
* * * *
6488040 GTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTT
1 GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTT
* *
6488085 GTCTTCCTGTATTGGCAGCAAAGTAGATCGAAA-ACAGCAGATCTT
1 GTCTTCCTGTATTGGCAGCGAAGTAGATC-AAAGATAGCAGATCTT
*
6488130 ATCTTCCTGTATTGGCAGCGAAGTAGA
1 GTCTTCCTGTATTGGCAGCGAAGTAGA
6488157 CCGAAGACAG
Statistics
Matches: 183, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 181 0.99
46 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (45 bp):
GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTT
Found at i:6488058 original size:90 final size:90
Alignment explanation
Indices: 6487905--6488163 Score: 430
Period size: 90 Copynumber: 2.9 Consensus size: 90
6487895 AAGCTTTATA
*
6487905 GTCTTCCTGTATTGGCAACGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCG
1 GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCG
6487970 AAGTAGATCGAAGATAACAGATCTT
66 AAGTAGATCGAAGATAACAGATCTT
*
6487995 GTCTTCCTGTACTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCG
1 GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCG
6488060 AAGTAGATCGAAGATAACAGATCTT
66 AAGTAGATCGAAGATAACAGATCTT
* * * * *
6488085 GTCTTCCTGTATTGGCAGCAAAGTAGATCGAAA-ACAGCAGATCTTATCTTCCTGTATTGGCAGC
1 GTCTTCCTGTATTGGCAGCGAAGTAGATC-AAAGATAGCAGATCTTGTCTTCCTATATTGGTAGC
*
6488149 GAAGTAGACCGAAGA
65 GAAGTAGATCGAAGA
6488164 CAGAAGTAAC
Statistics
Matches: 159, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
90 156 0.98
91 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (90 bp):
GTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCG
AAGTAGATCGAAGATAACAGATCTT
Found at i:6488322 original size:44 final size:43
Alignment explanation
Indices: 6488170--6488376 Score: 197
Period size: 44 Copynumber: 4.8 Consensus size: 43
6488160 AAGACAGAAG
* * *
6488170 TAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGGTT-AA
1 TAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
* * * *
6488212 -AACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCA
1 TAA-C-CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
* * * *
6488257 T--CCAATCTCATCACCCCGAGGTTGCAGTGGAGCAGATTGAA
1 TAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
* * *
6488298 TAAGCCAATCTTATCTCCCTGAGGTTGTAGTGGAACAGATTGAA
1 TAA-CCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
* *
6488342 GAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAG
1 -TAACCAATCTTATCTCCCTGAAGTTGCAGTGGAG
6488377 TGGATCAGAA
Statistics
Matches: 131, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
41 32 0.24
42 3 0.02
43 3 0.02
44 90 0.69
45 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (43 bp):
TAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
Found at i:6488788 original size:22 final size:23
Alignment explanation
Indices: 6488760--6488804 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6488750 CTGCAATCTT
6488760 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
6488782 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
6488805 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:6490428 original size:65 final size:65
Alignment explanation
Indices: 6490344--6490470 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
6490334 AAAAGATTGG
* * *
6490344 TGGCGACTTCATTTTCGTTTTAAAAGTCGAGCCCGTTTTTCAAAATAAAAATGGTTTCGACAGCT
1 TGGCGACTCCACTTTCGTTTTAAAAGTCGACCCCGTTTTTCAAAATAAAAATGGTTTCGACAGCT
6490409 TGGCGACTCCACTTTCGTTTTAAAAGTCGACCCCGTTTTTCAAAATAAAAATGGTTTCGACA
1 TGGCGACTCCACTTTCGTTTTAAAAGTCGACCCCGTTTTTCAAAATAAAAATGGTTTCGACA
6490471 CAAATTAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (65 bp):
TGGCGACTCCACTTTCGTTTTAAAAGTCGACCCCGTTTTTCAAAATAAAAATGGTTTCGACAGCT
Found at i:6497398 original size:26 final size:26
Alignment explanation
Indices: 6497319--6497398 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 26
6497309 TCATCCAAAC
* *
6497319 TCAAAACAAAATATAAAATAAAATAAAA
1 TCAAAA-AAAATATATAA-AAAATAAAT
**
6497347 T-AATGAAAATAT-TAAAAAGCAT-AAT
1 TCAAAAAAAATATATAAAAA--ATAAAT
6497372 TCAAAAAAAATATATAAAAAATAAAT
1 TCAAAAAAAATATATAAAAAATAAAT
6497398 T
1 T
6497399 GGAATTCATC
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
24 3 0.07
25 7 0.17
26 22 0.54
27 8 0.20
28 1 0.02
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.24
Consensus pattern (26 bp):
TCAAAAAAAATATATAAAAAATAAAT
Found at i:6501109 original size:3 final size:3
Alignment explanation
Indices: 6501103--6501156 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
6501093 TTTGACATTG
* *
6501103 TAT TAT TAT TATT TAC TAT TAT TAT TAT TAT TAT TAT TAT T-T CAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
6501148 TAT TTT TAT
1 TAT TAT TAT
6501157 ATCCATATGC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 39 0.91
4 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6502810 original size:16 final size:16
Alignment explanation
Indices: 6502789--6502819 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6502779 GTTTCACTTT
6502789 GACTGCATGGCATTTA
1 GACTGCATGGCATTTA
6502805 GACTGCATGGCATTT
1 GACTGCATGGCATTT
6502820 CATTATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (16 bp):
GACTGCATGGCATTTA
Found at i:6503280 original size:19 final size:18
Alignment explanation
Indices: 6503256--6503301 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
6503246 AACGTCTCTT
*
6503256 TTTGCATTCATTTCATGCA
1 TTTGCATTCATTACAT-CA
6503275 TTTGCATTTCATTACATCA
1 TTTGCA-TTCATTACATCA
*
6503294 TATGCATT
1 TTTGCATT
6503302 AAACACCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.48
Consensus pattern (18 bp):
TTTGCATTCATTACATCA
Found at i:6505211 original size:20 final size:20
Alignment explanation
Indices: 6505186--6505226 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6505176 GCAAATGTTC
6505186 TTTCATTCTTTACGATTTTT
1 TTTCATTCTTTACGATTTTT
**
6505206 TTTCATTCTTTTGGATTTTT
1 TTTCATTCTTTACGATTTTT
6505226 T
1 T
6505227 CTGCCAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTCATTCTTTACGATTTTT
Found at i:6506142 original size:7 final size:7
Alignment explanation
Indices: 6506130--6506172 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
6506120 AAATGACGAT
6506130 ATGAAAA
1 ATGAAAA
6506137 ATGAAAA
1 ATGAAAA
6506144 AGTG-AAA
1 A-TGAAAA
6506151 ATGAAAA
1 ATGAAAA
*
6506158 TTGAAAA
1 ATGAAAA
6506165 ATGGAAAA
1 AT-GAAAA
6506173 GTAAAATGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 22 0.71
8 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (7 bp):
ATGAAAA
Found at i:6506151 original size:14 final size:13
Alignment explanation
Indices: 6506134--6506180 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
6506124 GACGATATGA
6506134 AAAATGAAAAAGTG
1 AAAATG-AAAAGTG
*
6506148 AAAATGAAAATTG
1 AAAATGAAAAGTG
6506161 AAAAATGGAAAAGT-
1 -AAAAT-GAAAAGTG
6506175 AAAATG
1 AAAATG
6506181 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 1 0.03
13 11 0.38
14 11 0.38
15 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (13 bp):
AAAATGAAAAGTG
Found at i:6507541 original size:44 final size:44
Alignment explanation
Indices: 6507475--6508382 Score: 708
Period size: 44 Copynumber: 20.3 Consensus size: 44
6507465 TAAAAAGTAG
*
6507475 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAAAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
* * * *
6507519 CATATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
** * **
6507563 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGGTAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
** * *
6507607 TGGATCTTGTCTTCATCTA-TGGACATGAAGTAGATTAGAGAAAA
1 CAGATCTTGTCTTCATGTATTGG-CATGAAGTAGATCAGAGAAAA
* * * *
6507651 TAGATCTTATCTTCATGTATTGACATGAAGTAGATC-GAAGATAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAG-AGAAAA
** * * *
6507695 TGGATATTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
** * * * *
6507739 TGGATATTGTCTTCATATATTGGCATGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
** * * * *
6507783 TGGATATTGTCTTCATATATTGACATGAAGTAGATCAGATG-TAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGA-GAAAA
** *
6507827 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAAAA
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
* *
6507871 CAGGTCTTGTCTTCATGTATTGG-AGTGAAGTAGATC-GAAGAAAG
1 CAGATCTTGTCTTCATGTATTGGCA-TGAAGTAGATCAG-AGAAAA
* * * * *
6507915 CAGATCTTGTCTTCATGTATTAGCGTGAAGTAGGTCAAAGAAAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
* *
6507959 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCCA-AGAAAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT-CAGAGAAAA
* ** **** * ** * * * *
6508003 TAGATCCAAGAAAGCA-GATATTGTCTTCATTTATTGGCGTGAAGTAGATCAAAGA
1 CAGAT-CTTGTCTTCATG-TATTG---GCATGAAGTAG-AT-CAG-AG---AAA-A
* ** * * *
6508058 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGAAAG
1 CAG-ATCT-TG-TCTTCATGTATTGGCATGAAGTAGATCAG-AGAAAA
* * * *
6508105 CAGGTCTTATCTTCATGTATTGGCGTGAAGTAGATC-GAAGAAAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAG-AGAAAA
** *
6508149 CAGATCTTGTCTTCATGTATTGGGGTGAAGTAGATCCA-AGAAAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT-CAGAGAAAA
* *
6508193 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCCA-AGAAAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT-CAGAGAAAA
* * *
6508237 CAGATATTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGAAAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAG-AGAAAA
* * *
6508281 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAG-AGAAAA
* * * *
6508325 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
6508369 CAGATCTTGTCTTC
1 CAGATCTTGTCTTC
6508383 CCATATTGGG
Statistics
Matches: 740, Mismatches: 92, Indels: 64
0.83 0.10 0.07
Matches are distributed among these distances:
43 7 0.01
44 679 0.92
45 16 0.02
46 1 0.00
47 2 0.00
48 8 0.01
49 2 0.00
51 5 0.01
53 1 0.00
54 8 0.01
55 2 0.00
56 1 0.00
57 7 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (44 bp):
CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGAAAA
Found at i:6507714 original size:132 final size:133
Alignment explanation
Indices: 6507476--6508382 Score: 931
Period size: 132 Copynumber: 6.8 Consensus size: 133
6507466 AAAAAGTAGC
* * * *
6507476 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAAAACATATCTTGTCTTCATGTATTG
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAGAGAAAGCAGATCTTGTCTTCATGTATTG
* *
6507541 ACATGAAGTAGATCAAAGATAATG-GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGGT
66 ACGTGAAGTAGATCAAAGATAA-GAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGGT
*
6507605 AATG
130 AAAG
* * * ** *
6507609 -GATCTTGTCTTCATCTA-TGGACATGAAGTAGATTAGAGAAAATAGATCTTATCTTCATGTATT
1 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAGAGAAAGCAGATCTTGTCTTCATGTATT
* * * * *
6507672 GACATGAAGTAGATCGAAGATAATG-GATATTGTCTTCATGTATTGGCATGAAGTAGATCAAAGA
65 GACGTGAAGTAGATCAAAGATAA-GAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGG
*
6507736 TAATG
129 TAAAG
* * * * * *
6507741 -GATATTGTCTTCATATATTGGCATGAAGTAGATCAAAGATAATG--GATATTGTCTTCATATAT
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAGAGA-AA-GCAGATCTTGTCTTCATGTAT
* * *
6507803 TGACATGAAGTAGATCAGATG-TAATG-GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGA
64 TGACGTGAAGTAGATCA-AAGATAA-GAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGA
* *
6507866 -GAAAAC
127 GGTAAAG
* *
6507872 AGGTCTTGTCTTCATGTATTGGAGTGAAGTAGATC-GAAGAAAGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAG-AGAAAGCAGATCTTGTCTTCATGTATT
* *
6507936 -AGCGTGAAGTAGGTCAAAGA-AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCCAAG
65 GA-CGTGAAGTAGATCAAAGATAAG-AGATCTTGTCTTCATGTATTGGCATGAAGTAGAT-C-AG
6507999 AAAGTAGATCCAAGAAAG
126 --AG--G-T-----AAAG
* * *
6508017 CAGATATTGTCTTCATTTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATT
1 -AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAGAGAAAGCAGATCTTGTCTTCATGTATT
* * * * * *
6508082 GGCGTGAAGTAGATCGAAGA-AAGCAGGTCTTATCTTCATGTATTGGCGTGAAGTAGATC-GAAG
65 GACGTGAAGTAGATCAAAGATAAG-AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGG
6508145 -AAAG
129 TAAAG
*
6508149 CAGATCTTGTCTTCATGTATTGGGGTGAAGTAGATCCA-AGAAAGCAGATCTTGTCTTCATGTAT
1 -AGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT-CAGAGAAAGCAGATCTTGTCTTCATGTAT
* * * * *
6508213 TGGCGTGAAGTAGATCCAAGA-AAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATC-GAA
64 TGACGTGAAGTAGATCAAAGATAAG-AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAG
6508276 G-AAAG
128 GTAAAG
*
6508281 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAGCAGATCTTGTCTTCATGTAT
1 -AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAG-AGAAAGCAGATCTTGTCTTCATGTAT
*
6508345 TGGCGTGAAGTAGATCAAAGAT-AGCAGATCTTGTCTTC
64 TGACGTGAAGTAGATCAAAGATAAG-AGATCTTGTCTTC
6508383 CCATATTGGG
Statistics
Matches: 676, Mismatches: 65, Indels: 67
0.84 0.08 0.08
Matches are distributed among these distances:
130 2 0.00
131 12 0.02
132 531 0.79
133 10 0.01
134 2 0.00
136 1 0.00
139 2 0.00
141 1 0.00
143 1 0.00
145 4 0.01
146 110 0.16
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (133 bp):
AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAGAGAAAGCAGATCTTGTCTTCATGTATTG
ACGTGAAGTAGATCAAAGATAAGAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAGAGGTA
AAG
Found at i:6508005 original size:14 final size:14
Alignment explanation
Indices: 6507986--6508021 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6507976 TATTGGCGTG
6507986 AAGTAGATCCAAGA
1 AAGTAGATCCAAGA
6508000 AAGTAGATCCAAGA
1 AAGTAGATCCAAGA
*
6508014 AAGCAGAT
1 AAGTAGAT
6508022 ATTGTCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.22, T:0.14
Consensus pattern (14 bp):
AAGTAGATCCAAGA
Found at i:6508016 original size:58 final size:58
Alignment explanation
Indices: 6507942--6508066 Score: 196
Period size: 58 Copynumber: 2.2 Consensus size: 58
6507932 TATTAGCGTG
* * *
6507942 AAGTAGGTCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCCAAGA
1 AAGTAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGA
* *
6508000 AAGTAGATCCAAGAAAGCAGATATTGTCTTCATTTATTGGCGTGAAGTAGATCAAAGA
1 AAGTAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGA
*
6508058 AAGCAGATC
1 AAGTAGATC
6508067 TTGTCTTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (58 bp):
AAGTAGATCAAAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGA
Found at i:6508390 original size:44 final size:44
Alignment explanation
Indices: 6508000--6508427 Score: 649
Period size: 44 Copynumber: 9.7 Consensus size: 44
6507990 AGATCCAAGA
* * *
6508000 AAGTAGATCCAAGAAAGCAGATATTGTCTTCATTTATTGGCGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
*
6508044 AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* *
6508088 AAGTAGATCGAAGAAAGCAGGTCTTATCTTCATGTATTGGCGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
*
6508132 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGGGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
*
6508176 AAGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* *
6508220 AAGTAGATCCAAGAAAGCAGATATTGTCTTCATGTATTGGCGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
6508264 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
*
6508308 AAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * *** * *
6508352 AAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATATTGGGGGCG
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTG
*** *
6508397 AAGTAGATTTTAGAAAGTAGATCTTGTCTTC
1 AAGTAGATCGAAGAAAGCAGATCTTGTCTTC
6508428 CCATATATTA
Statistics
Matches: 357, Mismatches: 26, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
44 327 0.92
45 30 0.08
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (44 bp):
AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
Found at i:6509913 original size:3 final size:3
Alignment explanation
Indices: 6509907--6509946 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
6509897 TTTGACATTG
*
6509907 TAT TAT TAT TATT TAC TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6509947 GTTTTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6512435 original size:56 final size:55
Alignment explanation
Indices: 6512350--6512456 Score: 169
Period size: 56 Copynumber: 1.9 Consensus size: 55
6512340 TTATGGATTG
* *
6512350 CAAATTAATTCTTCATGAGCACTATTCAAATTAAAAGTGATAATTTATCATATTA
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATATTA
* *
6512405 CAAATTTAATTATTCATAAGCATTATTCAAATTAAAAGTGATGATTTATCAT
1 CAAA-TTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCAT
6512457 CTAATGGATA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 4 0.09
56 43 0.91
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.39
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATATTA
Found at i:6530602 original size:33 final size:33
Alignment explanation
Indices: 6530560--6530627 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
6530550 CTATGCACAT
6530560 TCTCATCATACCCATAAACAACATTATTTGCAA
1 TCTCATCATACCCATAAACAACATTATTTGCAA
6530593 TCTCATCATACCCATAAACAACATTATTTGCAA
1 TCTCATCATACCCATAAACAACATTATTTGCAA
6530626 TC
1 TC
6530628 ACATGTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (33 bp):
TCTCATCATACCCATAAACAACATTATTTGCAA
Found at i:6532095 original size:9 final size:9
Alignment explanation
Indices: 6532065--6532164 Score: 69
Period size: 9 Copynumber: 10.7 Consensus size: 9
6532055 ACGGTCATTG
*
6532065 ATTTTAATA
1 ATTTTTATA
*
6532074 TTTTTTACT-
1 ATTTTTA-TA
6532083 ATTTTTATA
1 ATTTTTATA
*
6532092 ATTTTT-TT
1 ATTTTTATA
6532100 ATTTTCTAATA
1 ATTTT-T-ATA
* *
6532111 AATTTTAAA
1 ATTTTTATA
6532120 TATTTTTATTAA
1 -ATTTTTA-T-A
*
6532132 AATTTTATA
1 ATTTTTATA
*
6532141 ACTTTTATA
1 ATTTTTATA
6532150 ATTTTTATA
1 ATTTTTATA
6532159 ATTTTT
1 ATTTTT
6532165 TTGCCACATG
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
8 7 0.10
9 43 0.61
10 9 0.13
11 11 0.15
12 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:6532095 original size:19 final size:18
Alignment explanation
Indices: 6532073--6532164 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 18
6532063 TGATTTTAAT
6532073 ATTTTTTACTATTTTTATA
1 ATTTTTTA-TATTTTTATA
6532092 ATTTTTT-TATTTTCTAATAA
1 ATTTTTTATATTTT-T-AT-A
**
6532112 ATTTTAAATATTTTTATTA
1 ATTTTTTATATTTTTA-TA
** *
6532131 AAATTTTATAACTTTTATA
1 ATTTTTTAT-ATTTTTATA
6532150 A-TTTTTATAATTTTT
1 ATTTTTTAT-ATTTTT
6532165 TTGCCACATG
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
17 6 0.10
18 13 0.22
19 19 0.33
20 14 0.24
21 6 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTTATATTTTTATA
Found at i:6532125 original size:21 final size:21
Alignment explanation
Indices: 6532099--6532138 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6532089 ATAATTTTTT
6532099 TATTTTCTAAT-AAATTTTAAA
1 TATTTT-TAATAAAATTTTAAA
*
6532120 TATTTTTATTAAAATTTTA
1 TATTTTTAATAAAATTTTA
6532139 TAACTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTAATAAAATTTTAAA
Found at i:6532374 original size:76 final size:78
Alignment explanation
Indices: 6532231--6532377 Score: 201
Period size: 76 Copynumber: 1.9 Consensus size: 78
6532221 AAAGTGTCTT
** * * * *
6532231 TTTGATACATTTTGACCGTTCAAATTACCAAATTGAGTGAGAAAAAAGTAGAGGTTTAATTGTTT
1 TTTGATACATTTTGAAAGTTCAAATTACCAAATTGAG-GAGAAAAAAATAAAGGTTTAAATATTT
6532296 TTTTTTTTAAGTTC
65 TTTTTTTTAAGTTC
6532310 TTTGATACATTTTGAAAGTTCAAA-TATCC-AATTGA-GAGAAAAAAATAAAGGTTTAAATATTT
1 TTTGATACATTTTGAAAGTTCAAATTA-CCAAATTGAGGAGAAAAAAATAAAGGTTTAAATATTT
6532372 TTTTTT
65 TTTTTT
6532378 AAAAAATTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
76 29 0.48
78 8 0.13
79 24 0.39
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (78 bp):
TTTGATACATTTTGAAAGTTCAAATTACCAAATTGAGGAGAAAAAAATAAAGGTTTAAATATTTT
TTTTTTTAAGTTC
Found at i:6532962 original size:15 final size:13
Alignment explanation
Indices: 6532935--6532990 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 13
6532925 GAATTTTATA
6532935 AATTAAAAATAAT
1 AATTAAAAATAAT
6532948 AATTATAAAAGTAATT
1 AATTA-AAAA-TAA-T
6532964 ATATTAAAAATAAAT
1 A-ATTAAAAAT-AAT
6532979 AATATAAAAATA
1 AAT-TAAAAATA
6532991 TTCAATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.14
14 7 0.19
15 13 0.35
16 8 0.22
17 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
AATTAAAAATAAT
Found at i:6539397 original size:22 final size:22
Alignment explanation
Indices: 6539366--6539413 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
6539356 AATCAAAGTC
* * *
6539366 AAAATGAAAATGAAAAAAATCA
1 AAAATCAAAATAAAAAAAAACA
6539388 AAAATCAAAATAAAAAAAAACA
1 AAAATCAAAATAAAAAAAAACA
6539410 AAAA
1 AAAA
6539414 GAAGAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.10
Consensus pattern (22 bp):
AAAATCAAAATAAAAAAAAACA
Found at i:6540460 original size:7 final size:6
Alignment explanation
Indices: 6540398--6540457 Score: 102
Period size: 6 Copynumber: 9.7 Consensus size: 6
6540388 GAAAATATGA
6540398 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG -AAAATG
6540447 AAAAATG AAAA
1 -AAAATG AAAA
6540458 ATGGAGAGGC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 40 0.75
7 13 0.25
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:6542044 original size:44 final size:43
Alignment explanation
Indices: 6541981--6542292 Score: 135
Period size: 44 Copynumber: 6.7 Consensus size: 43
6541971 CCGATAATCC
*
6541981 TATCTCCCTAAAGTTACAGTGGAGCGGATTAAAACAAATGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAA-GATCT
* **
6542025 TATCTCTCTGAAGTTACAGTCGAGTAGATCGTATCCGATTGAAGCCAGAA-ATCT
1 TATCTCCCTGAAGTTACAGT-G-G-AG--CG-----GATT-AAAACA-AAGATCT
* *
6542079 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCC
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAA-GATCT
* * *
6542123 TATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTCGATTGAAGACAGAGATCT
1 TATCTCCCTGAAGTTACAGT-G-G-AG--CG-----GATT-AAAACAAAGATCT
** * * * ** *
6542177 TATCTCCCTG-AGATTACAGCAGAGCAGATCGAAGAC-ACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGCGGAT-TAAAACAAAGATCT
* **
6542220 TATCTCCTTGAAGTTACAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAA-AGATCT
* * * *
6542264 TATCTCTCTGAAGTTGCAGTAGAGTGGAT
1 TATCTCCCTGAAGTTACAGTGGAGCGGAT
6542293 CGCATTAGGT
Statistics
Matches: 199, Mismatches: 39, Indels: 60
0.67 0.13 0.20
Matches are distributed among these distances:
42 4 0.02
43 30 0.15
44 81 0.41
45 2 0.01
46 2 0.01
47 4 0.02
49 5 0.03
51 4 0.02
52 2 0.01
53 3 0.02
54 50 0.25
55 10 0.05
56 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAGATCT
Found at i:6542133 original size:98 final size:98
Alignment explanation
Indices: 6541964--6542205 Score: 344
Period size: 98 Copynumber: 2.5 Consensus size: 98
6541954 AAGGAAGCAA
* * * * *
6541964 ATTGAAGCC-GATAATCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAAAACAAATGATCTTAT
1 ATTGAAGCCAGA-AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCCTAT
* *
6542028 CTCTCTGAAGTTACAGTCGAGTAGATCGTATCCG
65 CTCTCTGAAGTTACAGTAGAGTAGATCGCATCCG
6542062 ATTGAAGCCAGAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCCTATC
1 ATTGAAGCCAGAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCCTATC
*
6542127 TCTCTGAAGTTACAGTAGAGTAGATCGCATTCG
66 TCTCTGAAGTTACAGTAGAGTAGATCGCATCCG
* * **
6542160 ATTGAAGACAGAGATCTTATCTCCCTG-AGATTACAGCAGAGCAGAT
1 ATTGAAGCCAGAAATCTTATCTCCCTGAAG-TTACAGTGGAGCAGAT
6542206 CGAAGACACT
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
97 2 0.02
98 126 0.97
99 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (98 bp):
ATTGAAGCCAGAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCCTATC
TCTCTGAAGTTACAGTAGAGTAGATCGCATCCG
Found at i:6542350 original size:44 final size:44
Alignment explanation
Indices: 6542301--6542420 Score: 152
Period size: 44 Copynumber: 2.7 Consensus size: 44
6542291 ATCGCATTAG
* *
6542301 GTCTTATCACCCTGAGGTTGCATTGGAGCAGACTG-AGAAAACAA
1 GTCTTATCACCCTGAGGTTGCAGTGGAGCAGACCGAAG-AAACAA
* * * *
6542345 GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACCGAAGAAGCAA
1 GTCTTATCACCCTGAGGTTGCAGTGGAGCAGACCGAAGAAACAA
* *
6542389 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
1 GTCTTATCACCCTGAGGTTGCAGTGGAGCAGA
6542421 TTGAAGTCGA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 63 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.23
Consensus pattern (44 bp):
GTCTTATCACCCTGAGGTTGCAGTGGAGCAGACCGAAGAAACAA
Done.