Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 86 of 135
Found at i:29304015 original size:15 final size:15
Alignment explanation
Indices: 29303995--29304023 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29303985 CCACTTGTTG
29303995 AGTTTAAATACCACT
1 AGTTTAAATACCACT
29304010 AGTTTAAATACCAC
1 AGTTTAAATACCAC
29304024 CATCACACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
AGTTTAAATACCACT
Found at i:29315676 original size:23 final size:22
Alignment explanation
Indices: 29315650--29315693 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
29315640 AAAATATTTC
*
29315650 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
29315673 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
29315694 TTATTTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:29320271 original size:19 final size:19
Alignment explanation
Indices: 29320235--29320334 Score: 137
Period size: 19 Copynumber: 5.3 Consensus size: 19
29320225 CACATCTGAC
*
29320235 ATTCACATCAATGACACAT
1 ATTCACATCAATGTCACAT
* *
29320254 ATTCATATCCATGTCACAT
1 ATTCACATCAATGTCACAT
*
29320273 ATTCACATCAATGTCACGT
1 ATTCACATCAATGTCACAT
* *
29320292 ATTCACATCAATTTCACAA
1 ATTCACATCAATGTCACAT
29320311 ATTCACATCAATGTCACAT
1 ATTCACATCAATGTCACAT
*
29320330 GTTCA
1 ATTCA
29320335 TTGATTCCAC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 69 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (19 bp):
ATTCACATCAATGTCACAT
Found at i:29320693 original size:45 final size:45
Alignment explanation
Indices: 29320629--29320763 Score: 153
Period size: 45 Copynumber: 3.0 Consensus size: 45
29320619 CAACAATGAC
** * * *
29320629 TTGCTACCCCTAGTTGCCCGGTAATGATTGCTCACTTATATTGAA
1 TTGCTACCCCGGGTTGCCCGGAAATGATAGCTCACTTATATCGAA
* * * *
29320674 TTGCTACCCCGGGTTGCCCGAAAACGATAGCTCCCTTATGTCGAA
1 TTGCTACCCCGGGTTGCCCGGAAATGATAGCTCACTTATATCGAA
* * * *
29320719 TTGCTACCTCGGGTTGTCCGGCAATGATAGCTCACTTATGTCGAA
1 TTGCTACCCCGGGTTGCCCGGAAATGATAGCTCACTTATATCGAA
29320764 ATGTAGTTAA
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (45 bp):
TTGCTACCCCGGGTTGCCCGGAAATGATAGCTCACTTATATCGAA
Found at i:29321387 original size:46 final size:47
Alignment explanation
Indices: 29321320--29321416 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 47
29321310 ACAATCCATG
*
29321320 TCACGATTTACACATTTTAGCATGTAGCATGCCCACATAT-CACATT
1 TCACGATTTACACATTTTAGCATGTAGCATGCCCACATATCCACATA
* * *
29321366 TCACGATTTCCACATTTTAGCATGTATCATGCTCACATATCCACATA
1 TCACGATTTACACATTTTAGCATGTAGCATGCCCACATATCCACATA
29321413 TCAC
1 TCAC
29321417 ATAATTTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 37 0.80
47 9 0.20
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (47 bp):
TCACGATTTACACATTTTAGCATGTAGCATGCCCACATATCCACATA
Found at i:29330482 original size:19 final size:21
Alignment explanation
Indices: 29330458--29330496 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29330448 GAGTCAATAA
29330458 TAAATTTT-A-TATTGAATTT
1 TAAATTTTAATTATTGAATTT
29330477 TAAATTTTAATTATTGAATT
1 TAAATTTTAATTATTGAATT
29330497 AAAAGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TAAATTTTAATTATTGAATTT
Found at i:29330499 original size:19 final size:18
Alignment explanation
Indices: 29330458--29330496 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
29330448 GAGTCAATAA
29330458 TAAATTTTATATTGAATTT
1 TAAATTTTATATTGAA-TT
29330477 TAAATTTTAATTATTGAATT
1 TAAATTTT-A-TATTGAATT
29330497 AAAAGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTTTATATTGAATT
Found at i:29349772 original size:26 final size:26
Alignment explanation
Indices: 29349729--29349783 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
29349719 TTTTGGACGT
* * *
29349729 AATTTTGGACGTGCTCATGTAGCGAC
1 AATTCTGGACATGCTCATGTAACGAC
*
29349755 AATTCTGGACATGTTCATGTAACGAC
1 AATTCTGGACATGCTCATGTAACGAC
29349781 AAT
1 AAT
29349784 AGTAGTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (26 bp):
AATTCTGGACATGCTCATGTAACGAC
Found at i:29374006 original size:17 final size:17
Alignment explanation
Indices: 29373957--29374007 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
29373947 ATGCTATGGC
*
29373957 AAAAATATAATAAGTATT
1 AAAAATATAATAAG-AAT
*
29373975 AGAAATAT-ATAAAGAAT
1 AAAAATATAAT-AAGAAT
29373992 AAAAATATAATAAGAA
1 AAAAATATAATAAGAA
29374008 ATGATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (17 bp):
AAAAATATAATAAGAAT
Found at i:29374242 original size:15 final size:15
Alignment explanation
Indices: 29374224--29374271 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
29374214 AAATTGTTAA
29374224 TGCAAGAAAGTAAAT
1 TGCAAGAAAGTAAAT
* *
29374239 TGCAAGAAAAATGAAT
1 TGCAAG-AAAGTAAAT
29374255 TGCAAGAAAGTAAAT
1 TGCAAGAAAGTAAAT
29374270 TG
1 TG
29374272 GTAAACTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (15 bp):
TGCAAGAAAGTAAAT
Found at i:29378470 original size:21 final size:21
Alignment explanation
Indices: 29378444--29378487 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29378434 TTGGATACAT
29378444 GGGCGTGTGGGATG-GCCACAC
1 GGGCGTGTGGGA-GAGCCACAC
*
29378465 GGGCGTGTGTGAGAGCCACAC
1 GGGCGTGTGGGAGAGCCACAC
29378486 GG
1 GG
29378488 CCTTGTGACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.16, C:0.23, G:0.48, T:0.14
Consensus pattern (21 bp):
GGGCGTGTGGGAGAGCCACAC
Found at i:29380407 original size:41 final size:41
Alignment explanation
Indices: 29380238--29380543 Score: 307
Period size: 41 Copynumber: 7.4 Consensus size: 41
29380228 AAAAGGTAAA
*
29380238 TCATTAGAGGCGCTTACACA-AAGCGCCGCTAAAGGTCGGG
1 TCATTAGCGGCGCTTACACACAAGCGCCGCTAAAGGTCGGG
* * * **
29380278 CCTTTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGAC
1 TCATTAGCGGCGC-TTACACACAAGCGCCGCTAAAGGTCGGG
* * *
29380320 TCATTAGCGGCGCTTTACA-A-AAGCACCGCTAAAAGTCAGG
1 TCATTAGCGGCGC-TTACACACAAGCGCCGCTAAAGGTCGGG
* * * *
29380360 TTATTAGCGGCGCTTAGACACAAGCGCCACTAAAAGTCGGG
1 TCATTAGCGGCGCTTACACACAAGCGCCGCTAAAGGTCGGG
* *
29380401 TCATTAGCGGCGCTTAGC-CACAAGCGTCGCTAATGGTCGGG
1 TCATTAGCGGCGCTTA-CACACAAGCGCCGCTAAAGGTCGGG
* *
29380442 TCATTAGCGGCGCTTCACCACCAGCAAGCACCGCTAAAAGT-GGAG
1 TCATTAGCGGCGCTT-A-CA-CA-CAAGCGCCGCTAAAGGTCGG-G
** * * *
29380487 TCATTAGCGATGCTTACCCACAAACGCCGCTAAAGGTCGTG
1 TCATTAGCGGCGCTTACACACAAGCGCCGCTAAAGGTCGGG
29380528 TCATTAGCGGCGCTTA
1 TCATTAGCGGCGCTTA
29380544 TATAGAAAGC
Statistics
Matches: 216, Mismatches: 39, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
39 4 0.02
40 38 0.18
41 102 0.47
42 39 0.18
43 1 0.00
44 5 0.02
45 27 0.12
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (41 bp):
TCATTAGCGGCGCTTACACACAAGCGCCGCTAAAGGTCGGG
Found at i:29380520 original size:127 final size:122
Alignment explanation
Indices: 29380238--29380543 Score: 346
Period size: 127 Copynumber: 2.5 Consensus size: 122
29380228 AAAAGGTAAA
* * * * *
29380238 TCATTAGAGGCGCTTACACA-AAGCGCCGCTAAAGGTCGGGCCTTTAGCGGCGCTTTACCCACAA
1 TCATTAGCGACGCTTACACACAAACGCCGCTAAAGGTCGGGTCATTAGCGGCGC-TTACCCACAA
*
29380302 GCGCCGCTAAAGGTCGACTCATTAGCGGCGCTTTACAAAAGCACCGCTAAAAGTCAGG
65 GCGCCGCTAAAGGTCGACTCATTAGCGGCGCTTCACAAAAGCACCGCTAAAAGTCAGG
* * * * * * *
29380360 TTATTAGCGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCGGCGCTTAGCCACAAG
1 TCATTAGCGACGCTTACACACAAACGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTACCCACAAG
* * ** *
29380425 CGTCGCTAATGGTCGGGTCATTAGCGGCGCTTCACCACCAGCAAGCACCGCTAAAAGT-GGAG
66 CGCCGCTAAAGGTCGACTCATTAGCGGCGCTTCA-CA--A--AAGCACCGCTAAAAGTCAG-G
* * *
29380487 TCATTAGCGATGCTTACCCACAAACGCCGCTAAAGGTCGTGTCATTAGCGGCGCTTA
1 TCATTAGCGACGCTTACACACAAACGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTA
29380544 TATAGAAAGC
Statistics
Matches: 154, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
122 56 0.36
123 31 0.20
125 1 0.01
126 1 0.01
127 65 0.42
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (122 bp):
TCATTAGCGACGCTTACACACAAACGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTACCCACAAG
CGCCGCTAAAGGTCGACTCATTAGCGGCGCTTCACAAAAGCACCGCTAAAAGTCAGG
Found at i:29381758 original size:45 final size:44
Alignment explanation
Indices: 29381654--29381800 Score: 195
Period size: 44 Copynumber: 3.3 Consensus size: 44
29381644 CCCCAGACCG
* * * *** ***
29381654 CAGAACCCTCTTCTGTTTCCCTCACTCCGTTGGGTCTTCACTTG
1 CAGAACCCGCTTCTCTTCCCCTCACTCCGTTCCCTCTTCACCCC
*
29381698 CAGAACCCGCTTCTCTTCCCCTCACTCTGTTCCCTCTTCACCCCC
1 CAGAACCCGCTTCTCTTCCCCTCACTCCGTTCCCTCTTCA-CCCC
29381743 CAGAACCCGCTTCTCTTCCCCTCACTCCGTTCCCTCTTCACCCC
1 CAGAACCCGCTTCTCTTCCCCTCACTCCGTTCCCTCTTCACCCC
29381787 CAGAACCCGCTTCT
1 CAGAACCCGCTTCT
29381801 TGAGCAGATC
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
44 51 0.56
45 40 0.44
ACGTcount: A:0.12, C:0.48, G:0.10, T:0.30
Consensus pattern (44 bp):
CAGAACCCGCTTCTCTTCCCCTCACTCCGTTCCCTCTTCACCCC
Found at i:29384554 original size:18 final size:18
Alignment explanation
Indices: 29384510--29385458 Score: 160
Period size: 18 Copynumber: 52.7 Consensus size: 18
29384500 AAAGATTTAT
*
29384510 TTATTTATTTATATTAAA
1 TTATTTAATTATATTAAA
* ** *
29384528 GTAAATAATTACATTAAA
1 TTATTTAATTATATTAAA
* *
29384546 TTATTTAATCATATTTAA
1 TTATTTAATTATATTAAA
* *
29384564 TTATGTATTTA-ATTATAAA
1 TTATTTAATTATA-T-TAAA
* *
29384583 TAATATCAATTA-ATTAAA
1 TTAT-TTAATTATATTAAA
* *
29384601 -TATTTAACTATAAGATTTAA
1 TTATTTAA-T-T-ATATTAAA
29384621 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* **
29384639 GTAAATAATTATATTAAA
1 TTATTTAATTATATTAAA
*
29384657 TTAACATTTAATTATTTATTATA
1 TT---ATTTAATTA--TATTAAA
** * *
29384680 TTAAAGTAAATA-ATTATA
1 TT-ATTTAATTATATTAAA
* * *
29384698 TTAATTTAA-AAGATTTAA
1 TT-ATTTAATTATATTAAA
29384716 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* **
29384734 CTAACTAATTATATTAAA
1 TTATTTAATTATATTAAA
* * *
29384752 TTATTTAATCATGTTTAA
1 TTATTTAATTATATTAAA
** * *
29384770 TTATGTTTTTTTTTTTTAAA
1 TTA--TTTAATTATATTAAA
* **
29384790 -CACTATCGATTA-ATTAAA
1 TTA-T-TTAATTATATTAAA
* *
29384808 -TATTTAAGTTAAAAGATTTAA
1 TTATTTAA-TT---ATATTAAA
29384829 TTATTTAATTATATT-AA
1 TTATTTAATTATATTAAA
* ** *
29384846 CTAAATAATTATATTAAG
1 TTATTTAATTATATTAAA
* *
29384864 TTA---AA--AGATTTAA
1 TTATTTAATTATATTAAA
29384877 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* **
29384895 GTAAATAATTATATT-AA
1 TTATTTAATTATATTAAA
* **
29384912 TT-TTAAAAGATA-T-AA
1 TTATTTAATTATATTAAA
29384927 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* **
29384945 CTAAATAATTATATT-AA
1 TTATTTAATTATATTAAA
** *
29384962 TTATTTAAGCATGTTTAATA
1 TTATTTAATTAT-ATTAA-A
29384982 TGTATTTAATTATA--AACA
1 T-TATTTAATTATATTAA-A
* **
29385000 CTA-TCGATTA-ATTAAA
1 TTATTTAATTATATTAAA
* *
29385016 -TATTTAAGTTAAAGATTTAA
1 TTATTTAA-TT--ATATTAAA
29385036 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* ** *
29385054 GTAAATAATTACATTAAA
1 TTATTTAATTATATTAAA
* *
29385072 TTATTTAATCATGTTTAATTA
1 TTATTTAATTAT-ATTAA--A
29385093 TGTATTTAATTATA--AACA
1 T-TATTTAATTATATTAA-A
* **
29385111 CTA-TCGATTA-ATTAAA
1 TTATTTAATTATATTAAA
* *
29385127 -TATTTAAGTTAAAAGATTTAA
1 TTATTTAA-TT---ATATTAAA
29385148 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* ** *
29385166 GTAAATAATTATATTAAG
1 TTATTTAATTATATTAAA
*
29385184 TTA---AA--AGATT-AA
1 TTATTTAATTATATTAAA
29385196 TTATTTAATTATATTTAAA
1 TTATTTAATTATA-TTAAA
* **
29385215 GTAAATAA-TATATT--A
1 TTATTTAATTATATTAAA
* * *
29385230 --ATTTAA-AAGATTTAA
1 TTATTTAATTATATTAAA
29385245 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* **
29385263 CTAAATAATTATATTTAAA
1 TTATTTAATTATA-TTAAA
* *
29385282 TTATTTAATCATGTTTAATTA
1 TTATTTAATTAT-ATTAA--A
*
29385303 TGTATTTAATTATA--AAC
1 T-TATTTAATTATATTAAA
* **
29385320 CTA-TCGATTA-ATTAAA
1 TTATTTAATTATATTAAA
* *
29385336 -TATTTAAGTTAAAAGATTTAA
1 TTATTTAA-TT---ATATTAAA
29385357 TTATTTAATTATATTAAA
1 TTATTTAATTATATTAAA
* ** *
29385375 GTAAATAATTACATTAAA
1 TTATTTAATTATATTAAA
* * *
29385393 TTATTTAATCATGTTTAA
1 TTATTTAATTATATTAAA
* *
29385411 TTATGTATTTAT-TATAAA
1 TTATTTAATTATAT-TAAA
* *
29385429 TAATATCAATTA-ATTAAA
1 TTAT-TTAATTATATTAAA
29385447 -TATTTAATTATA
1 TTATTTAATTATA
29385459 AGATTTATAT
Statistics
Matches: 650, Mismatches: 193, Indels: 177
0.64 0.19 0.17
Matches are distributed among these distances:
12 4 0.01
13 20 0.03
14 1 0.00
15 26 0.04
16 47 0.07
17 69 0.11
18 289 0.44
19 52 0.08
20 32 0.05
21 61 0.09
22 41 0.06
23 8 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (18 bp):
TTATTTAATTATATTAAA
Found at i:29384598 original size:111 final size:112
Alignment explanation
Indices: 29384340--29384659 Score: 513
Period size: 111 Copynumber: 2.9 Consensus size: 112
29384330 AATAGTTAAA
* *
29384340 TAATTATGTATTTAATTATAAATAGTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
* *
29384405 TTAATTATATTAAAGTAAATAA-TACATT-AATTATTTAATGATGTT
66 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATATT
* * *
29384450 TAATTATGTATTTAATTATAAACACTATCAATTAATT-AATATTTAAGTTAAAAGATTTATTTAT
1 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
*
29384514 TTATTTATATTAAAGTAAATAATTACATTAAATTATTTAATCATATT
66 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATATT
* *
29384561 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA-CTATAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
*
29384625 TTAATTATATTAAAGTAAATAATTATATTAAATTA
66 TTAATTATATTAAAGTAAATAATTACATTAAATTA
29384660 ACATTTAATT
Statistics
Matches: 193, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
109 47 0.24
110 40 0.21
111 97 0.50
112 9 0.05
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (112 bp):
TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATATT
Found at i:29384772 original size:113 final size:112
Alignment explanation
Indices: 29384626--29385182 Score: 381
Period size: 112 Copynumber: 5.1 Consensus size: 112
29384616 TTTAATTATT
* **
29384626 TAATTATATTAAAGTAAATAATTATATTAAATTAACATTTAATTATTT-ATTA-TATTAAAGTAA
1 TAATTATATTAAAGTAAATAATCATATTAAATTAACATTTAATTATTTAAACACTA-TAAAGTAA
* * *
29384689 ATAATTATATTAATTTAAAAGATTTAATTATTTAATTATATTAAACTAAC
65 ATAAATAT-TTAAGTTAAAAGATTTAATTATTTAATTATATT-AACTAAA
* ** * * *** ** * ** * *
29384739 TAATTATATTAAATTATTTAATCATGTTTAATTATGTTTTTTTTTTTTAAACACTATCGATTAAT
1 TAATTATATTAAAGTAAATAATCATATTAAATTAACATTTAATTATTTAAACACTATAAAGTAAA
29384804 TAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAACTAAA
66 TAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAACTAAA
* *
29384851 TAATTATATT-AAGTTAA-AA-GAT-TT-AATT---ATTTAATTA--T----A-T-TAAAGTAAA
1 TAATTATATTAAAGTAAATAATCATATTAAATTAACATTTAATTATTTAAACACTATAAAGTAAA
* * *
29384900 TAATTATATTAATTTTAAAAGATATAATTATTTAATTATATTAAACTAAA
66 TAAATAT-TTAA-GTTAAAAGATTTAATTATTTAATTATATT-AACTAAA
* ** * * * ** ** *
29384950 TAATTATATT-AATTATTTAAGCATGTTTAA-TATGTATTTAATTA--TAAACACTATCGATTAA
1 TAATTATATTAAAGTAAATAATCATATTAAATTA-ACATTTAATTATTTAAACACTATAAAGTAA
* *
29385011 TTAAATATTTAAGTT-AAAGATTTAATTATTTAATTATATTAAAGTAAA
65 ATAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATT-AACTAAA
* * ** * * ** ** *
29385059 TAATTACATTAAATTATTTAATCATGTTTAATTATGTATTTAATTA--TAAACACTATCGATTAA
1 TAATTATATTAAAGTAAATAATCATATTAAATTA-ACATTTAATTATTTAAACACTATAAAGTAA
* *
29385122 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
65 ATAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATT-AACTAAA
29385171 TAATTATATTAA
1 TAATTATATTAA
29385183 GTTAAAAGAT
Statistics
Matches: 369, Mismatches: 53, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
96 11 0.03
97 5 0.01
98 28 0.08
99 20 0.05
100 2 0.01
101 2 0.01
102 4 0.01
103 2 0.01
104 5 0.01
106 10 0.03
107 4 0.01
108 2 0.01
109 42 0.11
110 24 0.07
111 54 0.15
112 71 0.19
113 68 0.18
114 13 0.04
115 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (112 bp):
TAATTATATTAAAGTAAATAATCATATTAAATTAACATTTAATTATTTAAACACTATAAAGTAAA
TAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAACTAAA
Found at i:29384836 original size:8 final size:8
Alignment explanation
Indices: 29384823--29384969 Score: 50
Period size: 8 Copynumber: 17.8 Consensus size: 8
29384813 AAGTTAAAAG
29384823 ATTTAATT
1 ATTTAATT
29384831 ATTTAATT
1 ATTTAATT
*
29384839 ATATTAACT
1 AT-TTAATT
**
29384848 AAATAATT
1 ATTTAATT
29384856 ATATTAAGTT
1 AT-TTAA-TT
**
29384866 A---AAAG
1 ATTTAATT
29384871 ATTTAATT
1 ATTTAATT
29384879 ATTTAATT
1 ATTTAATT
*
29384887 ATATTAAAGT
1 AT-TT-AATT
**
29384897 AAATAATT
1 ATTTAATT
29384905 ATATTAATT
1 AT-TTAATT
* **
29384914 -TTAAAAG
1 ATTTAATT
*
29384921 ATATAATT
1 ATTTAATT
29384929 ATTTAATT
1 ATTTAATT
*
29384937 ATATTAAACT
1 AT-TT-AATT
**
29384947 AAATAATT
1 ATTTAATT
29384955 ATATTAATT
1 AT-TTAATT
29384964 ATTTAA
1 ATTTAA
29384970 GCATGTTTAA
Statistics
Matches: 96, Mismatches: 30, Indels: 26
0.63 0.20 0.17
Matches are distributed among these distances:
5 1 0.01
6 2 0.02
7 3 0.03
8 52 0.54
9 27 0.28
10 11 0.11
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (8 bp):
ATTTAATT
Found at i:29384836 original size:48 final size:48
Alignment explanation
Indices: 29384784--29384961 Score: 151
Period size: 50 Copynumber: 3.6 Consensus size: 48
29384774 GTTTTTTTTT
* * *
29384784 TTTAAACACTATCGATTAATTAAATAT-TTAAGTTAAAAGATTTAATTA
1 TTTAAACA-TATCAACTAAATAAATATATTAAGTTAAAAGATTTAATTA
** * *
29384832 TTTAATTATATTAACTAAATAATTATATTAAGTTAAAAGATTTAATTA
1 TTTAAACATATCAACTAAATAAATATATTAAGTTAAAAGATTTAATTA
** * * * * *
29384880 TTTAATTATATTAAAGTAAATAATTATATTAATTTTAAAAGATATAATTA
1 TTTAAACATA-TCAACTAAATAAATATATTAA-GTTAAAAGATTTAATTA
** * *
29384930 TTTAATTATATTAAACTAAATAATTATATTAA
1 TTTAAACATA-TCAACTAAATAAATATATTAA
29384962 TTATTTAAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
47 13 0.11
48 37 0.32
49 19 0.17
50 46 0.40
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (48 bp):
TTTAAACATATCAACTAAATAAATATATTAAGTTAAAAGATTTAATTA
Found at i:29385132 original size:111 final size:111
Alignment explanation
Indices: 29384917--29385727 Score: 767
Period size: 111 Copynumber: 7.4 Consensus size: 111
29384907 ATTAATTTTA
* * *
29384917 AAAGATATAATTATTTAATTATATTAAACTAAATAATTATATT-AATTATTTAAGCATGTTTAA-
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAAT
29384980 TATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
66 TATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
*
29385026 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTTTAAT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAAT
29385091 TATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
66 TATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
* *
29385137 AAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AA--A-GATTAA
1 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAA
* * * * *
29385196 TTATTTAATTATATT-T-AA-AGTA---AATAA-TATATTAATTT-A---
65 TTATGTATTTA-ATTATAAACACTATCGATTAATTA-AAT-ATTTAAGTT
*
29385235 AAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTTAAATTATTTAATCATGTTTAA
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA-TTAAATTATTTAATCATGTTTAA
29385300 TTATGTATTTAATTATAAAC-CTATCGATTAATTAAATATTTAAGTT
65 TTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
*
29385346 AAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTTTAA
1 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAA
* * *
29385411 TTATGTATTT-ATTATAAATAATATCAATTAATTAAATATTTAA-TT
65 TTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
* * *
29385456 ATAAGATTTATATTAATTATAAATTA-ATTAAAGTAAATAATTATATCAAA-CA-TT-AT-ATAT
1 A-AAGATTTA-ATT-ATT-T-AATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGT
* * * * * *** * **
29385516 TT-A--ATCT-CTTAATTATATACA--AGT-AAATAATTTCCTATTAATT-T
61 TTAATTATGTATTTAATTATAAACACTA-TCGATTAATTAAATATTTAAGTT
* **** *** * *
29385560 AAACCCGATTGTTACTTTTATTTAATTATATTCTCTTCTCCCTAATT-TATTATCATTATTTACC
1 AAA---GA-T-TTA--ATTATTTAATTATA-T-TAAAGTAAATAATTATATTA-AATTATTTA-A
*
29385624 TCATGTTTAATTATGTCTTTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
55 TCATGTTTAATTATGT-ATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
*
29385682 AAAGATTTAATTATTTAATTATATTAAACTAAATAACTTATATTAA
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAA-TTATATTAA
29385728 GTTAAAAGAT
Statistics
Matches: 571, Mismatches: 71, Indels: 115
0.75 0.09 0.15
Matches are distributed among these distances:
97 40 0.07
98 7 0.01
100 2 0.00
101 9 0.02
102 4 0.01
103 6 0.01
104 33 0.06
105 9 0.02
106 33 0.06
107 11 0.02
108 19 0.03
109 61 0.11
110 40 0.07
111 107 0.19
112 90 0.16
113 30 0.05
114 13 0.02
115 19 0.03
117 6 0.01
118 1 0.00
119 14 0.02
120 1 0.00
121 12 0.02
122 4 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (111 bp):
AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAAT
TATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT
Found at i:29385270 original size:209 final size:207
Alignment explanation
Indices: 29385014--29385391 Score: 686
Period size: 209 Copynumber: 1.8 Consensus size: 207
29385004 CGATTAATTA
*
29385014 AATATTTAAGTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACA-TTAAATTATTT
1 AATATTTAAGTTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTACATTTAAATTATTT
29385078 AATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGA
66 AATCATGTTTAATTATGTATTTAATTATAAAC-CTATCGATTAATTAAATATTTAAGTTAAAAGA
*
29385143 TTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTAATTATTTAATTAT
130 TTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAGTTAAAAGATTAATTATTTAATTAT
29385208 ATTTAAAGTAAAT
195 ATTTAAAGTAAAT
* *
29385221 AATATATTAATTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTTAAATTAT
1 AATAT-TTAAGTT-AAAGATTTAATTATTTAATTATATTAAACTAAATAATTACATTTAAATTAT
29385286 TTAATCATGTTTAATTATGTATTTAATTATAAACCTATCGATTAATTAAATATTTAAGTTAAAAG
64 TTAATCATGTTTAATTATGTATTTAATTATAAACCTATCGATTAATTAAATATTTAAGTTAAAAG
29385351 ATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAA
129 ATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAA
29385392 ATTATTTAAT
Statistics
Matches: 164, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
207 5 0.03
208 6 0.04
209 110 0.67
210 43 0.26
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (207 bp):
AATATTTAAGTTAAAGATTTAATTATTTAATTATATTAAACTAAATAATTACATTTAAATTATTT
AATCATGTTTAATTATGTATTTAATTATAAACCTATCGATTAATTAAATATTTAAGTTAAAAGAT
TTAATTATTTAATTATATTAAAGTAAATAATTACATTAAGTTAAAAGATTAATTATTTAATTATA
TTTAAAGTAAAT
Found at i:29385799 original size:30 final size:31
Alignment explanation
Indices: 29385765--29385823 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
29385755 TTAAAGTAAA
* * *
29385765 TAATTATCTTAAATTAAATATTTA-ATTATT
1 TAATTATATTAAAGTAAATAATTATATTATT
29385795 TAATTATATTAAAGTAAATAATTATATTA
1 TAATTATATTAAAGTAAATAATTATATTA
29385824 AATTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (31 bp):
TAATTATATTAAAGTAAATAATTATATTATT
Found at i:29385803 original size:18 final size:18
Alignment explanation
Indices: 29385690--29385846 Score: 84
Period size: 18 Copynumber: 9.3 Consensus size: 18
29385680 TTAAAGATTT
29385690 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
29385708 AACTAAATAACTTATATTA
1 AATTATTTAA-TTATATTA
* * *
29385727 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
*
29385740 AATTATTTAATTATCTTA
1 AATTATTTAATTATATTA
* ** *
29385758 AAGTAAATAATTATCTTA
1 AATTATTTAATTATATTA
29385776 AATTA---AA-TAT-TT-
1 AATTATTTAATTATATTA
29385788 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
29385806 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
29385824 AATTTTTTAATTATATTT
1 AATTATTTAATTATATTA
29385842 AATTA
1 AATTA
29385847 ACTATTTAAC
Statistics
Matches: 103, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
12 5 0.05
13 10 0.10
14 3 0.03
15 4 0.04
16 7 0.07
17 2 0.02
18 61 0.59
19 11 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (18 bp):
AATTATTTAATTATATTA
Found at i:29385807 original size:48 final size:48
Alignment explanation
Indices: 29385675--29385827 Score: 234
Period size: 48 Copynumber: 3.1 Consensus size: 48
29385665 AATTAAATAT
* *
29385675 TTAAGTTAAAGATTTAATTATTTAATTATATTAAACTAAATAACTTATA
1 TTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAA-TTATA
* * *
29385724 TTAAGTTAAAAGATTTAATTATTTAATTATCTTAAAGTAAATAATTATC
1 TTAAATT-AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
*
29385773 TTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
29385821 TTAAATT
1 TTAAATT
29385828 TTTTAATTAT
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
48 45 0.47
49 17 0.18
50 34 0.35
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (48 bp):
TTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:29385911 original size:8 final size:8
Alignment explanation
Indices: 29385875--29385967 Score: 57
Period size: 8 Copynumber: 10.8 Consensus size: 8
29385865 TGGTCGTAAA
29385875 TAATTATAT
1 TAATTAT-T
29385884 ATAATTATT
1 -TAATTATT
29385893 TAAGCTTATT
1 TAA--TTATT
29385903 TAATTATT
1 TAATTATT
29385911 TAATTGAAAGATT
1 TAATT-----ATT
*
29385924 TAAGTATT
1 TAATTATT
29385932 TAATTATAT
1 TAATTAT-T
29385941 TAA--A-T
1 TAATTATT
*
29385946 TAAATATT
1 TAATTATT
29385954 TAATTATT
1 TAATTATT
29385962 TAATTA
1 TAATTA
29385968 ATAAAAACAG
Statistics
Matches: 69, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
5 4 0.06
7 2 0.03
8 36 0.52
9 5 0.07
10 15 0.22
13 7 0.10
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (8 bp):
TAATTATT
Found at i:29385953 original size:22 final size:20
Alignment explanation
Indices: 29385923--29385968 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
29385913 ATTGAAAGAT
*
29385923 TTAAGTATTTAATTATATTAAA
1 TTAAATATTTAATTAT-TT-AA
29385945 TTAAATATTTAATTATTTAA
1 TTAAATATTTAATTATTTAA
29385965 TTAA
1 TTAA
29385969 TAAAAACAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 2 0.09
22 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTAAATATTTAATTATTTAA
Found at i:29385962 original size:30 final size:29
Alignment explanation
Indices: 29385889--29385967 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
29385879 TATATATAAT
29385889 TATTTAAGCTTATTTAATTATTTAATTGAAA
1 TATTTAA--TTATTTAATTATTTAATTGAAA
* *
29385920 GATTTAAGTATTTAATTATATTAAATT-AAA
1 TATTTAATTATTTAATTAT-TT-AATTGAAA
29385950 TATTTAATTATTTAATTA
1 TATTTAATTATTTAATTA
29385968 ATAAAAACAG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 11 0.26
30 21 0.50
31 10 0.24
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTTAATTATTTAATTATTTAATTGAAA
Found at i:29391591 original size:66 final size:66
Alignment explanation
Indices: 29391482--29391621 Score: 219
Period size: 65 Copynumber: 2.1 Consensus size: 66
29391472 CAAATTGCTC
* * *
29391482 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATCTA
1 AACTTAAAGAAGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACCTA
29391547 A
66 A
* *
29391548 AACTTAAAGAAGAGGCTGCAGTGAGAGAAGCAGA-TCTCAAAAAAAATATGAAGAACTCCACCTA
1 AACTTAAAGAAGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACCTA
*
29391612 C
66 A
29391613 AACTTAAAG
1 AACTTAAAG
29391622 TGGAGGTAGC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 36 0.53
66 32 0.47
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (66 bp):
AACTTAAAGAAGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACCTA
A
Found at i:29391649 original size:21 final size:21
Alignment explanation
Indices: 29391623--29391675 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
29391613 AACTTAAAGT
29391623 GGAGGTAGCAGCGAGGCAAGC
1 GGAGGTAGCAGCGAGGCAAGC
29391644 GGAGGTAGCAGCGAGGCAAGC
1 GGAGGTAGCAGCGAGGCAAGC
* *
29391665 GAAGGAAGCAG
1 GGAGGTAGCAG
29391676 AGGCTACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.47, T:0.04
Consensus pattern (21 bp):
GGAGGTAGCAGCGAGGCAAGC
Found at i:29391897 original size:15 final size:15
Alignment explanation
Indices: 29391877--29391905 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29391867 ATTTGAAGTT
29391877 ATTGGTTGGATTTGC
1 ATTGGTTGGATTTGC
29391892 ATTGGTTGGATTTG
1 ATTGGTTGGATTTG
29391906 AATTTACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.34, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTGC
Found at i:29392039 original size:43 final size:43
Alignment explanation
Indices: 29391980--29392071 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
29391970 TATATTAGAA
*
29391980 AAAGCGCCGCTAAAGAACATGGTCTTTAACGGCGCTTGTGGAG
1 AAAGCGCCGCTAAAGAACATGGCCTTTAACGGCGCTTGTGGAG
*
29392023 AAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGCTTGTGGAG
1 AAAGCGCCGCTAAAGAACATGGCCTTTAACGGCGCTTGTGGAG
29392066 AAAGCG
1 AAAGCG
29392072 TTATTGGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.28, C:0.22, G:0.32, T:0.18
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGAACATGGCCTTTAACGGCGCTTGTGGAG
Found at i:29392094 original size:15 final size:15
Alignment explanation
Indices: 29392074--29392102 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29392064 AGAAAGCGTT
29392074 ATTGGTTGGATTTGC
1 ATTGGTTGGATTTGC
29392089 ATTGGTTGGATTTG
1 ATTGGTTGGATTTG
29392103 AATTTACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.34, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTGC
Found at i:29394815 original size:29 final size:29
Alignment explanation
Indices: 29394783--29394853 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
29394773 ATAGGAAAGT
29394783 CTTTGTGGCAAATCTATGAAAAA-TAATGC
1 CTTTGTGGCAAATCTAT-AAAAAGTAATGC
* * *
29394812 CTTTGTGGCAAACCTCTAAAAAGTAATGT
1 CTTTGTGGCAAATCTATAAAAAGTAATGC
29394841 CTTTGTGGCAAAT
1 CTTTGTGGCAAAT
29394854 TTGTAAGGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.14
29 32 0.86
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (29 bp):
CTTTGTGGCAAATCTATAAAAAGTAATGC
Found at i:29394957 original size:29 final size:28
Alignment explanation
Indices: 29394918--29394988 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
29394908 CCATAAAGAA
29394918 AAGCCTTTGTGGCTAAACTTTGTTAAAAG
1 AAGCCTTTGTGGCTAAA-TTTGTTAAAAG
** * *
29394947 AAGCCTTTGTGATTGAATTTGTTAAAGG
1 AAGCCTTTGTGGCTAAATTTGTTAAAAG
*
29394975 AAGCCTCTGTGGCT
1 AAGCCTTTGTGGCT
29394989 GACTCCTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
28 21 0.60
29 14 0.40
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (28 bp):
AAGCCTTTGTGGCTAAATTTGTTAAAAG
Found at i:29395036 original size:28 final size:27
Alignment explanation
Indices: 29395005--29395081 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 27
29394995 TAAAGAACAT
*
29395005 GCCTTTGTGGCGATCTTTGTTGAAGGAA
1 GCCTTTGTGGC-ATCTCTGTTGAAGGAA
*
29395033 GCCTTTATGGCAGTCTCTGTTGAAGGAA
1 GCCTTTGTGGCA-TCTCTGTTGAAGGAA
*
29395061 ACCTTTGTGGCTATCTCTGTT
1 GCCTTTGTGGC-ATCTCTGTT
29395082 AAAATGACGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 41 0.95
29 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (27 bp):
GCCTTTGTGGCATCTCTGTTGAAGGAA
Found at i:29395066 original size:56 final size:56
Alignment explanation
Indices: 29395006--29395117 Score: 138
Period size: 56 Copynumber: 2.0 Consensus size: 56
29394996 AAAGAACATG
* *
29395006 CCTTTGTGGCGATCTTTGTT-GAAGGAAGCCTTTATGG-CAGTCTCTGTTGAAGGAAA
1 CCTTTGTGGCGATCTCTGTTAAAAGGAAGCCTTTATGGTCAGTCTCTG-T-AAGGAAA
* * * *
29395062 CCTTTGTGGCTATCTCTGTTAAAATGACGCCTTTATGGTGAGTCTCTGTAAGGAAA
1 CCTTTGTGGCGATCTCTGTTAAAAGGAAGCCTTTATGGTCAGTCTCTGTAAGGAAA
29395118 GCCCATGTGG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
56 25 0.52
57 15 0.31
58 8 0.17
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (56 bp):
CCTTTGTGGCGATCTCTGTTAAAAGGAAGCCTTTATGGTCAGTCTCTGTAAGGAAA
Found at i:29395487 original size:189 final size:189
Alignment explanation
Indices: 29395167--29395541 Score: 671
Period size: 189 Copynumber: 2.0 Consensus size: 189
29395157 CAAATCTTTA
29395167 AAATTGGACACCTTTGTGGCTATCTCCATAAAGGAAGCCCTCTGAAGAACGACTCTCGTGATGAC
1 AAATTGGACACCTTTGTGGCTATCTCCATAAAGGAAGCCCTCTGAAGAACGACTCTCGTGATGAC
* *
29395232 CATCTGAAGACAACATCGTTAGGTAGATACTAAATGATTGGCAAACACCGTACACCGAGAATTGA
66 CATCTGAAGACAACATCGTTAGGCAGACACTAAATGATTGGCAAACACCGTACACCGAGAATTGA
29395297 ATAGCATGGATTAACTATGAATG-AAAGTGCCAATTTGGAAGGATAAGGCGAAGCTTTTG
131 ATAGCATGGATTAACTATGAATGAAAAG-GCCAATTTGGAAGGATAAGGCGAAGCTTTTG
29395356 AAATTGGACACCTTTGTGGCTATCTCCATAAAGGAAGCCCTCTGAAGAACGACTCTCGTGATGAC
1 AAATTGGACACCTTTGTGGCTATCTCCATAAAGGAAGCCCTCTGAAGAACGACTCTCGTGATGAC
* * *
29395421 CATCTGAAGACAACGTCGTTGGGCAGACACTAAATGATTGGCAAACACCGTACACTGAGAATTGA
66 CATCTGAAGACAACATCGTTAGGCAGACACTAAATGATTGGCAAACACCGTACACCGAGAATTGA
* *
29395486 ATAGCATGGATTAACTCTGAATGAAAAGGCCAGTTTGGAAGGATAAGGCGAAGCTT
131 ATAGCATGGATTAACTATGAATGAAAAGGCCAATTTGGAAGGATAAGGCGAAGCTT
29395542 GTACATCTAT
Statistics
Matches: 178, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
189 174 0.98
190 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (189 bp):
AAATTGGACACCTTTGTGGCTATCTCCATAAAGGAAGCCCTCTGAAGAACGACTCTCGTGATGAC
CATCTGAAGACAACATCGTTAGGCAGACACTAAATGATTGGCAAACACCGTACACCGAGAATTGA
ATAGCATGGATTAACTATGAATGAAAAGGCCAATTTGGAAGGATAAGGCGAAGCTTTTG
Found at i:29399176 original size:28 final size:28
Alignment explanation
Indices: 29399139--29399194 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
29399129 ATTTTAATAA
* *
29399139 TATTTAATATTAAATTTAATCTAATATT
1 TATTAAATATTAAATTAAATCTAATATT
* *
29399167 TATTAAATATTAGATTAAATTTAATATT
1 TATTAAATATTAAATTAAATCTAATATT
29399195 AAAGTGATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TATTAAATATTAAATTAAATCTAATATT
Found at i:29415411 original size:29 final size:30
Alignment explanation
Indices: 29415356--29415413 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
29415346 TATATGAATT
*
29415356 AAATTTTGATTGTAATTCAAATGTGTATAA
1 AAATTTTGATTGTAATTCAAATATGTATAA
* * *
29415386 AAATTTT-ATTTTTATTCAATTATGTATA
1 AAATTTTGATTGTAATTCAAATATGTATA
29415414 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (30 bp):
AAATTTTGATTGTAATTCAAATATGTATAA
Found at i:29415449 original size:24 final size:25
Alignment explanation
Indices: 29415422--29415468 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
29415412 TATTTAAAAA
* *
29415422 ATTAAATACATA-AATTTTTTATAC
1 ATTAAATAAATATAATTATTTATAC
29415446 ATTAAATAAATATAATTATTTAT
1 ATTAAATAAATATAATTATTTAT
29415469 GTATGTATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTAAATAAATATAATTATTTATAC
Found at i:29416130 original size:25 final size:23
Alignment explanation
Indices: 29416089--29416135 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
29416079 CCAATTAAGG
29416089 AATTATTATTTAGATTTAATTTT
1 AATTATTATTTAGATTTAATTTT
*
29416112 AATTATTTTTTTAGAATTTAATTT
1 AATTA-TTATTTAG-ATTTAATTT
29416136 GGATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 7 0.33
25 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTTT
Found at i:29420139 original size:15 final size:14
Alignment explanation
Indices: 29420119--29420180 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 14
29420109 AGTACTTTTA
29420119 TTTTCATTTCTCATT
1 TTTTCATTT-TCATT
29420134 TTTTCATTTTTTTCATTT
1 TTTTCA---TTTTCA-TT
29420152 TTTTCATTTTCA--
1 TTTTCATTTTCATT
*
29420164 TTTTCATTTTTATT
1 TTTTCATTTTCATT
29420178 TTT
1 TTT
29420181 ATTTTACTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
12 11 0.28
14 3 0.08
15 12 0.30
17 3 0.08
18 11 0.28
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCATTTTCATT
Found at i:29420142 original size:8 final size:8
Alignment explanation
Indices: 29420119--29420161 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
29420109 AGTACTTTTA
29420119 TTTTCA-T
1 TTTTCATT
*
29420126 TTCTCATT
1 TTTTCATT
29420134 TTTTCATTT
1 TTTTCA-TT
29420143 TTTTCATTT
1 TTTTCA-TT
29420152 TTTTCATT
1 TTTTCATT
29420160 TT
1 TT
29420162 CATTTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 5 0.16
8 10 0.31
9 17 0.53
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTCATT
Found at i:29420143 original size:6 final size:6
Alignment explanation
Indices: 29420114--29420185 Score: 50
Period size: 6 Copynumber: 12.7 Consensus size: 6
29420104 AAAATAGTAC
29420114 TTTT-A TTTTCA TTTCTCA TTTTTTCA -TTT-- TTTTCA TTTT-- -TTTCA
1 TTTTCA TTTTCA TTT-TCA --TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
* *
29420158 TTTTCA TTTTCA TTTTTA TTTTTA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
29420186 ACTTTATTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 19
0.74 0.01 0.25
Matches are distributed among these distances:
3 3 0.05
4 3 0.05
5 7 0.12
6 34 0.61
7 3 0.05
8 3 0.05
9 3 0.05
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTCA
Found at i:29420146 original size:9 final size:9
Alignment explanation
Indices: 29420132--29420161 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
29420122 TCATTTCTCA
29420132 TTTTTTCAT
1 TTTTTTCAT
29420141 TTTTTTCAT
1 TTTTTTCAT
29420150 TTTTTTCAT
1 TTTTTTCAT
29420159 TTT
1 TTT
29420162 CATTTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:29423927 original size:8 final size:8
Alignment explanation
Indices: 29423914--29423938 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29423904 TATAATGACA
29423914 AAAAAAAT
1 AAAAAAAT
29423922 AAAAAAAT
1 AAAAAAAT
29423930 AAAAAAAT
1 AAAAAAAT
29423938 A
1 A
29423939 TACATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:29424445 original size:38 final size:38
Alignment explanation
Indices: 29424403--29424486 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
29424393 ATGAGCAAAG
***
29424403 AATAAATAATAAATAATTTCAATCATGCAAATTAAACA
1 AATAAATAATAAATAATCAAAATCATGCAAATTAAACA
*
29424441 AATAAAAAATAAATAATCAAAATCATGCAAATTAAACA
1 AATAAATAATAAATAATCAAAATCATGCAAATTAAACA
29424479 AA-AAATAA
1 AATAAATAA
29424487 AAAGGGATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 5 0.12
38 36 0.88
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (38 bp):
AATAAATAATAAATAATCAAAATCATGCAAATTAAACA
Found at i:29424937 original size:15 final size:16
Alignment explanation
Indices: 29424904--29424941 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
29424894 GTAAAAATAC
*
29424904 AAATAATTTGAATTAA
1 AAATAATATGAATTAA
*
29424920 AAATAATAT-AATTCA
1 AAATAATATGAATTAA
29424935 AAATAAT
1 AAATAAT
29424942 CAATGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
AAATAATATGAATTAA
Found at i:29435096 original size:13 final size:13
Alignment explanation
Indices: 29435080--29435122 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
29435070 CATGCCTCAC
29435080 CCACTTGCC-CTTG
1 CCACTTGCCTC-TG
29435093 CCACTTGCCTCTG
1 CCACTTGCCTCTG
*
29435106 CCACTTACCTCTG
1 CCACTTGCCTCTG
29435119 CCAC
1 CCAC
29435123 CATCTGACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
13 27 0.96
14 1 0.04
ACGTcount: A:0.12, C:0.49, G:0.12, T:0.28
Consensus pattern (13 bp):
CCACTTGCCTCTG
Found at i:29435383 original size:23 final size:21
Alignment explanation
Indices: 29435345--29435386 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
29435335 TTTTGGCAAG
*
29435345 GTATATTATTTTTTTATATGT
1 GTATATTATTTATTTATATGT
29435366 GTATATATATTATATTTATAT
1 GTATAT-TATT-TATTTATAT
29435387 CTTTTCGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
GTATATTATTTATTTATATGT
Found at i:29436199 original size:30 final size:28
Alignment explanation
Indices: 29436165--29436318 Score: 125
Period size: 29 Copynumber: 5.3 Consensus size: 28
29436155 CTTGTTTTAC
29436165 CCAAAAATCACATTTGACCCCTAAACTTTT
1 CCAAAAATCACATTTGA-CCCTAAAC-TTT
29436195 CC-AAAATCACATTTTGACCCTCAAACTTT
1 CCAAAAATCACA-TTTGACCCT-AAACTTT
* *
29436224 CCCAAAATCACATTTCGA-CCTAAAAATTT
1 CCAAAAATCACATTT-GACCCT-AAACTTT
* * *
29436253 CTAAAATTTCA-TTTTGACCCTAAACTTT
1 CCAAAA-ATCACATTTGACCCTAAACTTT
* * *
29436281 CCATAAATTACATTTTAACCCCTAAACTTT
1 CCAAAAATCACA-TTTGA-CCCTAAACTTT
*
29436311 CTAAAAAT
1 CCAAAAAT
29436319 TATATTTTAA
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.02
28 12 0.12
29 44 0.44
30 42 0.42
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
CCAAAAATCACATTTGACCCTAAACTTT
Found at i:29436312 original size:58 final size:57
Alignment explanation
Indices: 29436168--29436356 Score: 152
Period size: 58 Copynumber: 3.2 Consensus size: 57
29436158 GTTTTACCCA
* * * **
29436168 AAAATCACA-TTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTCAAACTTTCCC
1 AAAATTACATTTTAACCCCTAAAC-TTTCTAAAATTTCATTTTGACCCT-AAACTTT-CC
* ** *
29436227 AAAATCACATTTCGA--CCTAAAAATTTCTAAAATTTCATTTTGACCCTAAACTTTCC
1 AAAATTACATTTTAACCCCT-AAACTTTCTAAAATTTCATTTTGACCCTAAACTTTCC
* * *
29436283 ATAAATTACATTTTAACCCCTAAACTTTCTAAAAATTAT-ATTTTAACCTATAAACTTTCTA
1 A-AAATTACATTTTAACCCCTAAACTTTCT-AAAATT-TCATTTTGACC-CTAAACTTTC-C
*
29436344 AAAATTACGTTTT
1 AAAATTACATTTT
29436357 GACCTCAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
56 3 0.03
57 18 0.17
58 32 0.30
59 29 0.27
60 25 0.23
61 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.37
Consensus pattern (57 bp):
AAAATTACATTTTAACCCCTAAACTTTCTAAAATTTCATTTTGACCCTAAACTTTCC
Found at i:29436319 original size:30 final size:29
Alignment explanation
Indices: 29436167--29436390 Score: 163
Period size: 30 Copynumber: 7.6 Consensus size: 29
29436157 TGTTTTACCC
*
29436167 AAAAATCACA-TTTGACCCCTAAACTTT-T
1 AAAAATTACATTTTGA-CCCTAAACTTTCT
* * *
29436195 CCAAAATCACATTTTGACCCTCAAACTTTCC
1 -AAAAATTACATTTTGACCCT-AAACTTTCT
* * * *
29436226 CAAAATCACATTTCGA-CCTAAAAATTTCT
1 AAAAATTACATTTTGACCCT-AAACTTTCT
* *
29436255 -AAAATTTCATTTTGACCCTAAACTTTCC
1 AAAAATTACATTTTGACCCTAAACTTTCT
* *
29436283 ATAAATTACATTTTAACCCCTAAACTTTCT
1 AAAAATTACATTTTGA-CCCTAAACTTTCT
* * *
29436313 AAAAATTATATTTTAACCTATAAACTTTCT
1 AAAAATTACATTTTGACC-CTAAACTTTCT
* * *
29436343 AAAAATTACGTTTTGA-CCTCAAAATTCTCA
1 AAAAATTACATTTTGACCCT-AAACTT-TCT
29436373 AAAAACTT-CATTTTGACC
1 AAAAA-TTACATTTTGACC
29436391 TTTTTTTGTA
Statistics
Matches: 159, Mismatches: 25, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
28 20 0.13
29 46 0.29
30 90 0.57
31 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCTAAACTTTCT
Found at i:29441718 original size:18 final size:17
Alignment explanation
Indices: 29441692--29441725 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29441682 GGATTCGATG
*
29441692 AAGACAAATAAATAAAAA
1 AAGAAAAATAAA-AAAAA
29441710 AAGAAAAATAAAAAAA
1 AAGAAAAATAAAAAAA
29441726 TAAAAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (17 bp):
AAGAAAAATAAAAAAAA
Found at i:29441720 original size:14 final size:14
Alignment explanation
Indices: 29441701--29441731 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29441691 GAAGACAAAT
29441701 AAATAAAAAAAGAA
1 AAATAAAAAAAGAA
*
29441715 AAATAAAAAAATAA
1 AAATAAAAAAAGAA
29441729 AAA
1 AAA
29441732 AAGAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (14 bp):
AAATAAAAAAAGAA
Found at i:29454742 original size:50 final size:50
Alignment explanation
Indices: 29454677--29455425 Score: 727
Period size: 50 Copynumber: 15.1 Consensus size: 50
29454667 AAGGAAACAT
* * * * * *
29454677 GAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCAGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * * *
29454727 AAAGATGTGATGGGAAGGGTTGAGGCTGCAATGGTGAACTCAGTGCCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* ** * *
29454777 GAAGATGTGATGAGAAAGGTTGAGGCTACAACGGTGAACCCGGTACCAT-
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * **
29454826 GAAGATATGAAGGGAAATATTGAGGCCGCAATGGTGAACCCGGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * *
29454876 GAATATGTGATAGGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * *
29454926 AAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGATACCAT-
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* ** * * * **
29454975 GAAGATATGAAAGGAAAGGTTGAGGTCGTAATTGCAAACCCGGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * *
29455025 GAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTTT
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * *
29455075 GAAAATGTGATGGGAAAGGTTGAAGCCGCAATGATGAACCCGGTACCAT-
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * *
29455124 GAAGATATAAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* *** *
29455174 GAAGATGTGATGGGAAAGGTTGAGGTCGCAACAATGAACCCGGTACCATA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * ** *
29455224 -AATATATTAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCGATACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
** * *
29455273 GAAGATGTGATGGGAAAGGTTGAGGCCATAATGGCGAACCCGATACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * * * *
29455323 AAAGATGTGATGGG-AAGGATCGAGGCCGCGACGGTGAATCCGGCACCATA
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAATGGTGAACCCGGTACCTTA
* ** * *
29455373 -AAGATATGAAAGGAAAGGTTGAGGCCGTAATGATGAACCCGGTACCTTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACC-TTA
29455423 GAA
1 GAA
29455426 AGATTGAAGA
Statistics
Matches: 561, Mismatches: 130, Indels: 15
0.79 0.18 0.02
Matches are distributed among these distances:
49 190 0.34
50 369 0.66
51 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.19
Consensus pattern (50 bp):
GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
Found at i:29454944 original size:149 final size:149
Alignment explanation
Indices: 29454674--29455418 Score: 811
Period size: 149 Copynumber: 5.0 Consensus size: 149
29454664 ACCAAGGAAA
* * * * *
29454674 CATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCAGTACCTTAAAAGATGTGATG
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAGAAGATGTGATG
* * * * * * *
29454739 GGAAGGGTTGAGGCTGCAATGGTGAACTCAG-TGCCTTAGAAGATGTGATGAGAAAGGTTGAGGC
66 GGAAAGGTTGAGGCCGCAACGGTGAA-TCCGCTACCTTAAAAGATGTGATGGGAAAGGTTGAGGC
** * *
29454803 TACAACGGTGAACCCGGTAC
130 CGCAATGGTGAACCCGATAC
** * * *
29454823 CATGAAGATATGAAGGGAAATATTGAGGCCGCAATGGTGAACCCGGTACCTTAGAATATGTGATA
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAGAAGATGTGATG
29454888 GGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACCTTAAAAGATGTGATGGGAAAGGTTGAGGCC
66 GGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACCTTAAAAGATGTGATGGGAAAGGTTGAGGCC
29454953 GCAATGGTGAACCCGATAC
131 GCAATGGTGAACCCGATAC
* * * * *
29454972 CATGAAGATATGAAAGGAAAGGTTGAGGTCGTAATTGCAAACCCGGTACCTTAGAAGATGTGATG
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAGAAGATGTGATG
* * * * * *
29455037 GGAAAGGTTGAGGCTGCAACGGCGAACCCGATACCTTTGAAA-ATGTGATGGGAAAGGTTGAAGC
66 GGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACC-TTAAAAGATGTGATGGGAAAGGTTGAGGC
* *
29455101 CGCAATGATGAACCCGGTAC
130 CGCAATGGTGAACCCGATAC
* * * *
29455121 CATGAAGATATAAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACCTTAGAAGATGTGATG
1 CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAGAAGATGTGATG
* ** * * * * *
29455186 GGAAAGGTTGAGGTCGCAACAATGAACCCGGTACCATAAATATAT-T-AAGGGAAAGGTTGAGGC
66 GGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACCTTAAA-AGATGTGATGGGAAAGGTTGAGGC
**
29455249 CGCAATGGCAAACCCGATAC
130 CGCAATGGTGAACCCGATAC
* * * ** * *
29455269 CTTAGAAGATGTGATGGGAAAGGTTGAGGCCATAATGGCGAACCCGATACCTTAAAAGATGTGAT
1 CAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * **
29455334 GGG-AAGGATCGAGGCCGCGACGGTGAATCCGGC-ACCAT-AAAGATATGAAAGGAAAGGTTGAG
65 GGGAAAGG-TTGAGGCCGCAACGGTGAATCC-GCTACCTTAAAAGATGTGATGGGAAAGGTTGAG
* * *
29455396 GCCGTAATGATGAACCCGGTAC
128 GCCGCAATGGTGAACCCGATAC
29455418 C
1 C
29455419 TTTAGAAAGA
Statistics
Matches: 500, Mismatches: 87, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
147 3 0.01
148 46 0.09
149 443 0.89
150 8 0.02
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (149 bp):
CATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAGAAGATGTGATG
GGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACCTTAAAAGATGTGATGGGAAAGGTTGAGGCC
GCAATGGTGAACCCGATAC
Found at i:29455419 original size:99 final size:100
Alignment explanation
Indices: 29454677--29455429 Score: 712
Period size: 99 Copynumber: 7.6 Consensus size: 100
29454667 AAGGAAACAT
* * * *
29454677 GAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCCAGTACCTTAAAAGATGTGATGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGGA
* * * * *
29454742 AGGGTTGAGGCTGCAATGGTGAACTCAGTGCCTTA
66 AAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * ** * * * *
29454777 GAAGATGTGATGAGAAAGGTTGAGGCTACAACGGTGAACCCGGTACCAT-GAAGATATGAAGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGGA
**
29454841 AATATTGAGGCCGCAATGGTGAACCCGGTACCTTA
66 AAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * *
29454876 GAATATGTGATA-GGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACCTTAAAAGATGTGATGGG
1 GAAGATGTGA-AGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGG
* *
29454940 AAAGGTTGAGGCCGCAATGGTGAACCCGATACCAT-
65 AAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * ** ** *
29454975 GAAGATATGAAAGGAAAGGTTGAGGTCGTAATTGCAAACCCGGTACCTTAGAAGATGTGATGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGGA
* * * * *
29455040 AAGGTTGAGGCTGCAACGGCGAACCCGATACCTTT
66 AAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * * * * * * *
29455075 GAAAATGTGATGGGAAAGGTTGAAGCCGCAATGATGAACCCGGTACCAT-GAAGATATAAAGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGGA
* *
29455139 AAGGTTGAGGCCGCAACGGTGAACCTGGTACCTTA
66 AAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * ** * * *
29455174 GAAGATGTGATGGGAAAGGTTGAGGTCGCAACAATGAACCCGGTACCATAAATATAT-T-AAGGG
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAA-AGATGTGATGGG
** *
29455237 AAAGGTTGAGGCCGCAATGGCAAACCCGATACCTTA
65 AAAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
* ** * * *
29455273 GAAGATGTGATGGGAAAGGTTGAGGCCATAATGGCGAACCCGATACCTTAAAAGATGTGATGGG-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGGA
* * * * * *
29455337 AAGGATCGAGGCCGCGACGGTGAATCCGGCACCATA
66 AAGG-TTGAGGCCGCAATGGTGAACCCGGTACCTTA
* * * * *
29455373 -AAGATATGAAAGGAAAGGTTGAGGCCGTAATGATGAACCCGGTACCTTTAGAAAGAT
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC-TTA-AAAGAT
29455430 TGAAGACGCA
Statistics
Matches: 536, Mismatches: 106, Indels: 21
0.81 0.16 0.03
Matches are distributed among these distances:
98 4 0.01
99 371 0.69
100 152 0.28
101 9 0.02
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (100 bp):
GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAAAAGATGTGATGGGA
AAGGTTGAGGCCGCAATGGTGAACCCGGTACCTTA
Found at i:29455419 original size:248 final size:247
Alignment explanation
Indices: 29454677--29455425 Score: 824
Period size: 248 Copynumber: 3.0 Consensus size: 247
29454667 AAGGAAACAT
* * * *** * * **
29454677 GAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC-AGTACCTTAAAAGATGTGATGGG
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACAATGAACCCGA-TACCAT-AAAGATATGAAAGG
* * ** * * *
29454741 AAGGGTTGAGGCTGCAATGGTGAACTC-AGTGCCTTAGAAGATGTGATGAGAAAGGTTGAGGCTA
64 AAAGGTTGAGGCCGCAATGGCAAACCCGA-TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTA
* * * * * * **
29454805 CAACGGTGAACCCGGTACCATGAAGATATGAAGGGAAATATTGAGGCCGCAATGGTGAACCCGGT
128 CAACGGCGAACCCGATACCTTAAAGATGTGATGGGAAGGATTGAGGCCGCAATGGTGAACCCGGT
* * * * * *
29454870 ACCTTAGAATATGTGATAGGAAAGGTTGAGGCCGCAACGGTGAATCCGCTACCTTA
193 ACCATA-AAGATATGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* *** *
29454926 AAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGTGAACCCGATACCATGAAGATATGAAAGGAA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACAATGAACCCGATACCATAAAGATATGAAAGGAA
* * * * *
29454991 AGGTTGAGGTCGTAATTGCAAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTGCAA
66 AGGTTGAGGCCGCAATGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTACAA
* *
29455056 CGGCGAACCCGATACCTTTGAAA-ATGTGATGGGAAAGG-TTGAAGCCGCAATGATGAACCCGGT
131 CGGCGAACCCGATACC-TT-AAAGATGTGATGGG-AAGGATTGAGGCCGCAATGGTGAACCCGGT
* *
29455119 ACCATGAAGATAT-AAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACCTTA
193 ACCATAAAGATATGAAA-GGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * *
29455174 GAAGATGTGATGGGAAAGGTTGAGGTCGCAACAATGAACCCGGTACCATAAATATATTAAGGGAA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACAATGAACCCGATACCATAAAGATATGAAAGGAA
* *
29455239 AGGTTGAGGCCGCAATGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCATAA
66 AGGTTGAGGCCGCAATGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTACAA
* * * * * *
29455304 TGGCGAACCCGATACCTTAAAAGATGTGATGGGAAGGATCGAGGCCGCGACGGTGAATCCGGCAC
131 CGGCGAACCCGATACCTT-AAAGATGTGATGGGAAGGATTGAGGCCGCAATGGTGAACCCGGTAC
* * *
29455369 CATAAAGATATGAAAGGAAAGGTTGAGGCCGTAATGATGAACCCGGTACCTTTA
195 CATAAAGATATGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC-TTA
29455423 GAA
1 GAA
29455426 AGATTGAAGA
Statistics
Matches: 418, Mismatches: 72, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
247 11 0.03
248 317 0.76
249 85 0.20
250 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.19
Consensus pattern (247 bp):
GAAGATGTGATGGGAAAGGTTGAGGCCGCAACAATGAACCCGATACCATAAAGATATGAAAGGAA
AGGTTGAGGCCGCAATGGCAAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTGAGGCTACAA
CGGCGAACCCGATACCTTAAAGATGTGATGGGAAGGATTGAGGCCGCAATGGTGAACCCGGTACC
ATAAAGATATGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
Found at i:29456864 original size:33 final size:32
Alignment explanation
Indices: 29456826--29456901 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 32
29456816 CAAAATAAAT
29456826 GAAATAAAAACAAGAAGAAAAGATTCGAAAATCA
1 GAAATAAAAACAAG--GAAAAGATTCGAAAATCA
* *
29456860 -AAATAATTTAATAAGGAAAAGATTCGAAAATCA
1 GAAATAA--AAACAAGGAAAAGATTCGAAAATCA
29456893 TGAAATAAA
1 -GAAATAAA
29456902 CAAACTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
33 24 0.69
35 11 0.31
ACGTcount: A:0.62, C:0.07, G:0.13, T:0.18
Consensus pattern (32 bp):
GAAATAAAAACAAGGAAAAGATTCGAAAATCA
Found at i:29457463 original size:30 final size:30
Alignment explanation
Indices: 29457429--29457682 Score: 251
Period size: 30 Copynumber: 8.6 Consensus size: 30
29457419 TGTTTACCCA
*
29457429 AAAATCACATTTTAACCCTCAAACTTTCCT
1 AAAATTACATTTTAACCCTCAAACTTTCCT
29457459 AAAATTACATTTTAA-CCTCAAACTTTCCT
1 AAAATTACATTTTAACCCTCAAACTTTCCT
* * * *
29457488 AAAATCACATTTTAA-CCTTAAAATTTTCT
1 AAAATTACATTTTAACCCTCAAACTTTCCT
* * *
29457517 AAAATTTCATTTTAAACCTTAAACTTTCC-
1 AAAATTACATTTTAACCCTCAAACTTTCCT
*
29457546 ATAAATTACATTTTAACCCTTAAA-TTT-CT
1 A-AAATTACATTTTAACCCTCAAACTTTCCT
*
29457575 AAAATTACATTTTAAGCCCT-AAA-TTTCCA
1 AAAATTACATTTTAA-CCCTCAAACTTTCCT
*
29457604 AAAATTACATTTTAA-CCTCTAAATTTGTCC-
1 AAAATTACATTTTAACCCTC-AAACTT-TCCT
* *
29457634 AAAAATACATTTTGACCC-CTAAACTTTCCCT
1 AAAATTACATTTTAACCCTC-AAACTTT-CCT
*
29457665 -AAATTATATTTTAACCCT
1 AAAATTACATTTTAACCCT
29457683 AAAATTCTTA
Statistics
Matches: 193, Mismatches: 18, Indels: 25
0.82 0.08 0.11
Matches are distributed among these distances:
27 3 0.02
28 21 0.11
29 81 0.42
30 83 0.43
31 5 0.03
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTCAAACTTTCCT
Found at i:29457500 original size:59 final size:59
Alignment explanation
Indices: 29457429--29457688 Score: 268
Period size: 59 Copynumber: 4.4 Consensus size: 59
29457419 TGTTTACCCA
*
29457429 AAAATCACATTTTAACCCTCAAACTTTCCTAAAATTACATTTTAACCTC-AAACTTTCCT
1 AAAATTACATTTTAACCCTCAAA-TTTCCTAAAATTACATTTTAACCTCTAAACTTTCCT
* * * * *
29457488 AAAATCACATTTTAACCTTAAAATTTTCTAAAATTTCATTTTAAACCT-TAAACTTTCC-
1 AAAATTACATTTTAACCCTCAAATTTCCTAAAATTACATTTT-AACCTCTAAACTTTCCT
* *
29457546 ATAAATTACATTTTAACCCTTAAATTT-CTAAAATTACATTTTAAGCC-CTAAA-TTTCCA
1 A-AAATTACATTTTAACCCTCAAATTTCCTAAAATTACATTTTAA-CCTCTAAACTTTCCT
* * *
29457604 AAAATTACATTTTAA-CCTCTAAATTTGTCC-AAAAATACATTTTGACCCCTAAACTTTCCCT
1 AAAATTACATTTTAACCCTC-AAA-TT-TCCTAAAATTACATTTTAACCTCTAAACTTT-CCT
* *
29457665 -AAATTATATTTTAACCCTAAAATT
1 AAAATTACATTTTAACCCTCAAATT
29457689 CTTAAAAAAC
Statistics
Matches: 173, Mismatches: 14, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
56 3 0.02
57 24 0.14
58 43 0.25
59 78 0.45
60 20 0.12
61 5 0.03
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (59 bp):
AAAATTACATTTTAACCCTCAAATTTCCTAAAATTACATTTTAACCTCTAAACTTTCCT
Found at i:29457683 original size:29 final size:29
Alignment explanation
Indices: 29457429--29457685 Score: 267
Period size: 29 Copynumber: 8.8 Consensus size: 29
29457419 TGTTTACCCA
*
29457429 AAAATCACATTTTAACCCTCAAACTTTCCT
1 AAAATTACATTTTAACCCT-AAACTTTCCT
29457459 AAAATTACATTTTAA-CCTCAAACTTTCCT
1 AAAATTACATTTTAACCCT-AAACTTTCCT
* * * *
29457488 AAAATCACATTTTAACCTTAAAATTTTCT
1 AAAATTACATTTTAACCCTAAACTTTCCT
* *
29457517 AAAATTTCATTTTAAACCTTAAACTTTCC-
1 AAAATTACATTTT-AACCCTAAACTTTCCT
29457546 ATAAATTACATTTTAACCCTTAAA-TTT-CT
1 A-AAATTACATTTTAACCC-TAAACTTTCCT
*
29457575 AAAATTACATTTTAAGCCCTAAA-TTTCCA
1 AAAATTACATTTTAA-CCCTAAACTTTCCT
*
29457604 AAAATTACATTTTAACCTCTAAATTTGTCC-
1 AAAATTACATTTTAACC-CTAAACTT-TCCT
* *
29457634 AAAAATACATTTTGACCCCTAAACTTTCCCT
1 AAAATTACATTTT-AACCCTAAACTTT-CCT
*
29457665 -AAATTATATTTTAACCCTAAA
1 AAAATTACATTTTAACCCTAAA
29457686 ATTCTTAAAA
Statistics
Matches: 196, Mismatches: 18, Indels: 27
0.81 0.07 0.11
Matches are distributed among these distances:
28 24 0.12
29 89 0.45
30 77 0.39
31 6 0.03
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTCCT
Found at i:29459478 original size:18 final size:20
Alignment explanation
Indices: 29459455--29459493 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29459445 ATACGGACTC
29459455 AAAAACA-T-AGAAATCACT
1 AAAAACAGTGAGAAATCACT
29459473 AAAAACAGGTGAGAAATCACT
1 AAAAACA-GTGAGAAATCACT
29459494 CACCTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAAACAGTGAGAAATCACT
Found at i:29471586 original size:26 final size:26
Alignment explanation
Indices: 29471539--29471588 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29471529 TTTTTAAACT
* *
29471539 CTAATTTTCTCTAAATTTATTTTTCA
1 CTAACTTTCTCTAAATTGATTTTTCA
29471565 CTAACTTT-TCTAAATTCGATTTTT
1 CTAACTTTCTCTAAATT-GATTTTT
29471589 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (26 bp):
CTAACTTTCTCTAAATTGATTTTTCA
Found at i:29478239 original size:12 final size:12
Alignment explanation
Indices: 29478222--29478263 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
29478212 TTCTCAAGAG
29478222 GAAAAAGAAAAT
1 GAAAAAGAAAAT
*
29478234 GAAAAACAAGAA-
1 GAAAAAGAA-AAT
29478246 GAAAAAGAAAAT
1 GAAAAAGAAAAT
29478258 GAAAAA
1 GAAAAA
29478264 CAAGAAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (12 bp):
GAAAAAGAAAAT
Found at i:29478243 original size:24 final size:24
Alignment explanation
Indices: 29478216--29478271 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
29478206 GGAGAGTTCT
*
29478216 CAAGAGGAAAAAGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
29478240 CAAGAAGAAAAAGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
29478264 CAAGAAGA
1 CAAGAAGA
29478272 TACCCATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.71, C:0.05, G:0.20, T:0.04
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAATGAAAAA
Found at i:29482216 original size:28 final size:29
Alignment explanation
Indices: 29482184--29482239 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
29482174 CTAGACTTCT
29482184 TTTATTTTATTTTAATTAGAAT-AGGTGA
1 TTTATTTTATTTTAATTAGAATAAGGTGA
29482212 TTTATTTTATTTTAATTAGAATAAGGTG
1 TTTATTTTATTTTAATTAGAATAAGGTG
29482240 TTTCAACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (29 bp):
TTTATTTTATTTTAATTAGAATAAGGTGA
Found at i:29485838 original size:17 final size:17
Alignment explanation
Indices: 29485816--29485854 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29485806 AGGTGGAGAA
*
29485816 CTTGTTCGTTA-AGAGTT
1 CTTGTTCG-TAGAGAATT
29485833 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
29485850 CTTGT
1 CTTGT
29485855 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:29487916 original size:58 final size:58
Alignment explanation
Indices: 29487793--29487917 Score: 134
Period size: 58 Copynumber: 2.2 Consensus size: 58
29487783 TAATTAAAAA
* *
29487793 TTAATATTATTTTAATTGATTTAATATTAAATTTAATTTAATACTTATCTTAATAGTAT
1 TTAATATTAATTTAATTGATTTAATATTAAATTTAATCTAATACTTATCTTAATAG-AT
* * *
29487852 TT--TATTAATTTAATAAT-ATTTAATTTTAAATTTAATCTAATATTTAT-TATATTA-AT
1 TTAATATTAATTTAAT--TGATTTAATATTAAATTTAATCTAATACTTATCT-TAATAGAT
29487908 TTAATATTAA
1 TTAATATTAA
29487918 AGTGATTAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
56 4 0.07
57 12 0.21
58 37 0.66
59 3 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (58 bp):
TTAATATTAATTTAATTGATTTAATATTAAATTTAATCTAATACTTATCTTAATAGAT
Found at i:29492620 original size:87 final size:86
Alignment explanation
Indices: 29492537--29492855 Score: 335
Period size: 87 Copynumber: 3.7 Consensus size: 86
29492527 TTAAAGGTTA
*
29492537 GATGATGGAAATCCTGCATTTGTTGTGGATTTTCTATGGCATCGTGAGTTATCAAATTGAACCTA
1 GATGATGGAAATCCTGCATTTGTTGTGGATTTTCTATGACATCGTGAGTTATCAAATTGAACCTA
29492602 TGACAGCCGAGATGAAAGGTCC
66 TGAC-GCCGAGATGAAAGGTCC
* * * * **
29492624 GATGATGGAAATCCTGCATTTGTTGTAGATTTTCTATGGCATTGTGAGTCATCAAATTGGGCCTA
1 GATGATGGAAATCCTGCATTTGTTGTGGATTTTCTATGACATCGTGAGTTATCAAATTGAACCTA
* * *
29492689 TGACGACCAAGATTAAAGGTTC
66 TGACG-CCGAGATGAAAGGTCC
** * * **
29492711 GATGACAGAAATCCTGCATTTG-T-T--ATTTTCTATGACATTGTGAGTTATTAAATTGGGCCTA
1 GATGATGGAAATCCTGCATTTGTTGTGGATTTTCTATGACATCGTGAGTTATCAAATTGAACCTA
*
29492772 TGACGGTCGAGATGAAAGGTCC
66 TGAC-GCCGAGATGAAAGGTCC
** ** * *
29492794 GATG-TCGGAGGTTTTCGC-TTTGTTGTGGATTCTCTACGACATCGTGAGTTATCAAATGTGAA
1 GATGAT-GGAAATCCT-GCATTTGTTGTGGATTTTCTATGACATCGTGAGTTATCAAAT-TGAA
29492856 TTGAATCCAA
Statistics
Matches: 194, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
83 62 0.32
84 4 0.02
85 2 0.01
86 2 0.01
87 122 0.63
88 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (86 bp):
GATGATGGAAATCCTGCATTTGTTGTGGATTTTCTATGACATCGTGAGTTATCAAATTGAACCTA
TGACGCCGAGATGAAAGGTCC
Found at i:29492790 original size:83 final size:86
Alignment explanation
Indices: 29492537--29492797 Score: 357
Period size: 87 Copynumber: 3.0 Consensus size: 86
29492527 TTAAAGGTTA
* **
29492537 GATGATGGAAATCCTGCATTTGTTGTGGATTTTCTATGGCATCGTGAGTTATCAAATTGAACCTA
1 GATGATGGAAATCCTGCATTTGTTGT-GATTTTCTATGGCATTGTGAGTTATCAAATTGGGCCTA
*
29492602 TGACAGCCGAGATGAAAGGTCC
65 TGACGGCCGAGATGAAAGGTCC
*
29492624 GATGATGGAAATCCTGCATTTGTTGTAGATTTTCTATGGCATTGTGAGTCATCAAATTGGGCCTA
1 GATGATGGAAATCCTGCATTTGTTGT-GATTTTCTATGGCATTGTGAGTTATCAAATTGGGCCTA
* * * *
29492689 TGACGACCAAGATTAAAGGTTC
65 TGACGGCCGAGATGAAAGGTCC
** * *
29492711 GATGACAGAAATCCTGCATTTG-T-T-ATTTTCTATGACATTGTGAGTTATTAAATTGGGCCTAT
1 GATGATGGAAATCCTGCATTTGTTGTGATTTTCTATGGCATTGTGAGTTATCAAATTGGGCCTAT
*
29492773 GACGGTCGAGATGAAAGGTCC
66 GACGGCCGAGATGAAAGGTCC
29492794 GATG
1 GATG
29492798 TCGGAGGTTT
Statistics
Matches: 154, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
83 55 0.36
85 1 0.01
86 1 0.01
87 97 0.63
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (86 bp):
GATGATGGAAATCCTGCATTTGTTGTGATTTTCTATGGCATTGTGAGTTATCAAATTGGGCCTAT
GACGGCCGAGATGAAAGGTCC
Found at i:29492818 original size:170 final size:173
Alignment explanation
Indices: 29492525--29492850 Score: 410
Period size: 170 Copynumber: 1.9 Consensus size: 173
29492515 TCCTATTACG
** *
29492525 GATTAAAGGTTAGATGATGGAAATCCTGCATTTGTTGTGGATTTTCTATGGCATCGTGAGTTATC
1 GATTAAAGGTTAGATGACAGAAATCCTGCATTTGTTGT-GATTTTCTATGACATCGTGAGTTATC
29492590 AAATTGAACCTATGACAGCCGAGATGAAAGGTCCGATGATGGAAATCCTGCATTTGTTGTAGATT
65 AAATTGAACCTATGACAGCCGAGATGAAAGGTCCGATGATGGAAATCCTGCATTTGTTGTAGATT
* * * *
29492655 TTCTATGGCATTGTGAGTCATCAAATTGGGCCTATGACGACCAA
130 CTCTACGACATCGTGAGTCATCAAATTGGGCCTATGACGACCAA
* * *
29492699 GATTAAAGGTTCGATGACAGAAATCCTGCATTTG-T-T-ATTTTCTATGACATTGTGAGTTATTA
1 GATTAAAGGTTAGATGACAGAAATCCTGCATTTGTTGTGATTTTCTATGACATCGTGAGTTATCA
** * * ** ** *
29492761 AATTGGGCCTATGACGGTCGAGATGAAAGGTCCGATG-TCGGAGGTTTTCGC-TTTGTTGTGGAT
66 AATTGAACCTATGACAGCCGAGATGAAAGGTCCGATGAT-GGAAATCCT-GCATTTGTTGTAGAT
*
29492824 TCTCTACGACATCGTGAGTTATCAAAT
129 TCTCTACGACATCGTGAGTCATCAAAT
29492851 GTGAATTGAA
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
169 1 0.01
170 94 0.72
171 2 0.02
172 1 0.01
173 1 0.01
174 31 0.24
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (173 bp):
GATTAAAGGTTAGATGACAGAAATCCTGCATTTGTTGTGATTTTCTATGACATCGTGAGTTATCA
AATTGAACCTATGACAGCCGAGATGAAAGGTCCGATGATGGAAATCCTGCATTTGTTGTAGATTC
TCTACGACATCGTGAGTCATCAAATTGGGCCTATGACGACCAA
Found at i:29495149 original size:18 final size:19
Alignment explanation
Indices: 29495113--29495154 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
29495103 ATCTTAAATG
29495113 ATAAAAAAAATTAATAACT
1 ATAAAAAAAATTAATAACT
29495132 ATAAAATAAAATT-A-AACT
1 ATAAAA-AAAATTAATAACT
29495150 ATAAA
1 ATAAA
29495155 CTTTAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAAAAATTAATAACT
Found at i:29511322 original size:72 final size:70
Alignment explanation
Indices: 29511202--29511337 Score: 209
Period size: 72 Copynumber: 1.9 Consensus size: 70
29511192 TAATTAAATT
* * * *
29511202 TGTAACACCCAAAAACTGTAACATCTCCGGTCTAGGTCTTAGGGTTTACAGAACTTTATGAGTTT
1 TGTAACACACAAAAACCGTAACATCTCCGGTCTAGGTCTTAAGGTTTACAGAACTTTACGAGTTT
29511267 CTAAA
66 CTAAA
*
29511272 TGTAACATACAAAAACCGTAACCATCTCCGGTCTAGGGTCTTAAGGTTTACAGAACTTTACGAGT
1 TGTAACACACAAAAACCGTAA-CATCTCCGGTCTA-GGTCTTAAGGTTTACAGAACTTTACGAGT
29511337 T
64 T
29511338 CTTTTTTTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 18 0.31
71 13 0.22
72 28 0.47
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (70 bp):
TGTAACACACAAAAACCGTAACATCTCCGGTCTAGGTCTTAAGGTTTACAGAACTTTACGAGTTT
CTAAA
Found at i:29515598 original size:2 final size:2
Alignment explanation
Indices: 29515591--29515620 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29515581 AGTAGTCAAT
29515591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29515621 AATTGTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29516604 original size:72 final size:72
Alignment explanation
Indices: 29516482--29516622 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 72
29516472 GATACCACTA
** * * * * *
29516482 AATGTAACACCTAAAAATCATAACCATCTTCGGTATGGGGTCTCAAGGTTTACAGAACTTTACGA
1 AATGTAACACAAAAAAATCACAACCATCTCCGGTATAGGGTATCAAGGTTTACAAAACTTTACGA
29516547 GTTTCTG
66 GTTTCTG
* * *
29516554 AATGTAACACAAAAAAATCACAACCATCTCCGGTCTAGGGTATCAGGGTTTATAAAACTTTACGA
1 AATGTAACACAAAAAAATCACAACCATCTCCGGTATAGGGTATCAAGGTTTACAAAACTTTACGA
29516619 GTTT
66 GTTT
29516623 TTTTTAAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (72 bp):
AATGTAACACAAAAAAATCACAACCATCTCCGGTATAGGGTATCAAGGTTTACAAAACTTTACGA
GTTTCTG
Found at i:29528248 original size:13 final size:13
Alignment explanation
Indices: 29528232--29528256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29528222 ACAACCACCA
29528232 ATTCAACAAGTAT
1 ATTCAACAAGTAT
29528245 ATTCAACAAGTA
1 ATTCAACAAGTA
29528257 ATATCCACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
ATTCAACAAGTAT
Found at i:29532608 original size:124 final size:125
Alignment explanation
Indices: 29532384--29532680 Score: 404
Period size: 124 Copynumber: 2.4 Consensus size: 125
29532374 TCTCTTATGT
* * *
29532384 TTCGCTTCATTGATTTGGTTTACTGCTCTGTATGTCATCAAGAAGATGACTGCTTCATCATTTTG
1 TTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACTGCTTCATCATTTTG
29532449 ATAAACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTTACTCACA-TTAAGC
66 ATAAACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTTACTCACATTTAAGC
29532508 TTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGA-TCGCTTCATCATTTT
1 TTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACT-GCTTCATCATTTT
** * * * * *
29532572 GATCCACTTCTTTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTTACTCATATTTGAGC
65 GATAAACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTTACTCACATTTAAGC
* * * * *
29532633 TTCGCGTCATT-ATTTTAGTCCATTTCTCTATATCTCATC-AGAAAGATG
1 TTCGCTTCATTGA-TTTGGTCTACTTCTCTGTATCTCATCAAG-AAGATG
29532681 GGGGTTTGAA
Statistics
Matches: 154, Mismatches: 15, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
123 1 0.01
124 110 0.71
125 43 0.28
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (125 bp):
TTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACTGCTTCATCATTTTG
ATAAACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTTACTCACATTTAAGC
Found at i:29532694 original size:77 final size:77
Alignment explanation
Indices: 29532574--29532749 Score: 255
Period size: 77 Copynumber: 2.3 Consensus size: 77
29532564 ATCATTTTGA
* * * * *
29532574 TCCACTTCTTTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTTACTCATATTTGAGCTTCGCG
1 TCCACTTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTTACTCACATTTGAGCTTCACG
29532639 TCATTATTTTAG-
66 TCATT-TTTTAGT
* *
29532651 TCCATTTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTTACTCACATTTGAGCTTCACT
1 TCCACTTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTTACTCACATTTGAGCTTCACG
*
29532716 TCATTTTTTTGT
66 TCATTTTTTAGT
*
29532728 TCCACTTCTCTGTATCTCATCA
1 TCCACTTCTCTATATCTCATCA
29532750 AGAAGGTGAT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 5 0.06
77 83 0.94
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (77 bp):
TCCACTTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTTACTCACATTTGAGCTTCACG
TCATTTTTTAGT
Found at i:29532858 original size:108 final size:110
Alignment explanation
Indices: 29532656--29532862 Score: 276
Period size: 108 Copynumber: 1.9 Consensus size: 110
29532646 TTTAGTCCAT
* * *
29532656 TTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTTACTCACATTTGAGCTTCACTTCATT
1 TTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTCACTCACATTTAAGCTTCACTTCATG
* * *
29532721 TTTTTGTTCCACTTCTCTGTATCTCATCAAGAAGGTGATTGCCAC
66 TCTTGGTTCCACTTCTCTCTATCTCATCAAGAAGGTGATTGCCAC
* * ***
29532766 TTCTCTATATCTCATCAGGAAGGT-GGGGTTTGAAGTTTCACTCACA-TTAAGCTTTGTTTCAAT
1 TTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTCACTCACATTTAAGCTTCACTTC-AT
*
29532829 GTCTTGGTT-CACTTCTTTCTATCTCATCAAGAAG
65 GTCTTGGTTCCACTTCTCTCTATCTCATCAAGAAG
29532863 ATGACCACTT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 33 0.39
109 29 0.35
110 22 0.26
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (110 bp):
TTCTCTATATCTCATCAGAAAGATGGGGGTTTGAAGTTTCACTCACATTTAAGCTTCACTTCATG
TCTTGGTTCCACTTCTCTCTATCTCATCAAGAAGGTGATTGCCAC
Found at i:29532987 original size:124 final size:124
Alignment explanation
Indices: 29532762--29533113 Score: 501
Period size: 124 Copynumber: 2.8 Consensus size: 124
29532752 AAGGTGATTG
* * * *
29532762 CCACTTCTCTATATCTCATCAGGAAGGT-GGGGTTTGAAGTTTCACTCACATTAAGCTTTGTTTC
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
* * *
29532826 AATGTCTTGGTTCACTTCTTTCTATCTCATCAAGAAGATGACCACTTCATTATTCTGAT
66 ATTGTCTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTCTGAT
* *
29532885 TCACTTCTCTGTATCTTATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
* * * * *
29532950 ATTGTCTTGGTTCACTTCTCTGTATCTTATTAGGAAGATGACCGCTTCATTATTTTGAT
66 ATTGTCTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTCTGAT
* * * *
29533009 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTTAAAGCTTCACTCACATTGAGTTTTGCTTC
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
* *
29533074 ATGGAT-TTGGTCCACTTCTCTGTATCTCATCAAGAAGATG
66 ATTG-TCTTGGTTCACTTCTCTGTATCTCATCAAGAAGATG
29533114 GGATTTTGAA
Statistics
Matches: 202, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
123 24 0.12
124 177 0.88
125 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (124 bp):
CCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTC
ATTGTCTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTATTCTGAT
Found at i:29533130 original size:76 final size:76
Alignment explanation
Indices: 29533003--29533189 Score: 284
Period size: 76 Copynumber: 2.5 Consensus size: 76
29532993 GCTTCATTAT
* * * *
29533003 TTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTTAAAGCTTCACTCACATTGAGTTT
1 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGGGATTTTAAAGCTTCACTCACATTGAGCTT
*
29533068 TGCTTCATGGA
66 CGCTTCATGGA
* *
29533079 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGGGATTTTGAAGTTTCACTCACATTGAGCTT
1 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGGGATTTTAAAGCTTCACTCACATTGAGCTT
* *
29533144 CGCTTCGTTGA
66 CGCTTCATGGA
*
29533155 TTTGGTCCACTTCTTTGTATCTCATCAAGAAGATG
1 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATG
29533190 ATCGCTTCAT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 101 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (76 bp):
TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGGGATTTTAAAGCTTCACTCACATTGAGCTT
CGCTTCATGGA
Found at i:29533291 original size:124 final size:124
Alignment explanation
Indices: 29533079--29533313 Score: 382
Period size: 124 Copynumber: 1.9 Consensus size: 124
29533069 GCTTCATGGA
* * *
29533079 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGGGATTTTGAAGTTTCACTCACATTGAGCTT
1 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATGGGAGTTTAAAGTTTCACTCACATTGAGCTT
* *
29533144 CGCTTCGTTGATTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCATTAT
66 CGCTTCATTGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTAT
*
29533203 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCACATTGAGCTT
1 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATGGGAGTTTAAAGTTTCACTCACATTGAGCTT
* *
29533268 GGCTTCATT-ATTTTGGTCTACTTCTCTGTATCTCATCAAGAAGATG
66 CGCTTCATTGA-TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATG
29533314 GGGGTTTAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
123 1 0.01
124 101 0.99
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (124 bp):
TTTGATCCACTTCTCTGTATCTCATCAAGAAGATGGGAGTTTAAAGTTTCACTCACATTGAGCTT
CGCTTCATTGATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTAT
Found at i:29533319 original size:76 final size:76
Alignment explanation
Indices: 29533193--29533389 Score: 367
Period size: 76 Copynumber: 2.6 Consensus size: 76
29533183 GAAGATGATC
* *
29533193 GCTTCATTATTTTGATCCACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCA
1 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCA
29533258 CATTGAGCTTG
66 CATTGAGCTTG
29533269 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCA
1 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCA
29533334 CATTGAGCTTG
66 CATTGAGCTTG
*
29533345 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATG
1 GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAAGAAGATG
29533390 ATCGTTTCAT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 118 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (76 bp):
GCTTCATTATTTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCA
CATTGAGCTTG
Found at i:29533430 original size:124 final size:124
Alignment explanation
Indices: 29533271--29533514 Score: 346
Period size: 124 Copynumber: 2.0 Consensus size: 124
29533261 TGAGCTTGGC
* *
29533271 TTCATTATTTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCACA
1 TTCATTATTTTGATCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGCTTCACTCACA
* * *** * **
29533336 TTGAGCTTGGC-TTCATTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGT
66 TTGAGCTTCGCTTTC-TTAATTCAATCCACTTCTCTACATCTCATCAGGAAGATGATCGT
* * * *
29533395 TTCATTATTTTGATCTACTTCTCTGTATCTTATCAAGAAGATGGGGTTTTGAAGCTTCACTCATA
1 TTCATTATTTTGATCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGCTTCACTCACA
29533460 TTGAGCTTCGCTTTCTTAATTCAATCCACTTCTCTACATCTCATCAGGAAGATGA
66 TTGAGCTTCGCTTTCTTAATTCAATCCACTTCTCTACATCTCATCAGGAAGATGA
29533515 CTGCTTTATT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
124 102 0.97
125 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (124 bp):
TTCATTATTTTGATCTACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGCTTCACTCACA
TTGAGCTTCGCTTTCTTAATTCAATCCACTTCTCTACATCTCATCAGGAAGATGATCGT
Found at i:29533493 original size:200 final size:200
Alignment explanation
Indices: 29532886--29533513 Score: 875
Period size: 200 Copynumber: 3.1 Consensus size: 200
29532876 TATTCTGATT
* * *
29532886 CACTTCTCTGTATCTTATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 CACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCA
* * * * *
29532951 TTGTCTTGGT-TCACTTCTCTGTATCTTATTAGGAAGATGACCGCTTCATTATTTTGATCCACTT
66 TTATTTTGGTCT-ACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTATTTTGATCCACTT
* * * **
29533015 CTCTGTATCTCATCAGGAAGATGGGGTTTTAAAGCTTCACTCACATTGAGTTTTGCTTCATGGAT
130 CTCTGTATCTCATCAAGAAGATGGGGTTTTAAAGCTTCACTCACATTGAGCTTCGCTTCATTAAT
29533080 TTGGTC
195 TTGGTC
** *
29533086 CACTTCTCTGTATCTCATCAAGAAGATGGGATTTTGAAGTTTCACTCACATTGAGCTTCGCTTCG
1 CACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCA
* * *
29533151 TTGA-TTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGATCGCTTCATTATTTTGATCCACTT
66 TT-ATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTATTTTGATCCACTT
* * * *
29533215 CTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCACATTGAGCTTGGCTTCATTATT
130 CTCTGTATCTCATCAAGAAGATGGGGTTTTAAAGCTTCACTCACATTGAGCTTCGCTTCATTAAT
29533280 TTGGTC
195 TTGGTC
* * *
29533286 TACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTAAAGTTTCACTCACATTGAGCTTGGCTTCA
1 CACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCA
* *
29533351 TTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGTTTCATTATTTTGATCTACTTC
66 TTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTATTTTGATCCACTTC
* * *
29533416 TCTGTATCTTATCAAGAAGATGGGGTTTTGAAGCTTCACTCATATTGAGCTTCGCTTTC-TTAAT
131 TCTGTATCTCATCAAGAAGATGGGGTTTTAAAGCTTCACTCACATTGAGCTTCGC-TTCATTAAT
***
29533480 TCAATC
195 TTGGTC
** *
29533486 CACTTCTCTACATCTCATCAGGAAGATG
1 CACTTCTCTGTATCTCATCAAGAAGATG
29533514 ACTGCTTTAT
Statistics
Matches: 377, Mismatches: 47, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
199 1 0.00
200 373 0.99
201 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (200 bp):
CACTTCTCTGTATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCA
TTATTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTATTTTGATCCACTTC
TCTGTATCTCATCAAGAAGATGGGGTTTTAAAGCTTCACTCACATTGAGCTTCGCTTCATTAATT
TGGTC
Found at i:29533838 original size:49 final size:49
Alignment explanation
Indices: 29533764--29534054 Score: 259
Period size: 49 Copynumber: 6.0 Consensus size: 49
29533754 CTTTATCTTC
*
29533764 AGGGTATAAGATTCGTCGTTACGGCCTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * *
29533813 AGGGTATAAGATTCGTCGTTGCGGCCTCGA-CCTTCCCTTTTACATCTTT
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCC-TTCACATCTCT
* * ** * ** *
29533862 AGGGT-TCAAGATTCGCCGTTGCGGCTTCAATC-TGACTTTCTTATTTCT
1 AGGGTAT-AAGATTCGTCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
* * * * * *
29533910 AAGGTATAAGGTTCGTCATTGCAGCCTCAA-CTTTTCCCTTTAAATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATC-TTTCCCTTCACATCTCT
** * *
29533959 AGGGTACCAGATTCGCCGTTGCGGCCTTAATCTTTCCCTTCACAT-TCCT
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTTCACATCT-CT
* * * * *
29534008 AGGGTACAAAATTTGTTGTTGCGGCCTCAATCTTTCCCTTCGCATCT
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTTCACATCT
29534055 TGAGAGTATA
Statistics
Matches: 187, Mismatches: 46, Indels: 17
0.75 0.18 0.07
Matches are distributed among these distances:
47 1 0.01
48 36 0.19
49 147 0.79
50 3 0.02
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36
Consensus pattern (49 bp):
AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTTCACATCTCT
Found at i:29533971 original size:97 final size:97
Alignment explanation
Indices: 29533810--29533991 Score: 242
Period size: 97 Copynumber: 1.9 Consensus size: 97
29533800 CCTTCACATC
* * * * * * *
29533810 TCTAGGGTATAAGATTCGTCGTTGCGGCCTCGACCTTCCCTTTTACATCTTTAGGGTTCAAGATT
1 TCTAAGGTATAAGATTCGTCATTGCAGCCTCAACCTTCCCTTTTAAATCTCTAGGGTACAAGATT
29533875 CGCCGTTGCGG-CTTCAATCTGACTTTCTTATT
66 CGCCGTTGCGGCCTT-AATCTGACTTTCTTATT
* * *
29533907 TCTAAGGTATAAGGTTCGTCATTGCAGCCTCAACTTTTCCC-TTTAAATCTCTAGGGTACCAGAT
1 TCTAAGGTATAAGATTCGTCATTGCAGCCTCAAC-CTTCCCTTTTAAATCTCTAGGGTACAAGAT
29533971 TCGCCGTTGCGGCCTTAATCT
65 TCGCCGTTGCGGCCTTAATCT
29533992 TTCCCTTCAC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
97 65 0.89
98 8 0.11
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (97 bp):
TCTAAGGTATAAGATTCGTCATTGCAGCCTCAACCTTCCCTTTTAAATCTCTAGGGTACAAGATT
CGCCGTTGCGGCCTTAATCTGACTTTCTTATT
Found at i:29534030 original size:146 final size:146
Alignment explanation
Indices: 29533766--29534040 Score: 322
Period size: 146 Copynumber: 1.9 Consensus size: 146
29533756 TTATCTTCAG
* * * * *
29533766 GGTATAAGATTCGTCGTTACGGCCTCAATCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCG
1 GGTATAAGATTCGTCATTACAGCCTCAATCTTTCCCTTCAAATCTCTAGGGTACAAGATTCGCCG
* * * * * *
29533831 TTGCGGCCTCGACCTTCCCTTTTACATCTTTAGGGTTCAAGATTCGCCGTTGCGGCTTCAATCTG
66 TTGCGGCCTCAACCTTCCCTTTCACATCTCTAGGGTACAAAATTCGCCGTTGCGGCCTCAATCTG
29533896 ACTTTCTTATTTCTAA
131 ACTTTCTTATTTCTAA
* * * *
29533912 GGTATAAGGTTCGTCATTGCAGCCTCAA-CTTTTCCCTTTAAATCTCTAGGGTACCAGATTCGCC
1 GGTATAAGATTCGTCATTACAGCCTCAATC-TTTCCCTTCAAATCTCTAGGGTACAAGATTCGCC
* * * **
29533976 GTTGCGGCCTTAATCTTTCCC-TTCACAT-TCCTAGGGTACAAAATTTGTTGTTGCGGCCTCAAT
65 GTTGCGGCCTCAA-CCTTCCCTTTCACATCT-CTAGGGTACAAAATTCGCCGTTGCGGCCTCAAT
29534039 CT
128 CT
29534041 TTCCCTTCGC
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
145 2 0.02
146 98 0.92
147 6 0.06
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (146 bp):
GGTATAAGATTCGTCATTACAGCCTCAATCTTTCCCTTCAAATCTCTAGGGTACAAGATTCGCCG
TTGCGGCCTCAACCTTCCCTTTCACATCTCTAGGGTACAAAATTCGCCGTTGCGGCCTCAATCTG
ACTTTCTTATTTCTAA
Found at i:29534935 original size:16 final size:18
Alignment explanation
Indices: 29534916--29534949 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29534906 TTTCTTCTTC
29534916 TTCTTTT-T-TTTTTTTT
1 TTCTTTTCTCTTTTTTTT
29534932 TTCTTTTCTCTTTTTTTT
1 TTCTTTTCTCTTTTTTTT
29534950 GGGTAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTCTTTTCTCTTTTTTTT
Found at i:29534948 original size:21 final size:22
Alignment explanation
Indices: 29534894--29534949 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
29534884 CATCTTGACC
*
29534894 TCTCATTTTTCTTTTCTTCTTCT
1 TCTC-TTTTTTTTTTCTTCTTCT
* *
29534917 TCTTTTTTTTTTTTTTTCTT-T
1 TCTCTTTTTTTTTTCTTCTTCT
29534938 TCTCTTTTTTTT
1 TCTCTTTTTTTT
29534950 GGGTAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 12 0.41
22 14 0.48
23 3 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (22 bp):
TCTCTTTTTTTTTTCTTCTTCT
Found at i:29535578 original size:25 final size:25
Alignment explanation
Indices: 29535544--29535596 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
29535534 ATTCAGTGTG
* *
29535544 TTGTCAAATATGATCCTTTCTGGCA
1 TTGTCAAATATAATCCTTTCTAGCA
29535569 TTGTCAAATATAATCCTTTCTAGCA
1 TTGTCAAATATAATCCTTTCTAGCA
29535594 TTG
1 TTG
29535597 ACATGTAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (25 bp):
TTGTCAAATATAATCCTTTCTAGCA
Found at i:29535836 original size:5 final size:5
Alignment explanation
Indices: 29535826--29535868 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
29535816 TGACTTTTCC
* *
29535826 TTCTT TTCTT TTCTT TGCTT TTCTT TT-TC TT-TT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
29535869 GGGTTTTAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:29535875 original size:28 final size:29
Alignment explanation
Indices: 29535819--29535875 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
29535809 TTCATCTTGA
*
29535819 CTTTTCCTTCTTTTCTTTTCTTTGCTTTT
1 CTTTTCCTTCTTTTCTTTTCTTGGCTTTT
* *
29535848 CTTTTTCTT-TTTTCTTTTCTTGGGTTTT
1 CTTTTCCTTCTTTTCTTTTCTTGGCTTTT
29535876 AAGATGCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (29 bp):
CTTTTCCTTCTTTTCTTTTCTTGGCTTTT
Found at i:29535956 original size:21 final size:21
Alignment explanation
Indices: 29535927--29535982 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
29535917 TCTTTTTCTT
29535927 TCTTCTTTCTTTTATCTTTTA
1 TCTTCTTTCTTTTATCTTTTA
* *
29535948 TCTTTTTTCTTTTATCTTTTTT
1 TCTTCTTTCTTTTATC-TTTTA
29535970 TCTTCTTT-TTTTA
1 TCTTCTTTCTTTTA
29535983 CCTCTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (21 bp):
TCTTCTTTCTTTTATCTTTTA
Found at i:29535973 original size:15 final size:14
Alignment explanation
Indices: 29535914--29535969 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
29535904 ATCTCGACCC
29535914 TTTTCTTTT-TCTT
1 TTTTCTTTTATCTT
*
29535927 TCTTC--TT-TCTT
1 TTTTCTTTTATCTT
*
29535938 TTATCTTTTATCTT
1 TTTTCTTTTATCTT
29535952 TTTTCTTTTATCTT
1 TTTTCTTTTATCTT
29535966 TTTT
1 TTTT
29535970 TCTTCTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 9 0.25
13 6 0.17
14 21 0.58
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTATCTT
Found at i:29535990 original size:21 final size:21
Alignment explanation
Indices: 29535925--29535991 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
29535915 TTTCTTTTTC
29535925 TTTCTTCTTTCTTTTA-TCTT
1 TTTCTTCTTTCTTTTACTCTT
* *
29535945 TTATCTTTTTTCTTTTATCTTTT
1 TT-TCTTCTTTCTTTTA-CTCTT
29535968 TTTCTTCTTT-TTTTACCTCTT
1 TTTCTTCTTTCTTTTA-CTCTT
29535989 TTT
1 TTT
29535992 TAATAACACG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.05
21 25 0.64
22 7 0.18
23 5 0.13
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCTTCTTTCTTTTACTCTT
Found at i:29540192 original size:29 final size:29
Alignment explanation
Indices: 29540160--29540321 Score: 116
Period size: 30 Copynumber: 5.4 Consensus size: 29
29540150 TTTTGGGGCT
29540160 TTTGAGGGTCAAAATTGAATTTTGGAAAG
1 TTTGAGGGTCAAAATTGAATTTTGGAAAG
* ** *
29540189 TTTGAGGGTCGAAATCAAATTTTGGAGAG
1 TTTGAGGGTCAAAATTGAATTTTGGAAAG
* *
29540218 TTCGAGGGGTC-AAATATGAATTTTTGAAAAG
1 TTTGA-GGGTCAAAAT-TGAA-TTTTGGAAAG
*
29540249 TTT-AGGGGTTAAAA-TGTAATGTTTGGAAAG
1 TTTGA-GGGTCAAAATTG-AAT-TTTGGAAAG
* * * **
29540279 TTCGGGGGT-TAAATCCAAATTTTGGGAAAG
1 TTTGAGGGTCAAAAT-TGAATTTT-GGAAAG
29540309 TTTGAGGGTCAAA
1 TTTGAGGGTCAAA
29540322 TAGTAAGTTT
Statistics
Matches: 102, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
29 42 0.41
30 45 0.44
31 15 0.15
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.33
Consensus pattern (29 bp):
TTTGAGGGTCAAAATTGAATTTTGGAAAG
Found at i:29540343 original size:90 final size:90
Alignment explanation
Indices: 29540165--29540370 Score: 217
Period size: 90 Copynumber: 2.3 Consensus size: 90
29540155 GGGCTTTTGA
* *
29540165 GGGTCAAAAT-TGAAT-TTTGGAAAGTTTGAGGGTCGAAATCAAATTTTGGAGAGTTCGAGGGGT
1 GGGTCAAAATAT-AATGTTTGGAAAGTTCGAGGGTCGAAATCAAATTTTGGAAAGTTCGAGGGGT
*
29540228 CAAATATGAATTTTTGAAAAGTTTAG
65 CAAATATGAATTTTAGAAAAGTTTAG
* * * * *
29540254 GGGTTAAAATGTAATGTTTGGAAAGTTCGGGGGT-TAAATCCAAATTTTGGGAAAGTTTGA-GGG
1 GGGTCAAAATATAATGTTTGGAAAGTTCGAGGGTCGAAAT-CAAATTTT-GGAAAGTTCGAGGGG
* *
29540317 TCAAATA-GTAAGTTTTAG-TAATTTTAG
64 TCAAATATG-AA-TTTTAGAAAAGTTTAG
* *
29540344 GGGTCAAAATATTATTTTTGGAAAGTT
1 GGGTCAAAATATAATGTTTGGAAAGTT
29540371 TAAGGACCTC
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
89 17 0.17
90 67 0.68
91 14 0.14
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (90 bp):
GGGTCAAAATATAATGTTTGGAAAGTTCGAGGGTCGAAATCAAATTTTGGAAAGTTCGAGGGGTC
AAATATGAATTTTAGAAAAGTTTAG
Found at i:29541105 original size:2 final size:2
Alignment explanation
Indices: 29541100--29541129 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29541090 AAATAGATAA
*
29541100 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29541130 CGAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29541187 original size:23 final size:22
Alignment explanation
Indices: 29541156--29541198 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29541146 TAAACCAAAA
29541156 TATAAATAGATGTTATGTATATG
1 TATAAATAGATGTTA-GTATATG
* *
29541179 TATATATAGGTGTTAGTATA
1 TATAAATAGATGTTAGTATA
29541199 CCTTGCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (22 bp):
TATAAATAGATGTTAGTATATG
Found at i:29543175 original size:19 final size:20
Alignment explanation
Indices: 29543138--29543176 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29543128 GTTTTAAAGT
*
29543138 TTTTTATTTTTAATTAATCAC
1 TTTTTATTTATAA-TAATCAC
29543159 TTTTTATTTATAA-AATCA
1 TTTTTATTTATAATAATCA
29543177 AATAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTATTTATAATAATCAC
Found at i:29545882 original size:25 final size:25
Alignment explanation
Indices: 29545837--29545891 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
29545827 GCTAATGTGT
29545837 AAAAAGTATTAATAAAAATGAACA-A
1 AAAAAGTATTAATAAAAATGAA-ATA
* *
29545862 AAAAAGTTTTAA-ACAACATGAAATA
1 AAAAAGTATTAATA-AAAATGAAATA
29545887 AAAAA
1 AAAAA
29545892 TATAAATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.20
Consensus pattern (25 bp):
AAAAAGTATTAATAAAAATGAAATA
Found at i:29548261 original size:252 final size:252
Alignment explanation
Indices: 29547816--29548560 Score: 1472
Period size: 252 Copynumber: 3.0 Consensus size: 252
29547806 ACATAGAAGT
29547816 TAGTCTTTAGTCCTCTCTTATATAGTTATAATTGTTCATAAATATAGATATAATTATCTATAATT
1 TAGTCTTTAGTCCTCTCTTATATAGTTATAATTGTTCATAAATATAGATATAATTATCTATAATT
29547881 GGGACATGTCACATACCACAGATTACAAACTATGCAAATATAAATGTTTATTTTCTGCATTTTAG
66 GGGACATGTCACATACCACAGATTACAAACTATGCAAATATAAATGTTTATTTTCTGCATTTTAG
29547946 AGCTCTGAGTCTGTTGGGACAATTGGTGGGAGGAGATGGAAAAAGCAGCTTAAACCAACTTCCTT
131 AGCTCTGAGTCTGTTGGGACAATTGGTGGGAGGAGATGGAAAAAGCAGCTTAAACCAACTTCCTT
29548011 AAAACCATTCAAGCTAAGAACTGAGGTACAATTACATCTTTTGGACATGTCAAAAGA
196 AAAACCATTCAAGCTAAGAACTGAGGTACAATTACATCTTTTGGACATGTCAAAAGA
29548068 TAGTCTTTAGTCCTCTCTTATATAGTTATAATTGTTCATAAATATAGATATAATTATCTATAATT
1 TAGTCTTTAGTCCTCTCTTATATAGTTATAATTGTTCATAAATATAGATATAATTATCTATAATT
29548133 GGGACATGTCACATACCACAGATTACAAACTATGCAAATATAAATGTTTATTTTCTGCATTTTAG
66 GGGACATGTCACATACCACAGATTACAAACTATGCAAATATAAATGTTTATTTTCTGCATTTTAG
29548198 AGCTCTGAGTCTGTTGGGACAATTGGTGGGAGGAGATGGAAAAAGCAGCTTAAACCAACTTCCTT
131 AGCTCTGAGTCTGTTGGGACAATTGGTGGGAGGAGATGGAAAAAGCAGCTTAAACCAACTTCCTT
29548263 AAAACCATTCAAGCTAAGAACTGAGGTACAATTACATCTTTTGGACATGTCAAAAGA
196 AAAACCATTCAAGCTAAGAACTGAGGTACAATTACATCTTTTGGACATGTCAAAAGA
29548320 TAGTCTTTAGTCCTCTCTTATATAGTTATAATTGTTCATAAATATAGATATAATTATCTATAATT
1 TAGTCTTTAGTCCTCTCTTATATAGTTATAATTGTTCATAAATATAGATATAATTATCTATAATT
* *
29548385 GGGAAATGTCACAAACCACAGATTACAAACTATGCAAATATAAATGTTTATTTTCTGCATTTTAG
66 GGGACATGTCACATACCACAGATTACAAACTATGCAAATATAAATGTTTATTTTCTGCATTTTAG
29548450 AGCTCTGAGTCTGTTGGGACAATTGGTGGGAGGAGATGGAAAAAGCAGCTTAAACCAACTTCCTT
131 AGCTCTGAGTCTGTTGGGACAATTGGTGGGAGGAGATGGAAAAAGCAGCTTAAACCAACTTCCTT
29548515 AAAACCATTCAAGCTAAGAACTGAGGTACAATTACATCTTTTGGAC
196 AAAACCATTCAAGCTAAGAACTGAGGTACAATTACATCTTTTGGAC
29548561 TTGAGTTTCT
Statistics
Matches: 491, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
252 491 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (252 bp):
TAGTCTTTAGTCCTCTCTTATATAGTTATAATTGTTCATAAATATAGATATAATTATCTATAATT
GGGACATGTCACATACCACAGATTACAAACTATGCAAATATAAATGTTTATTTTCTGCATTTTAG
AGCTCTGAGTCTGTTGGGACAATTGGTGGGAGGAGATGGAAAAAGCAGCTTAAACCAACTTCCTT
AAAACCATTCAAGCTAAGAACTGAGGTACAATTACATCTTTTGGACATGTCAAAAGA
Found at i:29550147 original size:334 final size:336
Alignment explanation
Indices: 29549537--29550211 Score: 1282
Period size: 334 Copynumber: 2.0 Consensus size: 336
29549527 ACTCAGGGGC
29549537 AAAAAATGAATAATAAATTTTTAAAGTTAAATATAATTTTATCATTATATGACTTGCCCCTTGTC
1 AAAAAATGAATAATAAATTTTTAAAGTTAAATATAATTTTATCATTATATGACTTGCCCCTTGTC
*
29549602 TTCGCCTCTAGACTCAAGGATGAAAGTTAAAATGCGGGTCCGACACGACTATCCTGGATTAGTTT
66 TTCGCCTCTAGACTCAAGGATGAAAGTTAAAATGCGGGTCCGACACGACTATACTGGATTAGTTT
29549667 TTTCCATATATTTCAAGGATCAAACCTCATCTCCATGCTCATTTTTGGTTGTTTAAGGTCATCAA
131 TTTCCATATATTTCAAGGATCAAACCTCATCTCCATGCTCATTTTTGGTTGTTTAAGGTCATCAA
29549732 AGAATCCAACCATACCGAGGGAGCCAAAGTTCCAGATTCCACAGCATAAGAAGATAAAATGCTTC
196 AGAATCCAACCATACCGAGGGAGCCAAAGTTCCAGATTCCACAGCATAAGAAGATAAAATGCTTC
* *
29549797 ATGTCATTCCATGACATGAGCCCATACACTTTCCAAGGCAATGAAGCAAGAG-AATATAGGGGTT
261 ATGTCATGCAATGACATGAGCCCATACACTTTCCAAGGCAATGAAGCAAGAGAAATATAGGGGTT
29549861 TTTTCCTTTAA
326 TTTTCCTTTAA
29549872 AAAAAATGAATAATAAATTTTTAAAGTTAAATATAATTTTATCATTATATGACTTG-CCCTTGTC
1 AAAAAATGAATAATAAATTTTTAAAGTTAAATATAATTTTATCATTATATGACTTGCCCCTTGTC
29549936 TTCGCCTCTAGACTCAAGGATGAAAGTTAAAATGCGGGTCCGACACGACTATACTGGATTAGTTT
66 TTCGCCTCTAGACTCAAGGATGAAAGTTAAAATGCGGGTCCGACACGACTATACTGGATTAGTTT
*
29550001 TTTCCATATATTTCGAGGATCAAACCTCATCTCCATGCTCATTTTTGGTTGTTTAAGGTCATCAA
131 TTTCCATATATTTCAAGGATCAAACCTCATCTCCATGCTCATTTTTGGTTGTTTAAGGTCATCAA
*
29550066 AGAATCCAACTATACCGAGGGAGCCAAAGTTCCAGATTCCACAGCATAAGAAGATAAAATGCTTC
196 AGAATCCAACCATACCGAGGGAGCCAAAGTTCCAGATTCCACAGCATAAGAAGATAAAATGCTTC
*
29550131 ATGTCATGGAATGACATGAGCCCATACACTTTCCAAGGCAATGAAGCAAGAGAAATATAGGGGTT
261 ATGTCATGCAATGACATGAGCCCATACACTTTCCAAGGCAATGAAGCAAGAGAAATATAGGGGTT
29550196 TTTTCCTTTAA
326 TTTTCCTTTAA
29550207 AAAAA
1 AAAAA
29550212 GTGATTCTTT
Statistics
Matches: 333, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
334 249 0.75
335 84 0.25
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (336 bp):
AAAAAATGAATAATAAATTTTTAAAGTTAAATATAATTTTATCATTATATGACTTGCCCCTTGTC
TTCGCCTCTAGACTCAAGGATGAAAGTTAAAATGCGGGTCCGACACGACTATACTGGATTAGTTT
TTTCCATATATTTCAAGGATCAAACCTCATCTCCATGCTCATTTTTGGTTGTTTAAGGTCATCAA
AGAATCCAACCATACCGAGGGAGCCAAAGTTCCAGATTCCACAGCATAAGAAGATAAAATGCTTC
ATGTCATGCAATGACATGAGCCCATACACTTTCCAAGGCAATGAAGCAAGAGAAATATAGGGGTT
TTTTCCTTTAA
Found at i:29550964 original size:19 final size:18
Alignment explanation
Indices: 29550925--29550978 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
29550915 CAATACAAGC
*
29550925 AAAATTAATAATAAAATA
1 AAAATTAACAATAAAATA
29550943 AAAATTATACAATATAAA-A
1 AAAATTA-ACAATA-AAATA
*
29550962 AAAATT-ACAACAAAATA
1 AAAATTAACAATAAAATA
29550979 GTAGAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 3 0.10
17 6 0.19
18 7 0.23
19 12 0.39
20 3 0.10
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTAACAATAAAATA
Found at i:29556859 original size:209 final size:209
Alignment explanation
Indices: 29556499--29556916 Score: 836
Period size: 209 Copynumber: 2.0 Consensus size: 209
29556489 ATGTTAAATA
29556499 TGGTACAAAAGAGAAATAATACACAAATTTAGGGAGAAATTATGTGTCATTTCTAATGCTGTCAC
1 TGGTACAAAAGAGAAATAATACACAAATTTAGGGAGAAATTATGTGTCATTTCTAATGCTGTCAC
29556564 ACCCTCAAACTTGAGTGTTTACTTATCCTTAAATAAACAAAAATCAGCAAATCATAGACAAACAT
66 ACCCTCAAACTTGAGTGTTTACTTATCCTTAAATAAACAAAAATCAGCAAATCATAGACAAACAT
29556629 GTCACCGTAATTATTATTCTCACAACTTAAATTTTCTGAGATCCTAATGTGCAAATTGCATTCAC
131 GTCACCGTAATTATTATTCTCACAACTTAAATTTTCTGAGATCCTAATGTGCAAATTGCATTCAC
29556694 ATGATAGAATAATG
196 ATGATAGAATAATG
29556708 TGGTACAAAAGAGAAATAATACACAAATTTAGGGAGAAATTATGTGTCATTTCTAATGCTGTCAC
1 TGGTACAAAAGAGAAATAATACACAAATTTAGGGAGAAATTATGTGTCATTTCTAATGCTGTCAC
29556773 ACCCTCAAACTTGAGTGTTTACTTATCCTTAAATAAACAAAAATCAGCAAATCATAGACAAACAT
66 ACCCTCAAACTTGAGTGTTTACTTATCCTTAAATAAACAAAAATCAGCAAATCATAGACAAACAT
29556838 GTCACCGTAATTATTATTCTCACAACTTAAATTTTCTGAGATCCTAATGTGCAAATTGCATTCAC
131 GTCACCGTAATTATTATTCTCACAACTTAAATTTTCTGAGATCCTAATGTGCAAATTGCATTCAC
29556903 ATGATAGAATAATG
196 ATGATAGAATAATG
29556917 CGCTGACAAT
Statistics
Matches: 209, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 209 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (209 bp):
TGGTACAAAAGAGAAATAATACACAAATTTAGGGAGAAATTATGTGTCATTTCTAATGCTGTCAC
ACCCTCAAACTTGAGTGTTTACTTATCCTTAAATAAACAAAAATCAGCAAATCATAGACAAACAT
GTCACCGTAATTATTATTCTCACAACTTAAATTTTCTGAGATCCTAATGTGCAAATTGCATTCAC
ATGATAGAATAATG
Found at i:29574986 original size:21 final size:22
Alignment explanation
Indices: 29574961--29575001 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29574951 GTGACTTTTA
*
29574961 TATTTAGC-TTAGTTAATCACT
1 TATTTAGCTTTAATTAATCACT
29574982 TATTTAGCTTTAATTAATCA
1 TATTTAGCTTTAATTAATCA
29575002 TGTTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (22 bp):
TATTTAGCTTTAATTAATCACT
Found at i:29596374 original size:30 final size:30
Alignment explanation
Indices: 29596329--29596392 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29596319 AAAATCAATG
* * ** *
29596329 AGGTTGAACTGTGAATTAAGTGTATGTAGT
1 AGGTTGAACTATGAATGAAGCCTATGTACT
*
29596359 AGGTTGAATTATGAATGAAGCCTATGTACT
1 AGGTTGAACTATGAATGAAGCCTATGTACT
29596389 AGGT
1 AGGT
29596393 GAAAATGAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (30 bp):
AGGTTGAACTATGAATGAAGCCTATGTACT
Found at i:29602957 original size:50 final size:50
Alignment explanation
Indices: 29602881--29603099 Score: 257
Period size: 50 Copynumber: 4.3 Consensus size: 50
29602871 TTAATAAAGT
*
29602881 CATGCATTATGTAACTTTCATGTTAGTTAAGTATGCATCATAAATAATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAATGA
* * * *
29602931 CATGTATTAT-TAACTCTCATGATTAGTTAATTTTTCATCATAAATAATGA
1 CATGCATTATGTAACTCTCATG-TTAGTTAAGTATGCATCATAAATAATGA
* * *
29602981 CATGCATTATGTAACTCTCATGTTAATTAAG-ATTGCATCATAAATTATGT
1 CATGCATTATGTAACTCTCATGTTAGTTAAGTA-TGCATCATAAATAATGA
* * *
29603031 CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATCAA-GT
1 CATGCATTATGTAACTCTCATGTTAGTT-AAGTATGCATCA-TAAAT-AATGA
29603083 CATGCATT-TAGTAACTC
1 CATGCATTAT-GTAACTC
29603100 ATTAGTTCAT
Statistics
Matches: 145, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
49 10 0.07
50 90 0.62
51 22 0.15
52 22 0.15
53 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (50 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAATGA
Found at i:29603436 original size:91 final size:91
Alignment explanation
Indices: 29603313--29603493 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 91
29603303 TCTTGATCAG
* *
29603313 GTGACTCTTCCAAAGATCAAGGGAAGACTCTTCAAATGCTGATCGATTTT-GGTGCACTTAAAGA
1 GTGACTCTTCAAAAGACCAAGGGAAGACTCTTCAAATGCTGATCGATTTTAGG-GCACTTAAAGA
*
29603377 CCAATTCATGGCACCAATTAAAAGGAA
65 CCAATTCATGACACCAATTAAAAGGAA
* * *
29603404 GTGACTCTTCAAAAGACCAGGGGGAA-ACTCTTCAAATGCTGATCGGTTTTAGGGCACTTAAAGG
1 GTGACTCTTCAAAAGACCA-AGGGAAGACTCTTCAAATGCTGATCGATTTTAGGGCACTTAAAGA
* *
29603468 CCAATTCATGACATCACTTAAAAGGA
65 CCAATTCATGACACCAATTAAAAGGA
29603494 GGAAATGCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
91 73 0.91
92 7 0.09
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (91 bp):
GTGACTCTTCAAAAGACCAAGGGAAGACTCTTCAAATGCTGATCGATTTTAGGGCACTTAAAGAC
CAATTCATGACACCAATTAAAAGGAA
Found at i:29605501 original size:47 final size:47
Alignment explanation
Indices: 29605410--29605511 Score: 111
Period size: 47 Copynumber: 2.1 Consensus size: 47
29605400 CACATAGATA
* * *
29605410 CCGATGAACGGTCACATAGCACATCGTGGGTAAAGCACCTCATATTTGT
1 CCGAT-AACGATCACATAACACATCGTGGGAAAAGCACCTCATATTT-T
*
29605459 -CGATAACGATCACATAACACATC-TTGGAAAAGC-CACTACATATTTT
1 CCGATAACGATCACATAACACATCGTGGGAAAAGCAC-CT-CATATTTT
29605505 CCGATAA
1 CCGATAA
29605512 TGACGACATA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
45 1 0.02
46 11 0.24
47 30 0.65
48 4 0.09
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (47 bp):
CCGATAACGATCACATAACACATCGTGGGAAAAGCACCTCATATTTT
Found at i:29620420 original size:5 final size:5
Alignment explanation
Indices: 29620410--29620436 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
29620400 CGCACTGAAA
29620410 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
29620437 GATTAGCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:29644174 original size:921 final size:908
Alignment explanation
Indices: 29642421--29644255 Score: 3419
Period size: 921 Copynumber: 2.0 Consensus size: 908
29642411 GGGTAAATTA
29642421 GAGCCAGTGAAGGGAGTTGTGGATTCTTATCGTTTCCAAGGCTCCTTAGGACGTTATCTTCTCTT
1 GAGCCAGTGAAGGGAGTTGTGGATTCTTATCGTTTCCAAGGCTCCTTAGGACGTTATCTTCTCTT
29642486 TTCTATCTTTAATTTATCGTTCTTGTTTGATCTAGTTTATTTCTTACTGTTTTGGGTTGTTGATT
66 TTCTATCTTTAATTTATCGTTCTTGTTTGATCTAGTTTATTTCTTACTGTTTTGGGTTGTTGATT
29642551 TAGTTGTTTTTGTTCTAGGTTGAAATTTCTTCAAGAGGGACATTCTCCTACCTTGATCCATCAAG
131 TAGTTGTTTTTGTTCTAGGTTGAAATTTCTTCAAGAGGGACATTCTCCTACCTTGATCCATCAAG
29642616 AAACACATCAAAAATTAGGAGATCCAATCTTTTCTTGCTGTTTCAATCATTCTTGCCTAAACAGT
196 AAACACATCAAAAATTAGGAGATCCAATCTTTTCTTGCTGTTTCAATCATTCTTGCCTAAACAGT
29642681 TTGCTTTTATCTTTTAAATCACTTCTAACGAATCTATTTGTGTTCTTATTTTCTAGATTTGGTTG
261 TTGCTTTTATCTTTTAAATCACTTCTAACGAATCTATTTGTGTTCTTATTTTCTAGATTTGGTTG
29642746 GGACGTTTTCTTGAGGTCAAAGGACGGTTTCTTTCATCCAAGAAACATAAATTCGTTCTCTGTTG
326 GGACGTTTTCTTGAGGTCAAAGGACGGTTTCTTTCATCCAAGAAACATAAATTCGTTCTCTGTTG
*
29642811 GATCCGTTACCAGCCATTCATCTTTCTTTCGTTTTAATTTCGTTTGATTATTCTTCTTGTTAATT
391 GATCCGTTACCAGCCATTCATCTTTCTTTCGTTTTAATTACGTTTGATTATTCTTCTTGTTAATT
29642876 AATCTGTCTTTCGTTTCAGATTATATTTGTCTAGAGCTTTAGGGTAGATCCGCGACTTGACAACT
456 AATCTGTCTTTCGTTTCAGATTATATTTGTCTAGAGCTTTAGGGTAGATCCGCGACTTGACAACT
*
29642941 TTACGATCCACTTTCGCATTTGTTTTTCGTATCACATTTTGCACAAAGATTTGGCATTGATACGA
521 TTACGATCCACTTTCGCATTTCTTTTTCGTATCACATTTTGCACAAAGATTTGGCATTGATACGA
29643006 GTCGCAAGGCCCAAAATCCAGCATATGAACGTGATGGCTCAATCTTCCTCAAGGACCAATAACGA
586 GTCGCAAGGCCCAAAATCCAGCATATGAACGTGATGGCTCAATCTTCCTCAAGGACCAATAACGA
29643071 AGTCAAAAGCAAAGCAAATTCGAGCAAAATTGAATGGGAGCATCCAAGAAATCATTACCAAGGCC
651 AGTCAAAAGCAAAGCAAATTCGAGCAAAATTGAATGGGAGCATCCAAGAAATCATTACCAAGGCC
29643136 CTAGATGCGCAATGATCGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCATGAAACTTAAGAA
716 CTAGATGCGCAATGATCGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCATGAAACTTAAGAA
29643201 ACCGAATCTTGGTCCAATTATGCTGTTTAAATAATTTCAAGAATCAAGAAAATCAAGATTACAAT
781 ACCGAATCTTGGTCCAATTATGCTGTTTAAATAATTTCAAGAATCAAGAAAATCAAGATTACAAT
*
29643266 TCTTGGAGAAAGAAACTGAATCTTGTAGCCAAGGCACATTGGATTTCTTGTACGGCCTTGAAC
846 TCTTGGAGAAAGAAACCGAATCTTGTAGCCAAGGCACATTGGATTTCTTGTACGGCCTTGAAC
*
29643329 GAGCCAGTGAAGGTAGTTGTGGATTCTTATCG-TTCCAAGGCTCCTTAGGACGTTATCTTCTCTT
1 GAGCCAGTGAAGGGAGTTGTGGATTCTTATCGTTTCCAAGGCTCCTTAGGACGTTATCTTCTCTT
29643393 TTCTATCTTTAATTTATCGTTCTTGTTTGATCTAGTTTATTTCTTACTGTTTTGGGTTGTTGATT
66 TTCTATCTTTAATTTATCGTTCTTGTTTGATCTAGTTTATTTCTTACTGTTTTGGGTTGTTGATT
29643458 TAGTTG-TTTTGTTCTAGGTTGAAATTTCTTCAAGAGGGACATTCTCCTACCTTGATCCATCAAG
131 TAGTTGTTTTTGTTCTAGGTTGAAATTTCTTCAAGAGGGACATTCTCCTACCTTGATCCATCAAG
29643522 AAACACATCAAAAATTAGGAGATCCAATCTTTTCTTGCTGTTTCAATCATTCTTGCCTAAACAGT
196 AAACACATCAAAAATTAGGAGATCCAATCTTTTCTTGCTGTTTCAATCATTCTTGCCTAAACAGT
29643587 TTGCTTTTATCTTTTAAATCACTTCTAACGAATCTATTTGTGTTCTTATTTTCTAGATTTGGTTG
261 TTGCTTTTATCTTTTAAATCACTTCTAACGAATCTATTTGTGTTCTTATTTTCTAGATTTGGTTG
* *
29643652 GGACGTTTTTCTTGAGGTCAAAGGATGGTTTCTTTCATCCAAGAAACATTAAATTGGTTCTCTGT
326 GGACG-TTTTCTTGAGGTCAAAGGACGGTTTCTTTCATCCAAGAAACA-TAAATTCGTTCTCTGT
29643717 TGGATCCGTTACCAGCCATTCATCTTTCTTTCGTTTTAATTACGTTTGATTATTCTTCTTGTTAA
389 TGGATCCGTTACCAGCCATTCATCTTTCTTTCGTTTTAATTACGTTTGATTATTCTTCTTGTTAA
29643782 TTAATCTGTCTTTTTTTGTTTTCGTTTCAGATTATATTTGTCTAGAGCTTTAGGGTAGATCCGCG
454 TTAATCTGTC---------TTTCGTTTCAGATTATATTTGTCTAGAGCTTTAGGGTAGATCCGCG
29643847 ACTTGACAACTTTACGATCCACTTTCGCA-TTCTTTTTCGTATCACATTGTCTTTGCACTAAAGA
510 ACTTGACAACTTTACGATCCACTTTCGCATTTCTTTTTCGTATCACA---T-TTTGCAC-AAAGA
29643911 TTTGGCATTGATACGAGTCGCAAGG-CCAAAATCCAGCATATGAACGTGATGGGCTCAATCTTCC
570 TTTGGCATTGATACGAGTCGCAAGGCCCAAAATCCAGCATATGAACGTGAT-GGCTCAATCTTCC
29643975 TCAAGGACCAATAACGAAGTCAAAAGCAAAGCAAATTCGAGCAAAATTGAATGGGAGCATCCAAG
634 TCAAGGACCAATAACGAAGTCAAAAGCAAAGCAAATTCGAGCAAAATTGAATGGGAGCATCCAAG
29644040 AAATCATTACCAAGGCCCTAGATGCGCACATGATCGAAAAAGAAAATCAAGATTCACTTTCTTGT
699 AAATCATTACCAAGGCCCTAGATGCGCA-ATGATCGAAAAAGAAAATCAAGATTCACTTTCTTGT
29644105 TTTCATGAAAC-TAAGAAACCGAATCTTGGTCCAATTATGCTGTTTAAATAATTTCAAGAATCAA
763 TTTCATGAAACTTAAGAAACCGAATCTTGGTCCAATTATGCTGTTTAAATAATTTCAAGAATCAA
29644169 GAAAATCAAGATTACAATTCTTGGAGAAAGAAACCGAATCTTGTAGCCAAGGCACATTGGATTTC
828 GAAAATCAAGATTACAATTCTTGGAGAAAGAAACCGAATCTTGTAGCCAAGGCACATTGGATTTC
29644234 TTGTACGGCCTTGAAC
893 TTGTACGGCCTTGAAC
29644250 GAGCCA
1 GAGCCA
29644256 ATTTCAAGAG
Statistics
Matches: 903, Mismatches: 6, Indels: 23
0.97 0.01 0.02
Matches are distributed among these distances:
906 193 0.21
907 144 0.16
908 120 0.13
916 16 0.02
917 75 0.08
919 1 0.00
920 32 0.04
921 275 0.30
922 47 0.05
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (908 bp):
GAGCCAGTGAAGGGAGTTGTGGATTCTTATCGTTTCCAAGGCTCCTTAGGACGTTATCTTCTCTT
TTCTATCTTTAATTTATCGTTCTTGTTTGATCTAGTTTATTTCTTACTGTTTTGGGTTGTTGATT
TAGTTGTTTTTGTTCTAGGTTGAAATTTCTTCAAGAGGGACATTCTCCTACCTTGATCCATCAAG
AAACACATCAAAAATTAGGAGATCCAATCTTTTCTTGCTGTTTCAATCATTCTTGCCTAAACAGT
TTGCTTTTATCTTTTAAATCACTTCTAACGAATCTATTTGTGTTCTTATTTTCTAGATTTGGTTG
GGACGTTTTCTTGAGGTCAAAGGACGGTTTCTTTCATCCAAGAAACATAAATTCGTTCTCTGTTG
GATCCGTTACCAGCCATTCATCTTTCTTTCGTTTTAATTACGTTTGATTATTCTTCTTGTTAATT
AATCTGTCTTTCGTTTCAGATTATATTTGTCTAGAGCTTTAGGGTAGATCCGCGACTTGACAACT
TTACGATCCACTTTCGCATTTCTTTTTCGTATCACATTTTGCACAAAGATTTGGCATTGATACGA
GTCGCAAGGCCCAAAATCCAGCATATGAACGTGATGGCTCAATCTTCCTCAAGGACCAATAACGA
AGTCAAAAGCAAAGCAAATTCGAGCAAAATTGAATGGGAGCATCCAAGAAATCATTACCAAGGCC
CTAGATGCGCAATGATCGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCATGAAACTTAAGAA
ACCGAATCTTGGTCCAATTATGCTGTTTAAATAATTTCAAGAATCAAGAAAATCAAGATTACAAT
TCTTGGAGAAAGAAACCGAATCTTGTAGCCAAGGCACATTGGATTTCTTGTACGGCCTTGAAC
Found at i:29658632 original size:13 final size:12
Alignment explanation
Indices: 29658616--29658669 Score: 58
Period size: 12 Copynumber: 4.3 Consensus size: 12
29658606 GCAAACATTT
29658616 TTTTCTCCTTTTC
1 TTTTCT-CTTTTC
29658629 TTTTCTCTTTTC
1 TTTTCTCTTTTC
29658641 TTTT-TC-TTTC
1 TTTTCTCTTTTC
29658651 TTTTTCTCATTTTCC
1 -TTTTCTC-TTTT-C
29658666 TTTT
1 TTTT
29658670 TCAAGTGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.11
11 6 0.17
12 12 0.33
13 6 0.17
14 7 0.19
15 1 0.03
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTCTTTTC
Found at i:29658663 original size:18 final size:18
Alignment explanation
Indices: 29658615--29658669 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
29658605 AGCAAACATT
29658615 TTTTTCTCCTTTTCTTTTC
1 TTTTTCT-CTTTTCTTTTC
29658634 TCTTTTCT-TTTTC-TTTC
1 T-TTTTCTCTTTTCTTTTC
29658651 TTTTTCTCATTTTCCTTTT
1 TTTTTCTC-TTTT-CTTTT
29658670 TCAAGTGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 6 0.19
17 5 0.16
18 9 0.29
19 2 0.06
20 9 0.29
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCTCTTTTCTTTTC
Found at i:29669263 original size:51 final size:51
Alignment explanation
Indices: 29669198--29669320 Score: 210
Period size: 51 Copynumber: 2.4 Consensus size: 51
29669188 ACATAAGAGC
* * *
29669198 TGACAAATTCACCCTCTTAACTTAATTAAATTAATTAAAGAAATTGGGATG
1 TGACAACTTTACCCTCTTAACTTAATTAAATTAATTAAAGAAATTAGGATG
*
29669249 TGATAACTTTACCCTCTTAACTTAATTAAATTAATTAAAGAAATTAGGATG
1 TGACAACTTTACCCTCTTAACTTAATTAAATTAATTAAAGAAATTAGGATG
29669300 TGACAACTTTACCCTCTTAAC
1 TGACAACTTTACCCTCTTAAC
29669321 ATAAGATAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (51 bp):
TGACAACTTTACCCTCTTAACTTAATTAAATTAATTAAAGAAATTAGGATG
Found at i:29679695 original size:18 final size:17
Alignment explanation
Indices: 29679674--29679720 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 17
29679664 TCAACTTCGT
29679674 TTTCTTTTTCTCTTTCAA
1 TTTCTTTTTCTCTTTC-A
29679692 TTTCTTTTTCTC--TCA
1 TTTCTTTTTCTCTTTCA
*
29679707 TTTCTTTTTTTCTT
1 TTTCTTTTTCTCTT
29679721 CTCTCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.46
16 2 0.08
18 12 0.46
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCTTTTTCTCTTTCA
Found at i:29679700 original size:24 final size:23
Alignment explanation
Indices: 29679642--29679713 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
29679632 CTCTTATCAA
29679642 CAAC-TCTTCTTTCTTATTTCTTT
1 CAACTTCTT-TTTCTTATTTCTTT
* *
29679665 CAACTTCGTTTTCTTTTTCTCTTT
1 CAACTTCTTTTTCTTATT-TCTTT
*
29679689 CAATTTCTTTTTCTCTCATTTCTTT
1 CAACTTCTTTTTCT-T-ATTTCTTT
29679714 TTTTCTTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 12 0.30
24 20 0.50
25 6 0.15
26 2 0.05
ACGTcount: A:0.11, C:0.25, G:0.01, T:0.62
Consensus pattern (23 bp):
CAACTTCTTTTTCTTATTTCTTT
Done.