Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 14 of 143
Found at i:4424364 original size:61 final size:61
Alignment explanation
Indices: 4424110--4424370 Score: 257
Period size: 61 Copynumber: 4.3 Consensus size: 61
4424100 ATTTGGGGTA
* * *
4424110 TTGGCCATCAAATGACTGACA-CATCCCTTTTCTCGAGAAAAAAATTTTAAATTTTTTTGGTG
1 TTGGCCATCAAATGGCCGACATC--CCCTTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTG
* * * *
4424172 TTGGCCATCAAATAGTCGACA-CCCCTTTTTCTC--GAAAAAAAA-TTATA-TTTTTGGGTG
1 TTGGCCATCAAATGGCCGACATCCCC-TTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTG
* *** * * *
4424229 TTGGTCATTTGATGGCCGACACCCCCTATTCTCGAG-AAAAAATTTTAAATTTTTTTGGTG
1 TTGGCCATCAAATGGCCGACATCCCCTTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTG
** * * *
4424289 TCAGCCATCAAATGGTCGACATCCCCTTTGCTCGAGAAAAAAAATTCAAATTTTTTTGGTG
1 TTGGCCATCAAATGGCCGACATCCCCTTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTG
**
4424350 TTGGCCATGTAATGGCCGACA
1 TTGGCCATCAAATGGCCGACA
4424371 CCAACTTTTC
Statistics
Matches: 158, Mismatches: 34, Indels: 15
0.76 0.16 0.07
Matches are distributed among these distances:
57 30 0.19
58 14 0.09
59 13 0.08
60 38 0.24
61 45 0.28
62 18 0.11
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (61 bp):
TTGGCCATCAAATGGCCGACATCCCCTTTTCTCGAGAAAAAAAATTTAAATTTTTTTGGTG
Found at i:4424568 original size:31 final size:31
Alignment explanation
Indices: 4424533--4424592 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4424523 TACAATTGAA
* *
4424533 TTTCGGGGTTGAGCTATATACTGTCATGTAT
1 TTTCGGAGTTGAACTATATACTGTCATGTAT
* *
4424564 TTTCGTAGTTGAATTATATACTGTCATGT
1 TTTCGGAGTTGAACTATATACTGTCATGT
4424593 GAAGCGGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (31 bp):
TTTCGGAGTTGAACTATATACTGTCATGTAT
Found at i:4428125 original size:11 final size:12
Alignment explanation
Indices: 4428085--4428133 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
4428075 TATTTGTGTA
4428085 AAAATTAATTTG
1 AAAATTAATTTG
4428097 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
4428111 TTGAAATTAATTTG
1 --AAAATTAATTTG
4428125 AAAATTAAT
1 AAAATTAAT
4428134 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:4428409 original size:45 final size:45
Alignment explanation
Indices: 4428350--4428505 Score: 137
Period size: 45 Copynumber: 3.5 Consensus size: 45
4428340 TACAAATTAT
4428350 TATTATATTA-TAATTTT-TATCATATAATGTGTTGATTTGATAATA
1 TATTAT-TTATTAATTTTATATCATATAA-GTGTTGATTTGATAATA
* * * *** * *
4428395 CATTATTTATTAATTTTATATC-TTTAAAT-AAAAATT-ATTAT-
1 TATTATTTATTAATTTTATATCATATAAGTGTTGATTTGATAATA
4428436 TATTATTATATTACAATTTT-TATCATATAAGGTGTTGATTTGATAATA
1 TATTATT-TATT--AATTTTATATCATATAA-GTGTTGATTTGATAATA
4428484 TATTATTTATTAATTTTATATC
1 TATTATTTATTAATTTTATATC
4428506 TTTAAATAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 21
0.69 0.13 0.17
Matches are distributed among these distances:
41 6 0.07
42 8 0.10
43 7 0.08
44 14 0.17
45 23 0.27
46 11 0.13
47 8 0.10
48 7 0.08
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (45 bp):
TATTATTTATTAATTTTATATCATATAAGTGTTGATTTGATAATA
Found at i:4428471 original size:89 final size:89
Alignment explanation
Indices: 4428265--4428555 Score: 391
Period size: 89 Copynumber: 3.3 Consensus size: 89
4428255 AAAAAGATAG
* * * * * *
4428265 TTATTCTATTACAATTTATATCAAATATTGTGTTAATTTGATAATACATTATTTATCAAATTTTG
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTAT-TAATTTT-
*
4428330 ATA--TTTAAAGTACAAATTATTATTA
64 ATATCTTTAAA-TAAAAATTATTATTA
4428355 -TA-T-TA-T--AATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
4428414 ATCTTTAAATAAAAATTATTATTA
66 ATCTTTAAATAAAAATTATTATTA
* *
4428438 TTATTATATTACAATTTTTATCATATAAGGTGTTGATTTGATAATATATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
4428503 ATCTTTAAATAAAAATTATTATTTTTA
66 ATCTTTAAATAAAAATTATTA---TTA
4428530 TTATTATATTACAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
4428556 TTTAAATTTA
Statistics
Matches: 182, Mismatches: 8, Indels: 20
0.87 0.04 0.10
Matches are distributed among these distances:
82 3 0.02
83 20 0.11
84 48 0.26
85 1 0.01
86 3 0.02
87 3 0.02
88 1 0.01
89 74 0.41
92 29 0.16
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (89 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTAT
ATCTTTAAATAAAAATTATTATTA
Found at i:4431963 original size:57 final size:56
Alignment explanation
Indices: 4431862--4432133 Score: 246
Period size: 57 Copynumber: 4.8 Consensus size: 56
4431852 AGATGAATGG
* * *
4431862 CCAACACAAAAAAAATTGAATTTTTTTCTCGAGAAAAAGGGGTGTCGGCCATTTGATGA
1 CCAACAC-CAAAAAATT-AAATTTTTT-TCGAGAAAAAGGGGTGTCGACCATTTGATGA
* *
4431921 CCAACACCCAAAAATATAAATTTTTTTCGAGAAAAAGGGGTGTCGACCATTTGATGG
1 CCAACACCAAAAAAT-TAAATTTTTTTCGAGAAAAAGGGGTGTCGACCATTTGATGA
* ** * * * * *** *
4431978 CCAACACCAAAAAATTTTGAATTTTTTTC-TCAAACAGAGGTTGTGGGCCATGCAATGG
1 CCAACACCAAAAAA--TTAAATTTTTTTCGAGAAAAAG-GGGTGTCGACCATTTGATGA
*
4432036 CCAACACCCAAAAATGTAAATTTTTTT-GAG-AAAAGAGGGTGTCGACCATTTGATGA
1 CCAACACCAAAAAAT-TAAATTTTTTTCGAGAAAAAG-GGGTGTCGACCATTTGATGA
** *
4432092 CCAACACCAAAAAATTGTA-TTTTTTCTGACAAAAAGGGGTGT
1 CCAACACCAAAAAATTAAATTTTTTTC-GAGAAAAAGGGGTGT
4432134 TGGTCATGCA
Statistics
Matches: 172, Mismatches: 32, Indels: 21
0.76 0.14 0.09
Matches are distributed among these distances:
54 6 0.03
55 2 0.01
56 41 0.24
57 62 0.36
58 52 0.30
59 9 0.05
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (56 bp):
CCAACACCAAAAAATTAAATTTTTTTCGAGAAAAAGGGGTGTCGACCATTTGATGA
Found at i:4434429 original size:2 final size:2
Alignment explanation
Indices: 4434424--4434450 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4434414 TCTCTCTCTC
4434424 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4434451 CCAAAGTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4436340 original size:21 final size:21
Alignment explanation
Indices: 4436298--4436340 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
4436288 AACCAAAAAT
**
4436298 AAAAAAAATCACATTTACAAA
1 AAAAAAAATCACATAAACAAA
*
4436319 AAAAAAAAT-ACATAAACTAA
1 AAAAAAAATCACATAAACAAA
4436339 AA
1 AA
4436341 CCCAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (21 bp):
AAAAAAAATCACATAAACAAA
Found at i:4437303 original size:5 final size:5
Alignment explanation
Indices: 4437295--4437323 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4437285 ATTTAGTCAT
4437295 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
4437324 TGCCCCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:4437544 original size:4 final size:4
Alignment explanation
Indices: 4437535--4437627 Score: 51
Period size: 4 Copynumber: 24.5 Consensus size: 4
4437525 TTTGCATACC
* * *
4437535 TTAT TTAT TTAT TTAA AT-T TTAT AT-T TTA- TTAT TTAAT TTAAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TT-AT TTAT
*
4437582 TTAATT TTCT TTA- TTA- TTA- TTA- TTA- TTA- TTAT TTAT TTAT TTAT
1 TT-A-T TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
4437626 TT
1 TT
4437628 TATGTCATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
3 24 0.32
4 37 0.50
5 10 0.14
6 3 0.04
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:4437560 original size:21 final size:19
Alignment explanation
Indices: 4437536--4437630 Score: 60
Period size: 19 Copynumber: 5.1 Consensus size: 19
4437526 TTGCATACCT
4437536 TATTTATTTATTTAAATTTTA
1 TATTTATTTATTT-AA-TTTA
4437557 TATTT-TATTATTTAATTTA
1 TATTTAT-TTATTTAATTTA
**
4437576 -ATTTATTTAATTTTCTTTA
1 TATTTATTT-ATTTAATTTA
4437595 T-TATTA-TTA-TT-A-TTA
1 TAT-TTATTTATTTAATTTA
*
4437610 TTATTTATTTATTTATTTTA
1 -TATTTATTTATTTAATTTA
4437630 T
1 T
4437631 GTCATTTATG
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
15 3 0.05
16 4 0.07
17 6 0.10
18 9 0.15
19 17 0.29
20 9 0.15
21 11 0.19
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTATTTATTTAATTTA
Found at i:4437629 original size:9 final size:9
Alignment explanation
Indices: 4437535--4437630 Score: 67
Period size: 8 Copynumber: 10.4 Consensus size: 9
4437525 TTTGCATACC
4437535 TTATTTA-T
1 TTATTTATT
4437543 TTATTTAAATT
1 TTATTT--ATT
4437554 TTA--TATT
1 TTATTTATT
4437561 TTA-TTATT
1 TTATTTATT
* *
4437569 TAATTTAAT
1 TTATTTATT
4437578 TTATTTAATT
1 TTATTT-ATT
*
4437588 TTCTTTATT
1 TTATTTATT
4437597 ATTATTATTATT
1 -TTA-T-TTATT
4437609 ATTATTTA-T
1 -TTATTTATT
4437618 TTATTTATT
1 TTATTTATT
4437627 TTAT
1 TTAT
4437631 GTCATTTATG
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
7 6 0.08
8 19 0.26
9 19 0.26
10 13 0.18
11 6 0.08
12 9 0.12
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (9 bp):
TTATTTATT
Found at i:4437639 original size:26 final size:24
Alignment explanation
Indices: 4437539--4437627 Score: 64
Period size: 25 Copynumber: 3.8 Consensus size: 24
4437529 CATACCTTAT
*
4437539 TTATTTATTTAAATTT-TATATTTTA
1 TTATTTATTT--ATTTATTTATTTTA
*
4437564 TTATTTAATTTAATTTATTTA-ATT-
1 TTATTT-ATTT-ATTTATTTATTTTA
*
4437588 TTCTTTA-TTA-TTA-TTATTATTA
1 TTATTTATTTATTTATTTATT-TTA
4437610 TTATTTATTTATTTATTT
1 TTATTTATTTATTTATTT
4437628 TATGTCATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 3 0.06
22 8 0.16
23 4 0.08
24 8 0.16
25 15 0.29
26 7 0.14
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (24 bp):
TTATTTATTTATTTATTTATTTTA
Found at i:4437678 original size:32 final size:31
Alignment explanation
Indices: 4437642--4437707 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
4437632 TCATTTATGA
4437642 TTTTGCCCTTTAAATTACACTTTT-TTTTTTAT
1 TTTTGCCC-TTAAATTAC-CTTTTATTTTTTAT
* *
4437674 TTTTGCCCTTGAATTACTTTTTATTTTTTAT
1 TTTTGCCCTTAAATTACCTTTTATTTTTTAT
4437705 TTT
1 TTT
4437708 ATCTTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 4 0.13
31 19 0.61
32 8 0.26
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.65
Consensus pattern (31 bp):
TTTTGCCCTTAAATTACCTTTTATTTTTTAT
Found at i:4437767 original size:62 final size:61
Alignment explanation
Indices: 4437701--4437896 Score: 228
Period size: 62 Copynumber: 3.3 Consensus size: 61
4437691 TTTTTATTTT
4437701 TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATTGTTG
1 TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATTG-TG
* * * * * * * *
4437763 TTATTTTATCTTTTATTT---T-T--TATTTTATTCTTTTATTACTATT-TTACT-ATAGTG
1 TTATTTTATCTTTTATTTAAATGTGGTA-TTAATTATGTCATTATTGTTATTATTGATTGTG
*
4437817 TTATTTTATCTTTTATTTAAATGTGGTATTAATTGTGTCATTATTGTTATTATTGATTGGTG
1 TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATT-GTG
4437879 TTATTTTATCTTTTATTT
1 TTATTTTATCTTTTATTT
4437897 TTTATTTTAT
Statistics
Matches: 108, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
54 20 0.19
55 3 0.03
56 6 0.06
57 15 0.14
58 2 0.02
59 15 0.14
60 6 0.06
61 2 0.02
62 39 0.36
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (61 bp):
TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATTGTG
Found at i:4437782 original size:116 final size:115
Alignment explanation
Indices: 4437701--4437938 Score: 440
Period size: 116 Copynumber: 2.1 Consensus size: 115
4437691 TTTTTATTTT
*
4437701 TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATTGTTGTTA
1 TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATTGGTGTTA
4437766 TTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATAGTG
66 TTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATA-TG
*
4437817 TTATTTTATCTTTTATTTAAATGTGGTATTAATTGTGTCATTATTGTTATTATTGATTGGTGTTA
1 TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATTGGTGTTA
4437882 TTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATAGTG
66 TTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATA-TG
4437933 TTATTT
1 TTATTT
4437939 CATTTTTGTT
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 120 1.00
ACGTcount: A:0.22, C:0.05, G:0.09, T:0.64
Consensus pattern (115 bp):
TTATTTTATCTTTTATTTAAATGTGGTATTAATTATGTCATTATTGTTATTATTGATTGGTGTTA
TTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATATG
Found at i:4437805 original size:19 final size:19
Alignment explanation
Indices: 4437764--4437808 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4437754 TGATTGTTGT
**
4437764 TATTTTATCTTTTATTTTT
1 TATTTTATCTTTTATTTAC
4437783 TATTTTATTCTTTTA-TTAC
1 TATTTTA-TCTTTTATTTAC
4437802 TATTTTA
1 TATTTTA
4437809 CTATAGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTTATCTTTTATTTAC
Found at i:4437819 original size:54 final size:54
Alignment explanation
Indices: 4437761--4437938 Score: 196
Period size: 54 Copynumber: 3.1 Consensus size: 54
4437751 TATTGATTGT
4437761 TGTTATTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATAG
1 TGTTATTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATAG
* * * * * * * *
4437815 TGTTATTTTATCTTTTATTTAAATGTGGTA-TTAATTGTGTCATTATTGTTATTATTGATTGG
1 TGTTATTTTATCTTTTATTT---T-T--TATTTTATTCTTTTATTACTATT-TTACT-A-TAG
4437877 TGTTATTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATAG
1 TGTTATTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATAG
4437931 TGTTATTT
1 TGTTATTT
4437939 CATTTTTGTT
Statistics
Matches: 98, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
54 30 0.31
55 1 0.01
56 6 0.06
57 15 0.15
58 2 0.02
59 15 0.15
60 6 0.06
61 1 0.01
62 22 0.22
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (54 bp):
TGTTATTTTATCTTTTATTTTTTATTTTATTCTTTTATTACTATTTTACTATAG
Found at i:4437835 original size:27 final size:27
Alignment explanation
Indices: 4437761--4437835 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 27
4437751 TATTGATTGT
** **
4437761 TGTTATTTTATCTTTTATTTTTTATTT
1 TGTTATTTTATCTTTTATTTACTATAG
* * **
4437788 TATTCTTTTAT-TACTATTTTACTATAG
1 TGTTATTTTATCTTTTA-TTTACTATAG
4437815 TGTTATTTTATCTTTTATTTA
1 TGTTATTTTATCTTTTATTTA
4437836 AATGTGGTAT
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
26 3 0.09
27 28 0.82
28 3 0.09
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (27 bp):
TGTTATTTTATCTTTTATTTACTATAG
Found at i:4437921 original size:19 final size:19
Alignment explanation
Indices: 4437880--4437924 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4437870 TGATTGGTGT
**
4437880 TATTTTATCTTTTATTTTT
1 TATTTTATCTTTTATTTAC
4437899 TATTTTATTCTTTTA-TTAC
1 TATTTTA-TCTTTTATTTAC
4437918 TATTTTA
1 TATTTTA
4437925 CTATAGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTTATCTTTTATTTAC
Found at i:4439364 original size:29 final size:29
Alignment explanation
Indices: 4439327--4439386 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
4439317 CTGTTCCTCT
*
4439327 AAACACCACTACTTCATCTGTGTATTAGC
1 AAACACCACTACTTCATCTGTGTATCAGC
*
4439356 AAACGCCACTACTTCATCTGTGTATCAGC
1 AAACACCACTACTTCATCTGTGTATCAGC
4439385 AA
1 AA
4439387 GTAATGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (29 bp):
AAACACCACTACTTCATCTGTGTATCAGC
Found at i:4449302 original size:15 final size:14
Alignment explanation
Indices: 4449275--4449314 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 14
4449265 TAACATTTTT
4449275 TAATATTTACATTA
1 TAATATTTACATTA
4449289 TAATATTATACATTA
1 TAATATT-TACATTA
4449304 CTATATATTTA
1 -TA-ATATTTA
4449315 GTTTTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
16 4 0.17
17 5 0.22
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTTACATTA
Found at i:4451890 original size:29 final size:30
Alignment explanation
Indices: 4451849--4451905 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
4451839 ACATGAATTT
*
4451849 TGAAATATGAAAGTAGAG-TGACTAAATTCC
1 TGAAATATAAAAGTAGAGAT-ACTAAATTCC
*
4451879 TGAAA-ATAAAAGTATAGATACTAAATT
1 TGAAATATAAAAGTAGAGATACTAAATT
4451906 TCAAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (30 bp):
TGAAATATAAAAGTAGAGATACTAAATTCC
Found at i:4461690 original size:21 final size:21
Alignment explanation
Indices: 4461666--4461707 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4461656 ATATTAATAC
*
4461666 TTCTTGAATTTA-AAGTTTAAA
1 TTCTCGAATTTAGAA-TTTAAA
*
4461687 TTCTCGAGTTTAGAATTTAAA
1 TTCTCGAATTTAGAATTTAAA
4461708 ATAGGGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (21 bp):
TTCTCGAATTTAGAATTTAAA
Found at i:4467013 original size:6 final size:6
Alignment explanation
Indices: 4466995--4467077 Score: 68
Period size: 6 Copynumber: 14.0 Consensus size: 6
4466985 TTAAATTGAT
*
4466995 TTTAAA TTT--A TTTGAA TTTAAA TTT--A TCTTAAA TTTAATTA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA--A TTTAAA
* *
4467042 TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
4467078 ACAAATTTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
4 6 0.10
5 5 0.08
6 40 0.63
7 6 0.10
8 6 0.10
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:4467077 original size:25 final size:23
Alignment explanation
Indices: 4467004--4467069 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 23
4466994 TTTTAAATTT
*
4467004 ATTTGAATTTAAATTT-ATCTTAA
1 ATTTAAATTTAAATTTAAT-TTAA
**
4467027 ATTTAATTATTTAAATTTACCTTAA
1 ATTTAA--ATTTAAATTTAATTTAA
4467052 ATTTAAATTTAAATTTAA
1 ATTTAAATTTAAATTTAA
4467070 ATTATAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 16 0.44
25 20 0.56
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAATTTAA
Found at i:4469014 original size:29 final size:29
Alignment explanation
Indices: 4468901--4469143 Score: 197
Period size: 30 Copynumber: 8.2 Consensus size: 29
4468891 AAATTATCCA
*
4468901 AAAATTATATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAAC-TTTCC
*
4468931 AAAATTATATTTTAACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAAC-TTTCC
*
4468961 AAAA-TATAATTTTGACCCCAAAACTTTCA
1 AAAATTAT-ATTTTGACCCCAAAACTTTCC
* * *
4468990 AGAAATTACATTTTGA-CCCTAAACTTTCTG
1 A-AAATTATATTTTGACCCCAAAACTTTC-C
* *
4469020 GAAATTATATTTTAACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAAC-TTTCC
* *
4469050 AAAATCATATTTTAACCCCAAAA-TTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCC
* * * * * *
4469078 AAAAAATTGCTTTTTTTACCTCAAAATTTTCA
1 --AAAATT-ATATTTTGACCCCAAAACTTTCC
* *
4469110 AAAATTACCATTTT-ACCCCCAAACTTTCC
1 AAAATTA-TATTTTGACCCCAAAACTTTCC
*
4469139 TAAAT
1 AAAAT
4469144 CCCATTTTAA
Statistics
Matches: 174, Mismatches: 28, Indels: 23
0.77 0.12 0.10
Matches are distributed among these distances:
28 5 0.03
29 46 0.26
30 100 0.57
31 19 0.11
32 4 0.02
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCAAAACTTTCC
Found at i:4469054 original size:89 final size:90
Alignment explanation
Indices: 4468891--4469158 Score: 275
Period size: 89 Copynumber: 3.0 Consensus size: 90
4468881 GTAAATCCCT
*
4468891 AAATTATCC-AAAAATTATATTTTGACCCTAAAACTTTTCCAAAATTATATTTTAACCCCAAAAC
1 AAATT-TCCAAAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTATATTTTAACCCCAAAAC
*
4468955 TTTTCCAAAAT-ATAATTTTGACCCCA
65 TTTTCCAAAATCAT-ATTTTAACCCCA
* **
4468981 AAACTTT-CAAGAAATTACATTTTGACCCT-AAAC-TTTCTGGAAATTATATTTTAACCCCAAAA
1 AAA-TTTCCAAAAAATTACATTTTGACCCTAAAACTTTTC-CAAAATTATATTTTAACCCCAAAA
4469043 CTTTTCCAAAATCATATTTTAACCCCA
64 CTTTTCCAAAATCATATTTTAACCCCA
* * * * * *
4469070 AAATTTCCAAAAAATTGCTTTTTTTA-CCTCAAAA-TTTTCAAAAATTACCATTTT-ACCCCCAA
1 AAATTTCCAAAAAATTAC-ATTTTGACCCT-AAAACTTTTCCAAAATTA-TATTTTAACCCCAAA
* **
4469132 AC-TTTCCTAAATCCCATTTTAAACCCC
63 ACTTTTCCAAAATCATATTTT-AACCCC
4469159 GATTTCACTT
Statistics
Matches: 151, Mismatches: 16, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
88 7 0.05
89 80 0.53
90 50 0.33
91 14 0.09
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (90 bp):
AAATTTCCAAAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTATATTTTAACCCCAAAACT
TTTCCAAAATCATATTTTAACCCCA
Found at i:4469191 original size:58 final size:58
Alignment explanation
Indices: 4469110--4469239 Score: 179
Period size: 58 Copynumber: 2.2 Consensus size: 58
4469100 AAAATTTTCA
* * *
4469110 AAAATTACCATTTTACCCCCAAACTTTCCTAAATCCCATTTTAAACCCCGATTTCACT
1 AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
* * ** *
4469168 TAAATTACCATTTCACCCTCAAACTTCCCTAAATCTTATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
4469226 AAAATCTACCATTT
1 AAAAT-TACCATTT
4469240 TGCCCTCGGG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
58 54 0.87
59 8 0.13
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
Found at i:4481210 original size:76 final size:76
Alignment explanation
Indices: 4481082--4481637 Score: 690
Period size: 76 Copynumber: 7.4 Consensus size: 76
4481072 ATTGAAGTAG
* *
4481082 AGTCTTTATCTCTGAAATTGAAGTAAGAGC-AGCGTCATTTCCTATCCACTTGAAATTGAAGTAA
1 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG-ATCATTTCCTATCCTCTTGAAATTGAAGTAA
*
4481146 AGCTGGATATCA
65 AGTTGGATATCA
*
4481158 AGTCTTTATCTCTGAAATTGAAGTAAGAACAATG-TCATTTCCTAT-CTGCTTGAAATTGAAG-A
1 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAA-GATCATTTCCTATCCT-CTTGAAATTGAAGTA
*
4481220 AGAGTTGGATAGCA
64 A-AGTTGGATATCA
* *
4481234 AGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGATCAGTTCCTATCCTCTTGAAATTGAAGTAAA
1 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
4481299 GTTGGATATCA
66 GTTGGATATCA
* * * * *
4481310 AGTCTTTATCTCTGAAACTGAAGAAAGAGCAAGACCTTTTCCTATCCTCTTGAAATTGAAGTAGA
1 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
*
4481375 GTTGGATAGCA
66 GTTGGATATCA
* ** * * *
4481386 CGTCTTTATCTCCAAAATTGAAGTAAGGGC-A-A-C--GT-C-ATCCTCTTGAAATTGAAGTAGA
1 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
*
4481444 G-TGGATAACA
66 GTTGGATATCA
* *
4481454 CA-TCTTTATCTCTGAAATTGAAGTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAG
1 -AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAA
*
4481518 AG-TGGATAACA
65 AGTTGGATATCA
* * *
4481529 CGTCTTTATCTCTGGAATTGAAATAAGAGCAAGATCATTTTCCTATCCTCTTGAAATTGAAGTAA
1 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCA-TTTCCTATCCTCTTGAAATTGAAGTAA
*
4481594 AGCTGGATATCA
65 AGTTGGATATCA
*
4481606 AGTCTTTATCTCTCTGAAATTGAAGCAAGAGC
1 AGTCTTTA--TCTCTGAAATTGAAGTAAGAGC
4481638 TAGACGAAGC
Statistics
Matches: 420, Mismatches: 40, Indels: 37
0.85 0.08 0.07
Matches are distributed among these distances:
68 32 0.08
69 24 0.06
70 2 0.00
71 2 0.00
73 2 0.00
74 2 0.00
75 69 0.16
76 247 0.59
77 20 0.05
78 1 0.00
79 19 0.05
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (76 bp):
AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAA
GTTGGATATCA
Found at i:4482026 original size:6 final size:6
Alignment explanation
Indices: 4482008--4482090 Score: 66
Period size: 6 Copynumber: 14.0 Consensus size: 6
4481998 TTAAATTGAT
* * *
4482008 TTTAAA TTT--A TTTGAA TTTAAA TTT-AC CTTAAA TTTAATTA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA
* *
4482055 TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
4482091 ACAAATTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.07
5 6 0.10
6 41 0.67
7 4 0.07
8 6 0.10
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:4482057 original size:25 final size:25
Alignment explanation
Indices: 4482009--4482081 Score: 105
Period size: 25 Copynumber: 2.9 Consensus size: 25
4481999 TAAATTGATT
*
4482009 TTAAATTTATTTGAATTTAAATTTACC
1 TTAAATTTAATT--ATTTAAATTTACC
4482036 TTAAATTTAATTATTTAAATTTACC
1 TTAAATTTAATTATTTAAATTTACC
4482061 TTAAATTTAA--ATTTAAATTTA
1 TTAAATTTAATTATTTAAATTTA
4482082 AATTATAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
23 11 0.24
25 23 0.51
27 11 0.24
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.52
Consensus pattern (25 bp):
TTAAATTTAATTATTTAAATTTACC
Found at i:4483981 original size:30 final size:30
Alignment explanation
Indices: 4483945--4484121 Score: 164
Period size: 30 Copynumber: 5.9 Consensus size: 30
4483935 AAATTATCCA
*
4483945 AAAATTATATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* **
4483975 AAAATTATATTTTAACCCCAAAACTTTTTG
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* * *
4484005 GAAATTACATTTTGGCCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
4484035 AAGATCATATTTTGACCCCAAAA--TTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* * *
4484063 AAAAAATTACATTTTTTACCCCAAAA-TTTTCA
1 --AAAATTATA-TTTTGACCCCAAAACTTTTCC
* *
4484095 AAAATTACCATTTT-ACCCCCAAACTTT
1 AAAATTA-TATTTTGACCCCAAAACTTT
4484122 CCTAAATCCC
Statistics
Matches: 120, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.04
29 8 0.07
30 88 0.73
31 15 0.12
32 4 0.03
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCAAAACTTTTCC
Found at i:4484070 original size:60 final size:59
Alignment explanation
Indices: 4483935--4484123 Score: 182
Period size: 60 Copynumber: 3.1 Consensus size: 59
4483925 GTAAGTCCCT
* * *
4483935 AAATTATCCAAAAATTATATTTTGACCCTAAAACTTTTCCAAAATTATATTTTAACCCCA
1 AAATT-TCCAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATCATATTTTAACCCCA
**** * * *
4483995 AAACTTTTTGGAAATTACATTTTGGCCCCAAAACTTTTCCAAGATCATATTTTGACCCCA
1 AAA-TTTCCAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATCATATTTTAACCCCA
* * * * *
4484055 AAATTTCCAAAAAATTACATTTTTTACCCCAAAA-TTTTCAAAAATTACCATTTTACCCCCA
1 AAATTTCC-AAAAATTACA-TTTTGACCCCAAAACTTTTCCAAAATCA-TATTTTAACCCCA
*
4484116 AACTTTCC
1 AAATTTCC
4484124 TAAATCCCAT
Statistics
Matches: 102, Mismatches: 23, Indels: 7
0.77 0.17 0.05
Matches are distributed among these distances:
59 3 0.03
60 68 0.67
61 31 0.30
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (59 bp):
AAATTTCCAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATCATATTTTAACCCCA
Found at i:4484100 original size:90 final size:89
Alignment explanation
Indices: 4483951--4484121 Score: 204
Period size: 90 Copynumber: 1.9 Consensus size: 89
4483941 TCCAAAAATT
* * ***
4483951 ATATTTTGACCCTAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTTGGAAATTA-CAT
1 ATATTTTGACCCCAAAAC-TTTCCAAAATTACATTTTAACCCCAAAACTTTTCAAAAATTACCAT
*
4484015 TTTGGCCCCAAAACTTTTCCAAGATC
65 TTT-ACCCCAAAACTTTTCCAAGATC
*
4484041 ATATTTTGACCCCAAAA-TTTCCAAAAAATTACATTTTTTACCCCAAAA-TTTTCAAAAATTACC
1 ATATTTTGACCCCAAAACTTTCC--AAAATTACA-TTTTAACCCCAAAACTTTTCAAAAATTACC
*
4484104 ATTTTACCCCCAAACTTT
63 ATTTTACCCCAAAACTTT
4484122 CCTAAATCCC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 5 0.07
90 45 0.65
91 19 0.28
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (89 bp):
ATATTTTGACCCCAAAACTTTCCAAAATTACATTTTAACCCCAAAACTTTTCAAAAATTACCATT
TTACCCCAAAACTTTTCCAAGATC
Found at i:4484128 original size:29 final size:28
Alignment explanation
Indices: 4484076--4484194 Score: 80
Period size: 29 Copynumber: 4.1 Consensus size: 28
4484066 AAATTACATT
* * **
4484076 TTTTACCCCAAAATTTTCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCTAAA-TACCA
*
4484105 TTTTACCCCCAAACTTTCCTAAATCCCA
1 TTTTACCCCCAAACTTTCCTAAATACCA
* *
4484133 TTTTAAACCCC-GA-TTTCACTTAAATTACCA
1 TTTT-ACCCCCAAACTTTC-C-TAAA-TACCA
* * * *
4484163 TTTCACCCTCAAACTTCCCTAAATCCCA
1 TTTTACCCCCAAACTTTCCTAAATACCA
4484191 TTTT
1 TTTT
4484195 TAACCCCGAT
Statistics
Matches: 69, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
27 4 0.06
28 17 0.25
29 36 0.52
30 9 0.13
31 3 0.04
ACGTcount: A:0.32, C:0.32, G:0.01, T:0.35
Consensus pattern (28 bp):
TTTTACCCCCAAACTTTCCTAAATACCA
Found at i:4484176 original size:58 final size:58
Alignment explanation
Indices: 4484095--4484224 Score: 197
Period size: 58 Copynumber: 2.2 Consensus size: 58
4484085 AAAATTTTCA
* * *
4484095 AAAATTACCATTTTACCCCCAAACTTTCCTAAATCCCATTTTAAACCCCGATTTCACT
1 AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
* * *
4484153 TAAATTACCATTTCACCCTCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
4484211 AAAATCTACCATTT
1 AAAAT-TACCATTT
4484225 TGCCCCCGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 56 0.88
59 8 0.12
ACGTcount: A:0.32, C:0.33, G:0.02, T:0.33
Consensus pattern (58 bp):
AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
Found at i:4488781 original size:17 final size:18
Alignment explanation
Indices: 4488748--4488789 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
4488738 TTTGTATTTT
4488748 TATTTTATATTTATTAAA
1 TATTTTATATTTATTAAA
4488766 TATTTTATATTT-TTAAA
1 TATTTTATATTTATTAAA
4488783 TACTTTT
1 TA-TTTT
4488790 TTCTAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATATTTATTAAA
Found at i:4490001 original size:85 final size:85
Alignment explanation
Indices: 4489847--4490014 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 85
4489837 TCACCTCATT
* * * *
4489847 GATTTGGTCCACTTCTCTGTATATCATCAGGAAGATGACCGCCTTATTGTTTCAATCCACTTCTT
1 GATTTGGTCCACTTCTCTGTATATCATCAAGAAGATGACCGCCTTATTGCTTCAACCCACTTCTC
*
4489912 TGTATCTCATCAGGAAGACG
66 TGTATCTCATCAGAAAGACG
* * * * * * *
4489932 GATTTTGTTCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTGCTTCGACCCATTTCTC
1 GATTTGGTCCACTTCTCTGTATATCATCAAGAAGATGACCGCCTTATTGCTTCAACCCACTTCTC
4489997 TGTATCTCATCAGAAAGA
66 TGTATCTCATCAGAAAGA
4490015 TGGGGGTTTG
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTGTATATCATCAAGAAGATGACCGCCTTATTGCTTCAACCCACTTCTC
TGTATCTCATCAGAAAGACG
Found at i:4490129 original size:209 final size:208
Alignment explanation
Indices: 4489727--4490355 Score: 825
Period size: 209 Copynumber: 3.0 Consensus size: 208
4489717 GCTTCATCTC
* *
4489727 TTGGTCCACTTCTCTGTATCTCATTAGGAAGATGATCACTTTATTGCTTCGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTCGACCCACTTCTCTGT
* * * * * *
4489792 ATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTTACATTGAGCTTCACCTCATTGATTTGGTCC
66 ATCTCATCAGAAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATTGATTTGGTCT
* * *
4489857 ACTTCTCTGTATATCATCAGGAAGATGACCGCCTTATTGTTTCAATCCACTTCTTTGTATCTCAT
131 ACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCTTTGTATCTCAT
4489922 CAGGAAGACGGAT
196 CAGGAAGACGGAT
* * * *
4489935 TTTGTTCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTGCTTCGACCCATTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTCGACCCACTTCTCTGT
* *
4490000 ATCTCATCAGAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATCGATTTAGTC
66 ATCTCATCAGAAAGAT-GGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATTGATTTGGTC
* * *
4490065 TACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTATTTTAATCCACTTTTTTGTATCTCA
130 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCTTTGTATCTCA
*
4490130 TCAGGAAGATGGAT
195 TCAGGAAGACGGAT
*
4490144 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGA-CTGCTTTATTGCTTTGACCCACTTCTCTG
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATC-GCTTTATTGCTTCGACCCACTTCTCTG
** * * **
4490208 TATCTCATCA-AGAAGATAAGGTTTGAAGTCTCATTCGTATTGA-TCTTCGCTTCATTGATTTGG
65 TATCTCATCAGA-AAGATGGGGTTTGAAGTTTCACTCACATTGAGT-TTCGCTTCATTGATTTGG
* * * * * * * * *
4490271 TTTACTTCTCTATATCTCATCAGGAAGATTACCGCTTTATTGCTTT-GACCCACTTCTCTGTATC
128 TCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATT-ATTTCAATCCACTTCTTTGTATC
* *
4490335 TCATCAAGAAGATGGAGT
192 TCATCAGGAAGACGGA-T
4490353 TTG
1 TTG
4490356 AAGTCTCATT
Statistics
Matches: 369, Mismatches: 46, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
207 1 0.00
208 176 0.48
209 192 0.52
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (208 bp):
TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTCGACCCACTTCTCTGT
ATCTCATCAGAAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATTGATTTGGTCT
ACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCTTTGTATCTCAT
CAGGAAGACGGAT
Found at i:4490201 original size:85 final size:85
Alignment explanation
Indices: 4490056--4490224 Score: 223
Period size: 85 Copynumber: 2.0 Consensus size: 85
4490046 TCGCTTCATC
* * * * *
4490056 GATTTAGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTATTTTAATCCACTTTTT
1 GATTTAGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTACTTTAACCCACTTCTC
*
4490121 TGTATCTCATCAGGAAGATG
66 TGTATCTCATCAAGAAGATG
* * * * *
4490141 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGA-CTGCTTTATTGCTTTGACCCACTTCT
1 GATTTAGTCCACTTCTCTGTATCTCATCAGGAAGATGATC-GCCTCATTACTTTAACCCACTTCT
4490205 CTGTATCTCATCAAGAAGAT
65 CTGTATCTCATCAAGAAGAT
4490225 AAGGTTTGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 1 0.01
85 71 0.99
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (85 bp):
GATTTAGTCCACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTACTTTAACCCACTTCTC
TGTATCTCATCAAGAAGATG
Found at i:4490469 original size:123 final size:123
Alignment explanation
Indices: 4490141--4490428 Score: 461
Period size: 123 Copynumber: 2.3 Consensus size: 123
4490131 CAGGAAGATG
* * * *
4490141 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCTACTTCTCTATATCTCATCAGGAAGATAACCGCTTTATTGCTTTGACCCACTTCTC
* * *
4490206 TGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCGTATTGATCTTCGCTTCATT
66 TGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATT
* *
4490264 GATTTGGTTTACTTCTCTATATCTCATCAGGAAGATTACCGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCTACTTCTCTATATCTCATCAGGAAGATAACCGCTTTATTGCTTTGACCCACTTCTC
*
4490329 TGTATCTCATCAAGAAGAT-GGAGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATT
66 TGTATCTCATCAAGAAGATAAG-GTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATT
*
4490387 GATTTGGTCTATTTCTCTATATCTCATCAGGAAGATAACCGC
1 GATTTGGTCTACTTCTCTATATCTCATCAGGAAGATAACCGC
4490429 CTCATTATTT
Statistics
Matches: 152, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
122 1 0.01
123 151 0.99
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (123 bp):
GATTTGGTCTACTTCTCTATATCTCATCAGGAAGATAACCGCTTTATTGCTTTGACCCACTTCTC
TGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATT
Found at i:4490479 original size:208 final size:208
Alignment explanation
Indices: 4490264--4490884 Score: 910
Period size: 208 Copynumber: 3.0 Consensus size: 208
4490254 TCGCTTCATT
* *
4490264 GATTTGGTTTACTTCTCTATATCTCATCAGGAAGATTACCGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTTCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTC
4490329 TGTATCTCATCAAGAAGATGGAGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATTGATTTGG
66 TGTATCTCATCAAGAAGATGGAGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATTGATTTGG
* * * * * *
4490394 TCTATTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAATCTACTTCTCTGTATCT
131 TCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTCAATCCACTTCTCTGTATCT
*
4490459 CATTAGGAAGAC-
196 CATCAGGAAGACA
* *
4490471 GAATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACGCACTTCT
1 G-ATTTGGTTCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCT
*
4490536 CTGTATCTCATCAAGAAGAT-GAGTTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTT
65 CTGTATCTCATCAAGAAGATGGAG-TTTGAAGTCTCATTCATATTAAGCTTCGCTTCATTGATTT
* * *
4490600 GGTCTACTTCTCTGCATCTCATCAGGAAGATGACCGCTTCATTGTTTCAATCCACTTTTCTCTAT
129 GGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTCAATCCACTTCTCTGTAT
*
4490665 CTCATCAAGAAGACA
194 CTCATCAGGAAGACA
* * *
4490680 GATTTGGTTCGCTTCTCTATATCTCATCAAGAAGATGATCGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTTCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTC
* * * * * * *
4490745 TGTATCTTATCAAGAAGATAGG-GTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGAATTG
66 TGTATCTCATCAAGAAGAT-GGAGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATTGATTTG
* * *
4490809 GTC-AGCTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTCT-AACCCACTTCTTTGTAT
130 GTCTA-CTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTCAATCCACTTCTCTGTAT
4490872 CTCATCAGGAAGA
194 CTCATCAGGAAGA
4490885 TGGGGTTTGA
Statistics
Matches: 372, Mismatches: 36, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
207 30 0.08
208 339 0.91
209 2 0.01
210 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (208 bp):
GATTTGGTTCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTC
TGTATCTCATCAAGAAGATGGAGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATTGATTTGG
TCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTCAATCCACTTCTCTGTATCT
CATCAGGAAGACA
Found at i:4490534 original size:85 final size:85
Alignment explanation
Indices: 4490388--4490546 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
4490378 CGCTTCATTG
* * *
4490388 ATTTGGTCTATTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAATCTACTTCTCT
1 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAAGCTACTTCTCT
4490453 GTATCTCATTAGGAAGACGA
66 GTATCTCATTAGGAAGACGA
* * * * * *
4490473 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACGC-ACTTCTC
1 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCGCCTCATT-ATTTCAAGCTACTTCTC
4490537 TGTATCTCAT
65 TGTATCTCAT
4490547 CAAGAAGATG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 59 0.92
86 5 0.08
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAAGCTACTTCTCT
GTATCTCATTAGGAAGACGA
Found at i:4490545 original size:331 final size:332
Alignment explanation
Indices: 4489932--4490677 Score: 1084
Period size: 331 Copynumber: 2.2 Consensus size: 332
4489922 CAGGAAGACG
* * * * * *
4489932 GATTTTGTTCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTGCTTCGACCCATTTCTC
1 GATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTC
* * * *
4489997 TGTATCTCATC-AGAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATCGATTT
66 TGTATCTCATCAAG-AAGATGGGAGTTTGAAGTCTCACTCACATTAAGCTTCGCTTCATCGATTT
* * * * * *
4490061 AGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTATTTTAATCCACTTTTTTGTAT
130 AGTCTACTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAATCCACTTCTCTGTAT
* * * *
4490126 CTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGC
195 CTCATCAGGAAGACGAATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGC
* *
4490191 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCGTATTGATCTTC
260 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCGTATTAAGCTTC
4490256 GCTTCATT
325 GCTTCATT
* *
4490264 GATTTGGTTTACTTCTCTATATCTCATCAGGAAGATTACCGCTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTC
* * * *
4490329 TGTATCTCATCAAGAAGAT-GGAGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATTGATTTG
66 TGTATCTCATCAAGAAGATGGGAGTTTGAAGTCTCACTCACATTAAGCTTCGCTTCATCGATTTA
* *
4490393 GTCTATTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAATCTACTTCTCTGTATC
131 GTCTACTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAATCCACTTCTCTGTATC
*
4490458 TCATTAGGAAGACGAATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCT
196 TCATCAGGAAGACGAATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCT
* * *
4490523 TTGACGCACTTCTCTGTATCTCATCAAGAAGATGAGTTTTGAAGTCTCATTCGTATTAAGCTTCG
261 TTGACCCACTTCTCTGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCGTATTAAGCTTCG
4490588 CTTCATT
326 CTTCATT
* * * * * *
4490595 GATTTGGTCTACTTCTCTGCATCTCATCAGGAAGATGACCGCTTCATTG-TTTCAATCCACTTTT
1 GATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTT-GACCCACTTCT
*
4490659 CTCTATCTCATCAAGAAGA
65 CTGTATCTCATCAAGAAGA
4490678 CAGATTTGGT
Statistics
Matches: 369, Mismatches: 43, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
330 3 0.01
331 291 0.79
332 73 0.20
333 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (332 bp):
GATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTC
TGTATCTCATCAAGAAGATGGGAGTTTGAAGTCTCACTCACATTAAGCTTCGCTTCATCGATTTA
GTCTACTTCTCTATATCTCATCAGGAAGATAACCGCCTCATTATTTCAATCCACTTCTCTGTATC
TCATCAGGAAGACGAATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCT
TTGACCCACTTCTCTGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCGTATTAAGCTTCG
CTTCATT
Found at i:4490740 original size:85 final size:85
Alignment explanation
Indices: 4490606--4490762 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
4490596 ATTTGGTCTA
* * * *
4490606 CTTCTCTGCATCTCATCAGGAAGATGACCGCTTCATTGTTTCAATCCACTTTTCTCTATCTCATC
1 CTTCTCTACATCTCATCAAGAAGATGACCGCTTCATTGTTTCAACCCACTTCTCTCTATCTCATC
4490671 AAGAAGACAGATTTGGTTCG
66 AAGAAGACAGATTTGGTTCG
* * * * * *
4490691 CTTCTCTATATCTCATCAAGAAGATGATCGCTTTATTGCTTT-GACCCACTTCTCTGTATCTTAT
1 CTTCTCTACATCTCATCAAGAAGATGACCGCTTCATTG-TTTCAACCCACTTCTCTCTATCTCAT
4490755 CAAGAAGA
65 CAAGAAGA
4490763 TAGGGTTTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 58 0.95
86 3 0.05
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (85 bp):
CTTCTCTACATCTCATCAAGAAGATGACCGCTTCATTGTTTCAACCCACTTCTCTCTATCTCATC
AAGAAGACAGATTTGGTTCG
Found at i:4490820 original size:331 final size:328
Alignment explanation
Indices: 4489942--4490894 Score: 804
Period size: 331 Copynumber: 2.9 Consensus size: 328
4489932 GATTTTGTTC
** * * * ** * *
4489942 ACTTCTCTGTATCTCATCAAGAAGATGATCGCTTTATTGCTTCGACCCATTTCTCTGTATCTCAT
1 ACTTCTCTACATCTCATCAGGAAGATGACCGCTTCATTGCTTTAACCCACTTCTCTCTATCTCAT
** * * * * * * * * *
4490007 C-AGAAAGATGGGGGTTTGAAGTTTCACTCACATTG-AGTTTCGCTTCATCGATTT-AGTCTACT
66 CAAG-AAGA-CAGAGTTTGAAGTCTCATTCATA-AGAAGATTCGCTTCATTGATTTGA-CCCACT
* * * * * * * * * *
4490069 TCTCTGTATCTCATCAGGAAGATGATCGCCTCATTATTTTAATCCACTTTTTTGTATCTCATCAG
127 TCTCTATATCTCATCAAGAAGATAACCGCCTCA-TATTTCAATCTAC-TATCTGTAGCT-ATTAG
* * * * *
4490134 GAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTTGACCC
189 CAACACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCC
* * *
4490199 ACTTCTCTGTATCTCATCAAGAAGATAAGGTTTGAAGTCTCATTCGTATTGATCTTCGCTTCATT
254 ACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATT
*
4490264 GATTTGGTTT
319 GATTTGGTCT
* * * * *
4490274 ACTTCTCTATATCTCATCAGGAAGATTACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCAT
1 ACTTCTCTACATCTCATCAGGAAGATGACCGCTTCATTGCTTTAACCCACTTCTCTCTATCTCAT
** ** * ** * *
4490339 CAAGAAGATGGAGTTTGAAGTCTCATTCATATTAAGCTTCGCTTCATTGATTTGGTCTATTTCTC
66 CAAGAAGACAGAGTTTGAAGTCTCATTCATAAGAAGATTCGCTTCATTGATTTGACCCACTTCTC
* * * * *
4490404 TATATCTCATCAGGAAGATAACCGCCTCATTATTTCAATCTACTTCTCTGTATCTCATTAGGAAG
131 TATATCTCATCAAGAAGATAACCGCCTCA-TATTTCAATCTAC-TATCTGTAGCT-ATTAGCAAC
* *
4490469 ACGAATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACGCACTT
193 ACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTT
*
4490534 CTCTGTATCTCATCAAGAAGATGAGTTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATT
258 CTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATT
4490599 TGGTCT
323 TGGTCT
* * *
4490605 ACTTCTCTGCATCTCATCAGGAAGATGACCGCTTCATTG-TTTCAATCCACTTTTCTCTATCTCA
1 ACTTCTCTACATCTCATCAGGAAGATGACCGCTTCATTGCTTT-AACCCACTTCTCTCTATCTCA
** * *
4490669 TCAAGAAGACAGA-TTTGGTTCGCTTCTCTATATCTCATCAAGAAGATGATCGCTTTATTGCTTT
65 TCAAGAAGACAGAGTTT-G-AAG--TCTC---AT-TCAT-AAGAAGAT--TCGCTTCATTGATTT
* * ** ** * *
4490733 GACCCACTTCTCTGTATCTTATCAAGAAGAT-AGGGTTTGA-AGTTTCACTC-AC-AT-TG-AGC
119 GACCCACTTCTCTATATCTCATCAAGAAGATAACCGCCTCATA-TTTCAATCTACTATCTGTAGC
** * *
4490792 T-TT-GCTTCATTGAA-TTGGT-CAGCTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTG-
183 TATTAGCAACA-CGAATTTGGTCCA-CTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGC
* * * * *
4490852 TCTAACCCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGA
246 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGA
4490895 TCTGCCCCTC
Statistics
Matches: 523, Mismatches: 80, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
330 45 0.09
331 334 0.64
332 70 0.13
333 2 0.00
334 7 0.01
335 2 0.00
336 1 0.00
337 2 0.00
338 7 0.01
339 12 0.02
340 4 0.01
341 37 0.07
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (328 bp):
ACTTCTCTACATCTCATCAGGAAGATGACCGCTTCATTGCTTTAACCCACTTCTCTCTATCTCAT
CAAGAAGACAGAGTTTGAAGTCTCATTCATAAGAAGATTCGCTTCATTGATTTGACCCACTTCTC
TATATCTCATCAAGAAGATAACCGCCTCATATTTCAATCTACTATCTGTAGCTATTAGCAACACG
AATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTC
TGTATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGG
TCT
Found at i:4491225 original size:99 final size:99
Alignment explanation
Indices: 4491040--4491280 Score: 281
Period size: 99 Copynumber: 2.4 Consensus size: 99
4491030 GAAGGTACCG
*
4491040 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCGTCGTCGCGAC
1 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCGTCATCGCGAC
* *
4491105 CTCGATCCTTCCCATCACATCTTTTAAAGTACT-
66 CTCGAACCTTCCCATCACATCTTCTAAAGTACTA
* * * ** ** *
4491138 GAGTTCGCCGTTGCGGCTTCAACCTTTCCCTTCATGTCTTCATGGTATTGGGTTC-TCCATTGCG
1 G-GTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCGT-CATCGCG
* ** * *
4491202 GCCTC-AACCTTTTTCATCTCATCTTCTAAGGTACTA
64 ACCTCGAACC-TTCCCATCACATCTTCTAAAGTACTA
*
4491238 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATG
1 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATG
4491281 TTTCCTTGGT
Statistics
Matches: 119, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
98 5 0.04
99 113 0.95
100 1 0.01
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (99 bp):
GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCGTCATCGCGAC
CTCGAACCTTCCCATCACATCTTCTAAAGTACTA
Found at i:4491276 original size:50 final size:50
Alignment explanation
Indices: 4491017--4491277 Score: 208
Period size: 49 Copynumber: 5.2 Consensus size: 50
4491007 ATTGGTGCGT
*
4491017 CTTC-AATCTTTCTGAAGGTACCGGGTTCGTCGTTGCGGCCTCAACCTTTCC
1 CTTCAAATC-TTCT-AAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCC
* * * ** * * *
4491068 CTTCATATCTTC-ATGGTACCGAATTCGTCGTCGCGACCTCGATCC-TTCC
1 CTTCAAATCTTCTAAGGTACTGGGTTCGTCGTTGCGGCCTC-AACCTTTCC
* * * * * * *
4491117 CATCACATCTTTTAAAGTACTGAGTTCGCCGTTGCGGCTTCAACCTTTCC
1 CTTCAAATCTTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCC
** * * * **
4491167 CTTCATGTCTTC-ATGGTATTGGGTTC-TCCATTGCGGCCTCAACCTTTTT
1 CTTCAAATCTTCTAAGGTACTGGGTTCGT-CGTTGCGGCCTCAACCTTTCC
* ** *
4491216 CATCTCATCTTCTAAGGTACTAGGTTCGTCGTTGCGGCCTCAACCTTTCC
1 CTTCAAATCTTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCC
4491266 CTTCAAATCTTC
1 CTTCAAATCTTC
4491278 ATGTTTCCTT
Statistics
Matches: 158, Mismatches: 45, Indels: 15
0.72 0.21 0.07
Matches are distributed among these distances:
49 74 0.47
50 73 0.46
51 8 0.05
52 3 0.02
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (50 bp):
CTTCAAATCTTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCC
Found at i:4491292 original size:50 final size:49
Alignment explanation
Indices: 4491040--4491292 Score: 158
Period size: 50 Copynumber: 5.1 Consensus size: 49
4491030 GAAGGTACCG
* * *
4491040 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTAC-C
1 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATGTTACTT
* * * * * * *
4491088 GAATTCGTCGTCGCGACCTCGATCC-TTCCCATCACATCTTTTAAAG-TAC-T
1 G-GTTCGTCGTTGCGGCCTC-AACCTTTCCCTTCACATC--TTCATGTTACTT
* * ** *
4491138 GAGTTCGCCGTTGCGGCTTCAACCTTTCCCTTCATGTCTTCATGGTA-TT
1 G-GTTCGTCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATGTTACTT
* ** * * * * *
4491187 GGGTTC-TCCATTGCGGCCTCAACCTTTTTCATCTCATCTTCTAAGGTACTA
1 -GGTTCGT-CGTTGCGGCCTCAACCTTTCCCTTCACATCTTC-ATGTTACTT
* *
4491238 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGTTTCCTT
1 GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATG-TTACTT
4491288 GGTTC
1 GGTTC
4491293 ATTTCACTAT
Statistics
Matches: 151, Mismatches: 41, Indels: 24
0.70 0.19 0.11
Matches are distributed among these distances:
48 5 0.03
49 63 0.42
50 77 0.51
51 6 0.04
ACGTcount: A:0.15, C:0.31, G:0.17, T:0.37
Consensus pattern (49 bp):
GGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCATGTTACTT
Found at i:4492260 original size:32 final size:35
Alignment explanation
Indices: 4492211--4492290 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 35
4492201 CCCTTTTTCC
*
4492211 ATTTTT-TTCTTT-TTTTTTTTTTTCTC-TTTT-TT
1 ATTTTTATT-TTTATTTTTATTTTTCTCTTTTTATT
*
4492243 ATTTTTATTTTTATTTTTATTTTTTTCTTTTTATT
1 ATTTTTATTTTTATTTTTATTTTTCTCTTTTTATT
4492278 ATTATTTATTTTT
1 ATT-TTTATTTTT
4492291 CTTTATCGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 9 0.22
33 14 0.34
34 4 0.10
35 5 0.12
36 9 0.22
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (35 bp):
ATTTTTATTTTTATTTTTATTTTTCTCTTTTTATT
Found at i:4492273 original size:20 final size:21
Alignment explanation
Indices: 4492214--4492294 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 21
4492204 TTTTTCCATT
* * * *
4492214 TTTTTCTTTTTTTTTTTTTTC
1 TTTTTATTATTTTTCTTTTTA
*
4492235 TCTTTT-TTATTTTTATTTTTA
1 T-TTTTATTATTTTTCTTTTTA
4492256 TTTTTATT-TTTTTCTTTTTA
1 TTTTTATTATTTTTCTTTTTA
*
4492276 TTATTATTTATTTTTCTTT
1 TTTTTA-TTATTTTTCTTT
4492295 ATCGAATCCG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
20 20 0.39
21 18 0.35
22 13 0.25
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTATTATTTTTCTTTTTA
Found at i:4492275 original size:26 final size:27
Alignment explanation
Indices: 4492205--4492284 Score: 96
Period size: 26 Copynumber: 3.1 Consensus size: 27
4492195 CTTTTCCCCT
*
4492205 TTTTCCATTTTTTTCTTTTT-TTTTT-
1 TTTTCTATTTTTTTCTTTTTATTTTTA
* *
4492230 TTTTCT-CTTTTTTATTTTTATTTTTA
1 TTTTCTATTTTTTTCTTTTTATTTTTA
*
4492256 TTTT-TATTTTTTTCTTTTTATTATTA
1 TTTTCTATTTTTTTCTTTTTATTTTTA
4492282 TTT
1 TTT
4492285 ATTTTTCTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
24 11 0.24
25 11 0.24
26 24 0.52
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTCTATTTTTTTCTTTTTATTTTTA
Found at i:4492282 original size:6 final size:6
Alignment explanation
Indices: 4492238--4492290 Score: 65
Period size: 6 Copynumber: 8.8 Consensus size: 6
4492228 TTTTTTCTCT
*
4492238 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT- TTCTTT- TTATTA TTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TT-TTTA
4492286 TTTTT
1 TTTTT
4492291 CTTTATCGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 4 0.10
6 33 0.79
7 5 0.12
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:4492290 original size:1 final size:1
Alignment explanation
Indices: 4492212--4492274 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
4492202 CCTTTTTCCA
* * * * * * * *
4492212 TTTTTTTCTTTTTTTTTTTTTTCTCTTTTTTATTTTTATTTTTATTTTTATTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4492275 ATTATTATTT
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:4492296 original size:20 final size:17
Alignment explanation
Indices: 4492212--4492294 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 17
4492202 CCTTTTTCCA
4492212 TTTTTTTCTTTTT-TTT
1 TTTTTTTCTTTTTATTT
4492228 TTTTTTCTCTTTTTTATTT
1 TTTTTT-TC-TTTTTATTT
*
4492247 TTATTTTTATTTTTATTT
1 TT-TTTTTCTTTTTATTT
*
4492265 TTTTCTTT-TTATTATTAT
1 TTTT-TTTCTTTTTATT-T
4492283 TTATTTTTCTTT
1 TT-TTTTTCTTT
4492295 ATCGAATCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
16 6 0.11
17 11 0.20
18 25 0.45
19 10 0.18
20 4 0.07
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTCTTTTTATTT
Found at i:4498753 original size:17 final size:18
Alignment explanation
Indices: 4498720--4498759 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
4498710 TTTGTATTTT
4498720 TATTTTATATTTATTAAA
1 TATTTTATATTTATTAAA
4498738 TATTTTATATTT-TTAAA
1 TATTTTATATTTATTAAA
4498755 TATTT
1 TATTT
4498760 GTTTCGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTATATTTATTAAA
Found at i:4499972 original size:85 final size:85
Alignment explanation
Indices: 4499826--4499992 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
4499816 CGCCTCATTG
* * * *
4499826 ATTTGGTCTACTTCTCTGTATCTTATCAAGAAAATGACCACCTCATTGTTTCAATCCACTTCTCT
1 ATTTGATCCACTTCTCTGTATCTCATCAAGAAAATGACCACCTCATTCTTTCAATCCACTTCTCT
4499891 GTATCTCATCAAGAAGACGA
66 GTATCTCATCAAGAAGACGA
* * * * *
4499911 ATTTGATCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTACTTT-AA-CCTACTTCT
1 ATTTGATCCACTTCTCTGTATCTCATCAAGAAAATGACCACCTCATT-CTTTCAATCC-ACTTCT
*
4499974 CTGTATCTCATCAGGAAGA
64 CTGTATCTCATCAAGAAGA
4499993 TGGGGTTCGA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 65 0.93
86 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.36
Consensus pattern (85 bp):
ATTTGATCCACTTCTCTGTATCTCATCAAGAAAATGACCACCTCATTCTTTCAATCCACTTCTCT
GTATCTCATCAAGAAGACGA
Found at i:4500084 original size:208 final size:208
Alignment explanation
Indices: 4499708--4500317 Score: 898
Period size: 208 Copynumber: 2.9 Consensus size: 208
4499698 TCATCTCTTG
* * * * *
4499708 GTCCACTTCTCTGTATCTCATTAGGAAGATGATCGCTTTATTGCTTCGACCCACTTTTCTGTATC
1 GTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTGTATC
* * ** *
4499773 TCATCAGGAAGATGGGGTTTAAAGTTTCACTCACATTGAGCTTCGCCTCATTGATTTGGTCTACT
66 TCATCAGGAAGATGGGGTTTAAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACT
* * * *
4499838 TCTCTGTATCTTATCAAGAAAATGACCACCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAA
131 TCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAA
4499903 GAAGACGAATTT-
196 GAAGACGAATTTA
* *
4499915 GATCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTACTTTAACCTACTTCTCTGTAT
1 G-TCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTGTAT
** * *
4499980 CTCATCAGGAAGATGGGGTTCGAAGTCACATTCGTATTGAGCTTCGCTTCATTGATTTGATCTAC
65 CTCATCAGGAAGATGGGGTTTAAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTAC
* *
4500045 TTCTCTGTATCTCATCAGGAAGATGACCGCCTTATTGTTTCAATCCACTTCTTTGTATCTCATCA
130 TTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCA
*
4500110 AGAAGACGGATTTA
195 AGAAGACGAATTTA
* * * *
4500124 GTTCACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTTCTTTGACCCACTTCTCTGTATC
1 GTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTGTATC
* * *
4500189 TCGTCAGAAAGATGGGGTTTAAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGCCTACT
66 TCATCAGGAAGATGGGGTTTAAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACT
* * * *
4500254 TCTCTATATCTCATAAGGAAGATGACCGCCTCATTGTTTCAATCCATTTTTCTGTATCTCATCA
131 TCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCA
4500318 GGACGATGAC
Statistics
Matches: 359, Mismatches: 42, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
207 1 0.00
208 357 0.99
209 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (208 bp):
GTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTACTTTGACCCACTTCTCTGTATC
TCATCAGGAAGATGGGGTTTAAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACT
TCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGTATCTCATCAA
GAAGACGAATTTA
Found at i:4500884 original size:22 final size:22
Alignment explanation
Indices: 4500862--4500903 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4500852 GGTAAGTTCA
4500862 AATT-CTAACCCATATTGCTTC
1 AATTACTAACCCATATTGCTTC
4500883 AATTACTAACCCATATTGCTT
1 AATTACTAACCCATATTGCTT
4500904 TTACAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (22 bp):
AATTACTAACCCATATTGCTTC
Found at i:4501267 original size:16 final size:15
Alignment explanation
Indices: 4501246--4501275 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
4501236 ATCACAAGTT
4501246 TTTTTTTAAATATTTA
1 TTTTTTT-AATATTTA
4501262 TTTTTTTAATATTT
1 TTTTTTTAATATTT
4501276 TCTTATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTAATATTTA
Found at i:4512062 original size:24 final size:24
Alignment explanation
Indices: 4512035--4512108 Score: 139
Period size: 24 Copynumber: 3.1 Consensus size: 24
4512025 TTAAGCGTCG
4512035 ATTAATACGAAATTTGAGAAATTA
1 ATTAATACGAAATTTGAGAAATTA
4512059 ATTAATACGAAATTTGAGAAATTA
1 ATTAATACGAAATTTGAGAAATTA
*
4512083 ATTAGTACGAAATTTGAGAAATTA
1 ATTAATACGAAATTTGAGAAATTA
4512107 AT
1 AT
4512109 CTTTTATTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.34
Consensus pattern (24 bp):
ATTAATACGAAATTTGAGAAATTA
Found at i:4512307 original size:20 final size:20
Alignment explanation
Indices: 4512275--4512315 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4512265 GTTAACTAAT
*
4512275 AATTGTTTCAATTTTTTTTA
1 AATTGTTTCAATTTTTATTA
4512295 AATT-TTTCTAATTTTTATTA
1 AATTGTTTC-AATTTTTATTA
4512315 A
1 A
4512316 GTATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
AATTGTTTCAATTTTTATTA
Found at i:4514108 original size:7 final size:7
Alignment explanation
Indices: 4514051--4514108 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
4514041 TCAATTCAAA
4514051 CTCAATT
1 CTCAATT
*
4514058 CTTAATT
1 CTCAATT
4514065 -TCAATT
1 CTCAATT
* *
4514071 ATCTATT
1 CTCAATT
4514078 CTCAATT
1 CTCAATT
*
4514085 CTTAATT
1 CTCAATT
*
4514092 CTTAATT
1 CTCAATT
4514099 CTCAATT
1 CTCAATT
4514106 CTC
1 CTC
4514109 TCAATAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
6 5 0.12
7 38 0.88
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (7 bp):
CTCAATT
Found at i:4526239 original size:12 final size:12
Alignment explanation
Indices: 4526222--4526246 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4526212 GCCAGCTAAA
4526222 TCATTTTAAAAT
1 TCATTTTAAAAT
4526234 TCATTTTAAAAT
1 TCATTTTAAAAT
4526246 T
1 T
4526247 AAATTTATTT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:4526314 original size:6 final size:6
Alignment explanation
Indices: 4526238--4526335 Score: 68
Period size: 6 Copynumber: 17.3 Consensus size: 6
4526228 TAAAATTCAT
* * * *
4526238 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
4526284 TTTATA -TTAAA TTTAGA TTT--A -TTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4526327 TTTAGAA TT
1 TTTA-AA TT
4526336 AATGTAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 16 0.23
6 45 0.63
7 5 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:4526322 original size:26 final size:26
Alignment explanation
Indices: 4526279--4526330 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4526269 TATGTTAAAG
* *
4526279 TTAAATTTATATTAAATTTAGATTTA
1 TTAAATTTAAATTAAATTTAAATTTA
*
4526305 TTAAATTTAAATTTAATTTAAATTTA
1 TTAAATTTAAATTAAATTTAAATTTA
4526331 GAATTAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAAATTTAAATTAAATTTAAATTTA
Found at i:4526324 original size:11 final size:11
Alignment explanation
Indices: 4526245--4526330 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 11
4526235 CATTTTAAAA
*
4526245 TTAAATTTATT
1 TTAAATTTAAT
*
4526256 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
4526268 TTATGTTAAAG
1 TTAAATTTAAT
4526279 TTAAATTT-AT
1 TTAAATTTAAT
4526289 ATTAAATTTAGAT
1 -TTAAATTTA-AT
*
4526302 TT--ATTAAAT
1 TTAAATTTAAT
4526311 TTAAATTTAAT
1 TTAAATTTAAT
4526322 TTAAATTTA
1 TTAAATTTA
4526331 GAATTAATGT
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
9 4 0.07
10 5 0.09
11 36 0.62
12 11 0.19
13 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:4526327 original size:17 final size:16
Alignment explanation
Indices: 4526238--4526366 Score: 125
Period size: 17 Copynumber: 7.7 Consensus size: 16
4526228 TAAAATTCAT
*
4526238 TTTAAAATTAAATTTA
1 TTTAAATTTAAATTTA
*
4526254 TTTTAAAATTAAATTTA
1 -TTTAAATTTAAATTTA
*
4526271 TGTTAAAGTTAAATTTA
1 T-TTAAATTTAAATTTA
*
4526288 TATTAAATTTAGATTTA
1 T-TTAAATTTAAATTTA
4526305 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTT-A
*
4526321 TTTAAATTTAGAATTAA
1 TTTAAATTTA-AATTTA
* *
4526338 TGTAAATTTTAAAATTA
1 TTTAAA-TTTAAATTTA
4526355 TTATAAATTTAA
1 TT-TAAATTTAA
4526367 TAGAGTGTCC
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
15 13 0.14
16 2 0.02
17 69 0.72
18 12 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:4527069 original size:22 final size:20
Alignment explanation
Indices: 4527032--4527082 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
4527022 CCCATTGAAT
4527032 ATTTTAAAT-GTATTAATTA
1 ATTTTAAATAGTATTAATTA
4527051 ATGTTTTAAATAGTATTAATTA
1 A--TTTTAAATAGTATTAATTA
4527073 ATTTTAAATA
1 ATTTTAAATA
4527083 AAAGCATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 9 0.31
21 8 0.28
22 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTTAAATAGTATTAATTA
Found at i:4528233 original size:30 final size:30
Alignment explanation
Indices: 4528197--4528312 Score: 96
Period size: 30 Copynumber: 3.9 Consensus size: 30
4528187 CCCTAGAGGT
4528197 CCCTAAAC-TATCCAAAAATTATATTTTGAC
1 CCCTAAACTTATCC-AAAATTATATTTTGAC
* *
4528227 CCCTAAACTTTTCCAAAATTATATTTT-AA
1 CCCTAAACTTATCCAAAATTATATTTTGAC
* * *** *
4528256 CCTTAAAACTTTTTGTAAATTACATTTTGA-
1 CCCT-AAACTTATCCAAAATTATATTTTGAC
*
4528286 CCCTAAAACTT-TCCAAAATTACATTTT
1 CCCT-AAACTTATCCAAAATTATATTTT
4528313 TATCCCCAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 17 0.24
30 50 0.69
31 5 0.07
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.40
Consensus pattern (30 bp):
CCCTAAACTTATCCAAAATTATATTTTGAC
Found at i:4528369 original size:55 final size:57
Alignment explanation
Indices: 4528298--4528432 Score: 152
Period size: 55 Copynumber: 2.4 Consensus size: 57
4528288 CTAAAACTTT
* *** *
4528298 CCAAAATTA-CATTTTTATCCCCAAGTTTTCCAAAATTC-CATTTTG-CCCGATTT-A
1 CCAAAATTACCA-TTTTACCCCCAAACCTTCCAAAATTCTCATTTTGACCCAATTTAA
*
4528352 CCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCTCGTTTTGACCCAATTTCAA
1 CC-AAAATTACCATTTTACCCCCAAACCTTCCAAAATTCTCATTTTGACCCAATTT-AA
*
4528411 CCAAAATTACCATTTTGCCCCC
1 CCAAAATTACCATTTTACCCCC
4528433 GGGTATCCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
54 2 0.03
55 29 0.43
56 8 0.12
57 7 0.10
58 19 0.28
59 3 0.04
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (57 bp):
CCAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCTCATTTTGACCCAATTTAA
Found at i:4528432 original size:58 final size:55
Alignment explanation
Indices: 4528325--4528432 Score: 146
Period size: 58 Copynumber: 1.9 Consensus size: 55
4528315 TCCCCAAGTT
*
4528325 TTCCAAAATTCCATTTTGCCCGATTTACCAAAAATTACCATTTTACCCCCAAACC
1 TTCCAAAATTCCATTTTGCCCAATTTACCAAAAATTACCATTTTACCCCCAAACC
* *
4528380 TTCCAAAATTCTCGTTTTGACCCAATTTCAACC-AAAATTACCATTTTGCCCCC
1 TTCCAAAATTC-CATTTTG-CCCAATTT--ACCAAAAATTACCATTTTACCCCC
4528433 GGGTATCCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
55 11 0.24
56 6 0.13
57 7 0.15
58 19 0.41
59 3 0.07
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.32
Consensus pattern (55 bp):
TTCCAAAATTCCATTTTGCCCAATTTACCAAAAATTACCATTTTACCCCCAAACC
Found at i:4540157 original size:40 final size:41
Alignment explanation
Indices: 4540102--4540348 Score: 146
Period size: 40 Copynumber: 5.6 Consensus size: 41
4540092 ATGTTAATTC
4540102 TTATC-CTCTTGAAGTTATAGTAAAGTTGGATAACGAATCT
1 TTATCTCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCT
*** *
4540142 TTATCTCTC-TGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATT
1 TTATCTCTCTTGAAGTTATAGTAA-AGTTGGAT-AA----CGAA--TC---T
4540193 CTTATCT-TCTTGAAGTTATAGTAAAGTTGGATAACGAATCT
1 -TTATCTCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCT
*** *
4540234 TTATCTCTC-TGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGCCAATT
1 TTATCTCTCTTGAAGTTATAGTAA-AGTTGGAT-AA----CGAAT--C---T
* *
4540285 CTTATC-CTCTTGAAATTATAGTAAAGTTGGATAATGAATCT
1 -TTATCTCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCT
4540326 TTATCTCTC-TGAAGTTATAGTAA
1 TTATCTCTCTTGAAGTTATAGTAA
4540349 GAACAAGATG
Statistics
Matches: 159, Mismatches: 19, Indels: 58
0.67 0.08 0.25
Matches are distributed among these distances:
40 57 0.36
41 20 0.13
42 4 0.03
44 3 0.02
46 13 0.08
48 3 0.02
50 4 0.03
51 17 0.11
52 38 0.24
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (41 bp):
TTATCTCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCT
Found at i:4540204 original size:92 final size:92
Alignment explanation
Indices: 4540042--4540430 Score: 699
Period size: 92 Copynumber: 4.2 Consensus size: 92
4540032 ATCCACGACG
*
4540042 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTTAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
4540107 CTCTTGAAGTTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
4540134 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
*
4540199 TTCTTGAAGTTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
*
4540226 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGCCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
*
4540291 CTCTTGAAATTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
* *
4540318 ATGAATCTTTATCTCTCTGAAGTTATAGTAAGAACAAGATGAATTTTCAAATGTCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
4540383 CTCTTGAAGTTATAGTAAA-TTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
* *
4540409 ATGAACCTTTATCTCTCTGAAG
1 ACGAATCTTTATCTCTCTGAAG
4540431 ATAAAACTTC
Statistics
Matches: 287, Mismatches: 10, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
91 28 0.10
92 259 0.90
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (92 bp):
ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
CTCTTGAAGTTATAGTAAAGTTGGATA
Found at i:4540723 original size:17 final size:17
Alignment explanation
Indices: 4540697--4540793 Score: 117
Period size: 17 Copynumber: 5.8 Consensus size: 17
4540687 AATCATTTTA
*
4540697 AAATTCATTTTAAAATT
1 AAATTTATTTTAAAATT
4540714 AAATTTATTTTAAAATT
1 AAATTTATTTTAAAATT
* *
4540731 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAAATT
*
4540748 AAATTTATTTTAAATTT
1 AAATTTATTTTAAAATT
* *
4540765 AGATTTA--TTAAATTT
1 AAATTTATTTTAAAATT
*
4540780 AAATTTAATTTAAA
1 AAATTTATTTTAAA
4540794 TTTAGAATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
15 14 0.20
17 57 0.80
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAAATT
Found at i:4540730 original size:12 final size:12
Alignment explanation
Indices: 4540689--4540713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4540679 GCCAGCCAAA
4540689 TCATTTTAAAAT
1 TCATTTTAAAAT
4540701 TCATTTTAAAAT
1 TCATTTTAAAAT
4540713 T
1 T
4540714 AAATTTATTT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:4540760 original size:11 final size:11
Alignment explanation
Indices: 4540712--4540797 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
4540702 CATTTTAAAA
*
4540712 TTAAATTTATT
1 TTAAATTTAAT
*
4540723 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
4540735 TTATGTTAAAG
1 TTAAATTTAAT
*
4540746 TTAAATTTATT
1 TTAAATTTAAT
4540757 TTAAATTTAGAT
1 TTAAATTTA-AT
*
4540769 TT--ATTAAAT
1 TTAAATTTAAT
4540778 TTAAATTTAAT
1 TTAAATTTAAT
4540789 TTAAATTTA
1 TTAAATTTA
4540798 GAATTAATGT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 38 0.66
12 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:4540765 original size:6 final size:6
Alignment explanation
Indices: 4540705--4540802 Score: 68
Period size: 6 Copynumber: 17.3 Consensus size: 6
4540695 TAAAATTCAT
* * * *
4540705 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
4540751 TTT-AT TTTAAA TTTAGA TTT--A -TTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4540794 TTTAGAA TT
1 TTTA-AA TT
4540803 AATGTAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 16 0.23
6 45 0.63
7 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:4540794 original size:17 final size:17
Alignment explanation
Indices: 4540705--4540833 Score: 115
Period size: 17 Copynumber: 7.6 Consensus size: 17
4540695 TAAAATTCAT
* *
4540705 TTTAAAATTAAATTTAT
1 TTTAAATTTAAATTTAA
*
4540722 TTTAAAATTAAATTT-A
1 TTTAAATTTAAATTTAA
* *
4540738 TGTTAAAGTTAAATTTAT
1 T-TTAAATTTAAATTTAA
*
4540756 TTTAAATTTAGATTT-A
1 TTTAAATTTAAATTTAA
4540772 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
4540788 TTTAAATTTAGAA-TTAA
1 TTTAAATTTA-AATTTAA
* *
4540805 TGTAAATTTTAATATT-A
1 TTTAAATTTAAAT-TTAA
4540822 TTATAAATTTAA
1 TT-TAAATTTAA
4540834 TAGAGTGTCC
Statistics
Matches: 93, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
15 13 0.14
16 4 0.04
17 63 0.68
18 13 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:4541536 original size:22 final size:20
Alignment explanation
Indices: 4541499--4541549 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
4541489 CCCATTGAAT
4541499 ATTTTAAAT-GTATTAATTA
1 ATTTTAAATAGTATTAATTA
4541518 ATGTTTTAAATAGTATTAATTA
1 A--TTTTAAATAGTATTAATTA
4541540 ATTTTAAATA
1 ATTTTAAATA
4541550 AAAGCATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 9 0.31
21 8 0.28
22 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTTAAATAGTATTAATTA
Found at i:4542767 original size:30 final size:28
Alignment explanation
Indices: 4542650--4542843 Score: 124
Period size: 30 Copynumber: 6.7 Consensus size: 28
4542640 CCCCAGAGGT
* * *
4542650 CCCTAAACTATCCAAAAATTATATATTAA
1 CCCTAAACTTTCC-AAAATTACATTTTAA
* *
4542679 CCACTAAACTTTTTCAAAATTATATTTTAA
1 CC-CTAAAC-TTTCCAAAATTACATTTTAA
**
4542709 CCCTAAAACTTTTTATAAATTACATTTTAA
1 CCCT-AAACTTTCCA-AAATTACATTTTAA
*
4542739 CCCTAAAACTTTCCAAAATTACATTTTTAT
1 CCCT-AAACTTTCCAAAATTACA-TTTTAA
* ** * *
4542769 CCCCAAGTTTTCCAAAATTCCATTTTTA
1 CCCTAAACTTTCCAAAATTACATTTTAA
* *
4542797 CAC--AA-TTTACCAAAAATTACCATTTTAC
1 CCCTAAACTTT-CC-AAAATTA-CATTTTAA
* *
4542825 CCCCAAACCTTCCAAAATT
1 CCCTAAACTTTCCAAAATT
4542844 CTCGTTTTGA
Statistics
Matches: 133, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.02
26 3 0.02
27 6 0.05
28 14 0.11
29 38 0.29
30 64 0.48
31 5 0.04
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTACATTTTAA
Found at i:4542823 original size:56 final size:57
Alignment explanation
Indices: 4542751--4542886 Score: 152
Period size: 56 Copynumber: 2.4 Consensus size: 57
4542741 CTAAAACTTT
* *** *
4542751 CCAAAATTA-CATTTTTATCCCCAAGTTTTCCAAAATTC-CATTTTTACACAATTT-A
1 CCAAAATTACCA-TTTTACCCCCAAACCTTCCAAAATTCTCATTTTGACACAATTTAA
* *
4542806 CCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCTCGTTTTGACCCAATTTCAA
1 CC-AAAATTACCATTTTACCCCCAAACCTTCCAAAATTCTCATTTTGACACAATTT-AA
*
4542865 CCAAAATTACCATTTTGCCCCC
1 CCAAAATTACCATTTTACCCCC
4542887 GGGTATCCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
55 2 0.03
56 29 0.43
57 15 0.22
58 19 0.28
59 3 0.04
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (57 bp):
CCAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCTCATTTTGACACAATTTAA
Found at i:4542886 original size:58 final size:56
Alignment explanation
Indices: 4542778--4542886 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 56
4542768 TCCCCAAGTT
*
4542778 TTCCAAAATTCCATTTTTACACAATTTACCAAAAATTACCATTTTACCCCCAAACC
1 TTCCAAAATTCCATTTTGACACAATTTACCAAAAATTACCATTTTACCCCCAAACC
* * *
4542834 TTCCAAAATTCTCGTTTTGACCCAATTTCAACC-AAAATTACCATTTTGCCCCC
1 TTCCAAAATTC-CATTTTGACACAATTT--ACCAAAAATTACCATTTTACCCCC
4542887 GGGTATCCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
56 11 0.24
57 13 0.28
58 19 0.41
59 3 0.07
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (56 bp):
TTCCAAAATTCCATTTTGACACAATTTACCAAAAATTACCATTTTACCCCCAAACC
Found at i:4547582 original size:21 final size:21
Alignment explanation
Indices: 4547557--4547603 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4547547 GCAGTAGCAG
4547557 ACATCAAAAAGCTAC-AATGCC
1 ACATCAAAAAGCTACAAAT-CC
* *
4547578 ACATCAGAAAGCTTCAAATCC
1 ACATCAAAAAGCTACAAATCC
4547599 ACATC
1 ACATC
4547604 CTCTTACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.45, C:0.30, G:0.09, T:0.17
Consensus pattern (21 bp):
ACATCAAAAAGCTACAAATCC
Found at i:4553685 original size:6 final size:6
Alignment explanation
Indices: 4553647--4553744 Score: 78
Period size: 6 Copynumber: 16.8 Consensus size: 6
4553637 TTTTTTAAGA
* * * * *
4553647 TTAAAT TT-GAT TTAAAT CTAGAT TT-ATT TTAAAT TTAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
4553693 TTAAACT TTAAAT TTGAAT TT-AAT TTAAGT CTAAAT TT-ATT TTAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
4553740 TTAAA
1 TTAAA
4553745 ATTATTATAA
Statistics
Matches: 70, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
5 16 0.23
6 49 0.70
7 5 0.07
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:4553688 original size:17 final size:17
Alignment explanation
Indices: 4553632--4553762 Score: 68
Period size: 17 Copynumber: 8.2 Consensus size: 17
4553622 GGGCCCCATC
*
4553632 AAATTTTTTTTAAGA-TT
1 AAATTTATTTTAA-ATTT
*
4553649 AAATTTGA-TTTAAATCT
1 AAATTT-ATTTTAAATTT
*
4553666 AGATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
4553683 AAATTTA----AAA-TT
1 AAATTTATTTTAAATTT
*
4553695 -AA---ACTTTAAATTT
1 AAATTTATTTTAAATTT
* * * *
4553708 GAATTTAATTTAAGTCT
1 AAATTTATTTTAAATTT
4553725 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
* * *
4553742 AAAATTATTATAAATTG
1 AAATTTATTTTAAATTT
4553759 AAAT
1 AAAT
4553763 CCAATTAATG
Statistics
Matches: 86, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
8 1 0.01
11 2 0.02
12 5 0.06
13 5 0.06
14 2 0.02
16 2 0.02
17 69 0.80
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:4555299 original size:32 final size:33
Alignment explanation
Indices: 4555258--4555320 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
4555248 TATAATGCTA
4555258 TTAAGTTTGGTCCTTTCGTAT-TTTTTAATTATT
1 TTAAGTTTGGTCCTTT-GTATATTTTTAATTATT
*
4555291 TTAA-TTTGGTCCTTTTTATATTTTTAATTA
1 TTAAGTTTGGTCCTTTGTATATTTTTAATTA
4555321 ATTGTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 3 0.11
32 21 0.75
33 4 0.14
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.62
Consensus pattern (33 bp):
TTAAGTTTGGTCCTTTGTATATTTTTAATTATT
Found at i:4555715 original size:57 final size:58
Alignment explanation
Indices: 4555607--4555745 Score: 165
Period size: 57 Copynumber: 2.4 Consensus size: 58
4555597 CTAAACTATC
* * * *
4555607 CATAAATTATATTTTGACCCCCAAACTTCTCTAAAATTACATTTTTGACACTG-AACTTTT
1 CATAAATTACATTTT--CCCCCGAACTTCTCGAAAATTACATTTTTAACACTGAAAC-TTT
*
4555667 CATAAATTACATTTTCCCCCGAACTT-TCGAAAATTTCATTTTTAACACTGAAACTTT
1 CATAAATTACATTTTCCCCCGAACTTCTCGAAAATTACATTTTTAACACTGAAACTTT
* *
4555724 CAAAAATTACCATTTTACCCCG
1 CATAAATTA-CATTTTCCCCCG
4555746 GGTATCCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
57 32 0.46
58 24 0.34
60 14 0.20
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (58 bp):
CATAAATTACATTTTCCCCCGAACTTCTCGAAAATTACATTTTTAACACTGAAACTTT
Found at i:4555740 original size:30 final size:29
Alignment explanation
Indices: 4555630--4555739 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 29
4555620 TTGACCCCCA
* *
4555630 AACTTCTCTAAAATTACATTTTTGACACTG
1 AACTT-TCAAAAATTACATTTTTAACACTG
* * * *
4555660 AACTTTTCATAAATTACA-TTTT-CCCCCG
1 AAC-TTTCAAAAATTACATTTTTAACACTG
* *
4555688 AACTTTCGAAAATTTCATTTTTAACACTG
1 AACTTTCAAAAATTACATTTTTAACACTG
4555717 AAACTTTCAAAAATTACCATTTT
1 -AACTTTCAAAAATTA-CATTTT
4555740 ACCCCGGGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
27 11 0.18
28 10 0.16
29 7 0.11
30 26 0.42
31 8 0.13
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (29 bp):
AACTTTCAAAAATTACATTTTTAACACTG
Found at i:4557005 original size:18 final size:17
Alignment explanation
Indices: 4556963--4557007 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4556953 AAAGCAGTCA
*
4556963 ACATTAACAAAGGAAAT
1 ACATTAACAGAGGAAAT
4556980 ACATTAACAGAGGAAAT
1 ACATTAACAGAGGAAAT
*
4556997 AGTATTAACAG
1 A-CATTAACAG
4557008 TTGCAATGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (17 bp):
ACATTAACAGAGGAAAT
Found at i:4557642 original size:53 final size:53
Alignment explanation
Indices: 4557584--4557688 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 53
4557574 TTAAATTGTA
* *
4557584 ATTTTTATTA-TCGTAAAATATTAAATTGAATTTTTATCATTTTAATAGACTAT
1 ATTTTTATAATTCGTAAAATATTAAATCGAATTTTTATCATTTTAA-AGACTAT
** *
4557637 ATTTTTATAATTTTTAAAATATTAAATCGAATTTTTATCATTTTTAAGACTA
1 ATTTTTATAATTCGTAAAATATTAAATCGAATTTTTATCATTTTAAAGACTA
4557689 AAAGTATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 15 0.33
54 31 0.67
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (53 bp):
ATTTTTATAATTCGTAAAATATTAAATCGAATTTTTATCATTTTAAAGACTAT
Found at i:4560013 original size:15 final size:16
Alignment explanation
Indices: 4559993--4560027 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4559983 TCTTCTAATC
*
4559993 ATTTT-AATTTAAATT
1 ATTTTAAATGTAAATT
4560008 ATTTTAAATGTAAATT
1 ATTTTAAATGTAAATT
4560024 ATTT
1 ATTT
4560028 GGGTGTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTTAAATGTAAATT
Found at i:4574920 original size:25 final size:25
Alignment explanation
Indices: 4574865--4574924 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
4574855 TTTCACAAAT
*
4574865 TATTTTAAAATTTATTATATATTTT
1 TATTTTAAAATTTATTATATATTTA
*
4574890 TGTTTTAAATATTTATT-TAT-TTTAA
1 TATTTTAAA-ATTTATTATATATTT-A
4574915 TATTTTAAAA
1 TATTTTAAAA
4574925 CACTTATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 4 0.13
25 19 0.63
26 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TATTTTAAAATTTATTATATATTTA
Found at i:4575159 original size:38 final size:37
Alignment explanation
Indices: 4575117--4575203 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 37
4575107 AAAAATCAAA
** *
4575117 TATTTAATAAATGGATCATATTTAA-AAATAGATAATGT
1 TATTTAATAAAT--ATCATATCCAATAAATAAATAATGT
**
4575155 TATTTAATCAAATATTTTATCCAATAAATAAATAATGT
1 TATTTAAT-AAATATCATATCCAATAAATAAATAATGT
4575193 TATTTAATAAA
1 TATTTAATAAA
4575204 AATTTAGGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
37 10 0.24
38 28 0.67
39 4 0.10
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (37 bp):
TATTTAATAAATATCATATCCAATAAATAAATAATGT
Found at i:4575590 original size:30 final size:27
Alignment explanation
Indices: 4575535--4575591 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
4575525 TTTATTAAGT
4575535 TCCTAAAATTTTAAAATTTCAATTAAA
1 TCCTAAAATTTTAAAATTTCAATTAAA
4575562 TCCTCAAAATTTTTGAAAATTCTC-ATTAAA
1 TCCT-AAAA-TTTT-AAAATT-TCAATTAAA
4575592 CCCCCTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 4 0.15
30 12 0.46
31 2 0.08
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (27 bp):
TCCTAAAATTTTAAAATTTCAATTAAA
Found at i:4579229 original size:15 final size:17
Alignment explanation
Indices: 4579201--4579234 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4579191 TCTTTCTGTT
4579201 TTTTCTACTCTTT-CAA
1 TTTTCTACTCTTTCCAA
4579217 TTTTCTA-TCTTTCCAA
1 TTTTCTACTCTTTCCAA
4579233 TT
1 TT
4579235 GTGTGTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTCTACTCTTTCCAA
Found at i:4580434 original size:28 final size:28
Alignment explanation
Indices: 4580403--4580458 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
4580393 TCAGCCATTG
*
4580403 AAGGATTTAAGTGCCCTCATGCAGGATC
1 AAGGATTTAAGTGCCCCCATGCAGGATC
*
4580431 AAGGATTTATGTGCCCCCATGCAGGATC
1 AAGGATTTAAGTGCCCCCATGCAGGATC
4580459 GAACTACAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (28 bp):
AAGGATTTAAGTGCCCCCATGCAGGATC
Found at i:4582603 original size:13 final size:13
Alignment explanation
Indices: 4582566--4582615 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
4582556 ATTCCAATAA
4582566 TAATTAAAATATT
1 TAATTAAAATATT
**
4582579 ATAATT-TGATATT
1 -TAATTAAAATATT
4582592 TAATTAAAATATT
1 TAATTAAAATATT
4582605 T-ATTAATAATA
1 TAATTAA-AATA
4582616 AAGTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.33
13 15 0.50
14 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TAATTAAAATATT
Found at i:4583340 original size:23 final size:23
Alignment explanation
Indices: 4583314--4583383 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
4583304 TTTATTTAAC
4583314 TTAATCGAACATGTTCACGAATA
1 TTAATCGAACATGTTCACGAATA
* * *
4583337 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAATA
*
4583360 TATAATTGAACATGTTCACGAATA
1 T-TAATCGAACATGTTCACGAATA
4583384 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAATA
Found at i:4595257 original size:39 final size:39
Alignment explanation
Indices: 4595214--4595304 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
4595204 TGAATTGATA
* ** * *
4595214 GTAACACTATAAATAC-CGTAACGCAATGCTGAACTGACG
1 GTAACACTGTAAAT-CTCGTAAAACAATACTGAACCGACG
4595253 GTAACACTGTAAATCTCGTAAAACAATACTGAACCGACG
1 GTAACACTGTAAATCTCGTAAAACAATACTGAACCGACG
*
4595292 GTGACACTGTAAA
1 GTAACACTGTAAA
4595305 CACTGTGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.21
Consensus pattern (39 bp):
GTAACACTGTAAATCTCGTAAAACAATACTGAACCGACG
Found at i:4597960 original size:17 final size:18
Alignment explanation
Indices: 4597940--4597981 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
4597930 TAATGATACA
*
4597940 TAAAATATTAATTA-ATT
1 TAAAATATTAAATACATT
*
4597957 TAAAATTTTAAATACATT
1 TAAAATATTAAATACATT
*
4597975 TTAAATA
1 TAAAATA
4597982 ACTAATATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATATTAAATACATT
Found at i:4598777 original size:61 final size:58
Alignment explanation
Indices: 4598620--4598783 Score: 184
Period size: 61 Copynumber: 2.8 Consensus size: 58
4598610 AAATTTGATA
* * * *
4598620 TTTTTTAATTTAGTATTTAAAATTTTTTGACTTAATTTGGTACATGAATTTGACACTT
1 TTTTTTAATTTAGTACTTAAATTTTTTTGATTTAATTTGGTACCTGAATTTGACACTT
* * * * * **
4598678 TTTTTTTATTTGGTACTTAAATTTTTTTGGATTCAATTTGCTACCTTAATTTGGTACTT
1 TTTTTTAATTTAGTACTTAAATTTTTTT-GATTTAATTTGGTACCTGAATTTGACACTT
*
4598737 TTTTTCCTAATTTAGTACTTAAGTTTTTTTAGATTTAATTTGGTACC
1 TTTTT--TAATTTAGTACTTAAATTTTTTT-GATTTAATTTGGTACC
4598784 AAAATTTATT
Statistics
Matches: 86, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
58 24 0.28
59 28 0.33
61 34 0.40
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.55
Consensus pattern (58 bp):
TTTTTTAATTTAGTACTTAAATTTTTTTGATTTAATTTGGTACCTGAATTTGACACTT
Found at i:4603925 original size:18 final size:18
Alignment explanation
Indices: 4603902--4603936 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4603892 TACTTGGGGT
4603902 CAAATAAAATATTCAGAG
1 CAAATAAAATATTCAGAG
* *
4603920 CAAATATAATGTTCAGA
1 CAAATAAAATATTCAGA
4603937 TCAATTCGGA
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:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (18 bp):
CAAATAAAATATTCAGAG
Found at i:4614821 original size:87 final size:87
Alignment explanation
Indices: 4614662--4614830 Score: 241
Period size: 87 Copynumber: 1.9 Consensus size: 87
4614652 CCTCTCAAAT
* *
4614662 TCAAATTCGGTGAATTCATCAAGTCCATCTTAATAGGACCACCCAAACTCTGGGATATGAATTCA
1 TCAAATTCAGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTGGGATATGAATTCA
*
4614727 TTGAGAGTAACAAACTCAATCTC
66 TTAAGAGTAA-AAACTCAATCTC
* * * * * *
4614750 TCAAA-TCAGTGAATTCATCAAGTCCGTCTCAATAGGACCATCCAAATTTTGGGCTATGAATTTA
1 TCAAATTCAGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTGGGATATGAATTCA
4614814 TTAAGAGTAAAAACTCA
66 TTAAGAGTAAAAACTCA
4614831 TCATTTTGCA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 7 0.10
87 60 0.83
88 5 0.07
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (87 bp):
TCAAATTCAGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTGGGATATGAATTCA
TTAAGAGTAAAAACTCAATCTC
Found at i:4614911 original size:24 final size:24
Alignment explanation
Indices: 4614879--4614927 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4614869 AAATGTACAC
4614879 TATGAGTCTTTTCATGGTTTCATT
1 TATGAGTCTTTTCATGGTTTCATT
4614903 TATGAGTCTTTTCATGGTTTCATT
1 TATGAGTCTTTTCATGGTTTCATT
4614927 T
1 T
4614928 GACCACATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.55
Consensus pattern (24 bp):
TATGAGTCTTTTCATGGTTTCATT
Found at i:4615728 original size:18 final size:17
Alignment explanation
Indices: 4615687--4615732 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
4615677 CCAAACCCAT
*
4615687 TTTAAATTTATCTTAAG
1 TTTAAATTTATCTAAAG
* *
4615704 ATTAAATTTGTTCTAAAG
1 TTTAAATTT-ATCTAAAG
4615722 TTTAAATTTAT
1 TTTAAATTTAT
4615733 TTTTAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATCTAAAG
Found at i:4615739 original size:12 final size:12
Alignment explanation
Indices: 4615722--4615791 Score: 70
Period size: 12 Copynumber: 5.9 Consensus size: 12
4615712 TGTTCTAAAG
*
4615722 TTTAAATTTATT
1 TTTAAATTTAAT
*
4615734 TTTAAATTTATT
1 TTTAAATTTAAT
*
4615746 TTTAAATTTAAA
1 TTTAAATTTAAT
*
4615758 TTT-AATTTAAG
1 TTTAAATTTAAT
**
4615769 TTTAAATTTGCT
1 TTTAAATTTAAT
*
4615781 TTCAAATTTAA
1 TTTAAATTTAA
4615792 AATTATTATA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
11 10 0.21
12 38 0.79
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (12 bp):
TTTAAATTTAAT
Found at i:4615739 original size:30 final size:30
Alignment explanation
Indices: 4615705--4615761 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4615695 TATCTTAAGA
4615705 TTAAATTT-GTTCTAAAGTTTAAATTTATTT
1 TTAAATTTAGTTCTAAA-TTTAAATTTATTT
* *
4615735 TTAAATTTATTTTTAAATTTAAATTTA
1 TTAAATTTAGTTCTAAATTTAAATTTA
4615762 ATTTAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (30 bp):
TTAAATTTAGTTCTAAATTTAAATTTATTT
Found at i:4615755 original size:6 final size:6
Alignment explanation
Indices: 4615717--4615777 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
4615707 AAATTTGTTC
** **
4615717 TAAAGTT TAAATT TATTTT TAAATT TATTTT TAAATT TAAATT T-AATT
1 TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
4615765 TAAGTT TAAATT T
1 TAAATT TAAATT T
4615778 GCTTTCAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
5 5 0.12
6 34 0.79
7 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (6 bp):
TAAATT
Found at i:4615808 original size:35 final size:35
Alignment explanation
Indices: 4615734--4615810 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
4615724 TAAATTTATT
* * * *
4615734 TTTAAATTTATTTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTACTTTCAAATTTAAAATTAATTTAAA
*
4615769 TTTAAATTTGCTTTCAAATTTAAAATT-ATTATAAA
1 TTTAAATTTACTTTCAAATTTAAAATTAATT-TAAA
4615804 TTTAAAT
1 TTTAAAT
4615811 GTCCAATTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTACTTTCAAATTTAAAATTAATTTAAA
Found at i:4616435 original size:15 final size:15
Alignment explanation
Indices: 4616417--4616459 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
4616407 TTAATTATAT
*
4616417 TATTAATAATATTAA
1 TATTAATAATAATAA
*
4616432 TATTGATAATAATAA
1 TATTAATAATAATAA
* *
4616447 TAATGATAATAAT
1 TATTAATAATAAT
4616460 GGCAGTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
TATTAATAATAATAA
Found at i:4617673 original size:162 final size:162
Alignment explanation
Indices: 4617490--4617834 Score: 568
Period size: 162 Copynumber: 2.1 Consensus size: 162
4617480 AATTAGTTTT
* *
4617490 CAATTTAATCTTTTGACTGTTTGACTGCACCAGAGGCTGCCATGTGTCACTTTTTGGCTTATTTA
1 CAATTTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTA
*
4617555 TGCATTTAGTCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTATTTAATT
66 TGCATTTAGTCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTACTTAATT
4617620 ACAAAATTGGCCCAAGAATTTTTCAAGGATTATA
131 ACAAAATTGGCCCAAGAATTTTTCAA-GATT-TA
* * *
4617654 -AA-TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGGTTATTTA
1 CAATTTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTA
* *
4617717 TGCATTTAGTCCCTGACTTTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTACTTAATT
66 TGCATTTAGTCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTACTTAATT
*
4617782 ACGAAATTGGCCCAAGAATTTTTCAAGATTTA
131 ACAAAATTGGCCCAAGAATTTTTCAAGATTTA
*
4617814 CAATTTAATCCCTTGACTGTT
1 CAATTTAATCCTTTGACTGTT
4617835 GGATGCCTGT
Statistics
Matches: 168, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
160 2 0.01
161 6 0.04
162 158 0.94
163 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (162 bp):
CAATTTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTA
TGCATTTAGTCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTACTTAATT
ACAAAATTGGCCCAAGAATTTTTCAAGATTTA
Found at i:4618140 original size:58 final size:58
Alignment explanation
Indices: 4617960--4618273 Score: 436
Period size: 58 Copynumber: 5.4 Consensus size: 58
4617950 CTCGAAACTT
**
4617960 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTT-CAAAATTCCATTTTTAACCCCGATTTCA
* *
4618019 CCAAAAATTACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTC-AAAATTCCATTTTTAACCCCGATTTCA
* * *
4618078 CAAAAAATTACCA-TTTACCCCCAAACATTTC-AAATTTCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAAC-TTTCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
4618135 CCAAAAATTACCATTTTACCCCCAAACATTCTAAATTCCATTTTAAACCCCAATTCCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCAAAATTCCATTTTTAACCCCGATTTCA
* * *
4618193 CCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACTCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTC-AAAATTCCATTTTTAACCCCGATTTCA
4618252 CC-AAAATTACCATTTTACCCCC
1 CCAAAAATTACCATTTTACCCCC
4618274 GGGTATCCAA
Statistics
Matches: 226, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
57 38 0.17
58 97 0.43
59 91 0.40
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.33
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:4618295 original size:58 final size:55
Alignment explanation
Indices: 4617960--4618273 Score: 301
Period size: 59 Copynumber: 5.4 Consensus size: 55
4617950 CTCGAAACTT
** *
4617960 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAA---TCCAAAATTCCATTTTTAA-CCTGATTTCA
* * *
4618019 CCAAAAATTACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAA---TCCAAAATTCCATTTTTAA-CCTGATTTCA
* * *
4618078 CAAAAAATTACCA-TTTACCCCCAAACATTTC-AAATTTCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCC-AA-A-TCCAAAATTCCATTTTTAACCT-GATTTCA
* * * ** *
4618135 CCAAAAATTACCATTTTACCCCCAAACATTCTAAATTCCATTTTAAACCCCAATTCCA
1 CCAAAAATTACCATTTTACCCCC-AA-ATCCAAAATTCCATTTTTAA-CCTGATTTCA
4618193 CCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACTCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAA-TC-C-AAAATTCCATTTTTAAC-CTGATTTCA
4618252 CC-AAAATTACCATTTTACCCCC
1 CCAAAAATTACCATTTTACCCCC
4618274 GGGTATCCAA
Statistics
Matches: 222, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
56 3 0.01
57 38 0.17
58 88 0.40
59 92 0.41
60 1 0.00
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.33
Consensus pattern (55 bp):
CCAAAAATTACCATTTTACCCCCAAATCCAAAATTCCATTTTTAACCTGATTTCA
Found at i:4618307 original size:58 final size:56
Alignment explanation
Indices: 4617960--4618309 Score: 319
Period size: 58 Copynumber: 6.0 Consensus size: 56
4617950 CTCGAAACTT
** *
4617960 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAA---TCCAAAATTCCATTTTAAACCCCGATTTCA
* * *
4618019 CCAAAAATTACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAA---TCCAAAATTCCATTTTAAACCCCGATTTCA
* * * * *
4618078 CAAAAAATTACCA-TTTACCCCCAAACATTTC-AAATTTCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCC-AA-A-TCCAAAATTCCATTTTAAACCCCGATTTCA
* * * *
4618135 CCAAAAATTACCATTTTACCCCCAAACATTCTAAATTCCATTTTAAACCCCAATTCCA
1 CCAAAAATTACCATTTTACCCCC-AA-ATCCAAAATTCCATTTTAAACCCCGATTTCA
* * *
4618193 CCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACTCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAA-TC-C-AAAATTCCATTTTAAACCCCGATTTCA
** * * *
4618252 CC-AAAATTACCATTTTACCCCCGGGTATCCAAAAGTCCCATTTTCACCCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCC--AAATCCAAAA-TTCCATTTTAAACCCCGATTTCA
4618310 TCGTTTCTTC
Statistics
Matches: 250, Mismatches: 31, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.00
57 45 0.18
58 109 0.44
59 93 0.37
60 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (56 bp):
CCAAAAATTACCATTTTACCCCCAAATCCAAAATTCCATTTTAAACCCCGATTTCA
Found at i:4620824 original size:44 final size:44
Alignment explanation
Indices: 4620737--4620824 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
4620727 CAAAACCCTC
* * * *
4620737 GCTGCACAACTAAATAGCAATGACCAAACCAGAAACTAGCAATA
1 GCTGCACAACTAAACAACAATGACCAAACCAGAAACCAACAATA
*
4620781 GCTGTACAACTAAACAACAATGACCAAACCAGAAACCAACAATA
1 GCTGCACAACTAAACAACAATGACCAAACCAGAAACCAACAATA
4620825 CACCAAGCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.50, C:0.26, G:0.11, T:0.12
Consensus pattern (44 bp):
GCTGCACAACTAAACAACAATGACCAAACCAGAAACCAACAATA
Found at i:4624587 original size:7 final size:7
Alignment explanation
Indices: 4624575--4624607 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
4624565 CTCTACATTT
4624575 TTTGAAA
1 TTTGAAA
4624582 TTTGAAA
1 TTTGAAA
4624589 TTTGAAA
1 TTTGAAA
4624596 TTTGAAA
1 TTTGAAA
*
4624603 GTTGA
1 TTTGA
4624608 CATGAACGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (7 bp):
TTTGAAA
Found at i:4624765 original size:31 final size:29
Alignment explanation
Indices: 4624714--4624779 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
4624704 ACTATTCGGG
4624714 ATTAAAATTTTAAAATTTAAAATATACAAAA
1 ATTAAAATTTTAAAATTTAAAATAT--AAAA
*
4624745 ATTAAAATTAATT-AAA-TTAAAGTATAAAA
1 ATTAAAATT--TTAAAATTTAAAATATAAAA
4624774 ATTAAA
1 ATTAAA
4624780 TCCATAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.31
31 17 0.53
32 3 0.09
33 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (29 bp):
ATTAAAATTTTAAAATTTAAAATATAAAA
Found at i:4627640 original size:22 final size:21
Alignment explanation
Indices: 4627614--4627657 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
4627604 TTTTTTCTAG
4627614 TTTTTTATCTGTCTTGATGGCA
1 TTTTTTATCTGTCTTG-TGGCA
*
4627636 TTTTTTTTCTGTCTTGTGGCA
1 TTTTTTATCTGTCTTGTGGCA
4627657 T
1 T
4627658 GCTTTTGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.09, C:0.14, G:0.18, T:0.59
Consensus pattern (21 bp):
TTTTTTATCTGTCTTGTGGCA
Done.