Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 8 of 190
Found at i:2453618 original size:2 final size:2
Alignment explanation
Indices: 2453613--2453638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2453603 AAATTCTTTA
2453613 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2453639 GAAATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2458382 original size:20 final size:20
Alignment explanation
Indices: 2458342--2458396 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2458332 TTTTACTTTT
*
2458342 TTTTAAATAATTTTT-T-GAA
1 TTTTAAAT-ATTTTTATCAAA
*
2458361 TTTTATATATTTTTATCAAA
1 TTTTAAATATTTTTATCAAA
*
2458381 TTTTAAATTTTTTTAT
1 TTTTAAATATTTTTAT
2458397 AATAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.20
19 8 0.27
20 16 0.53
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTAAATATTTTTATCAAA
Found at i:2458424 original size:19 final size:18
Alignment explanation
Indices: 2458378--2458424 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2458368 TATTTTTATC
2458378 AAAT-TTTAAATTTTTTT
1 AAATATTTAAATTTTTTT
*
2458395 ATAATA-ATAAATTTTTTTT
1 A-AATATTTAAA-TTTTTTT
2458414 AAATATTTAAA
1 AAATATTTAAA
2458425 ATTAAGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.04
18 11 0.46
19 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATATTTAAATTTTTTT
Found at i:2462270 original size:3 final size:3
Alignment explanation
Indices: 2462262--2462296 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2462252 ACTATATGAT
2462262 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
2462297 ATCATTGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:2475795 original size:55 final size:58
Alignment explanation
Indices: 2475736--2475846 Score: 147
Period size: 58 Copynumber: 2.0 Consensus size: 58
2475726 TTTTAATCAT
* *
2475736 TTTAATATTAAATTAAAT-TAA-A-TTAAATAGATAAGTATTCTATTAATTTAATAGA
1 TTTAATATTAAATTAAATATAATATTTAAATAGATAAGCATTATATTAATTTAATAGA
* ** *
2475791 TTTAATATTAAATTTAATATAATATTTATCTTGATAAGCATTATATTAATTTAATA
1 TTTAATATTAAATTAAATATAATATTTAAATAGATAAGCATTATATTAATTTAATA
2475847 TTAAAGTGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 17 0.36
56 3 0.06
57 1 0.02
58 26 0.55
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (58 bp):
TTTAATATTAAATTAAATATAATATTTAAATAGATAAGCATTATATTAATTTAATAGA
Found at i:2477984 original size:17 final size:17
Alignment explanation
Indices: 2477956--2478007 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
2477946 CTCAAATCCC
2477956 ATATTT-TGATACCCAT
1 ATATTTCTGATACCCAT
2477972 ATATTTCTGATACCCAT
1 ATATTTCTGATACCCAT
* *
2477989 ATCTTTCTGACACCCAT
1 ATATTTCTGATACCCAT
2478006 AT
1 AT
2478008 CTTTGACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
16 6 0.18
17 27 0.82
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.40
Consensus pattern (17 bp):
ATATTTCTGATACCCAT
Found at i:2481090 original size:36 final size:36
Alignment explanation
Indices: 2481043--2481117 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
2481033 CTCATTCTAC
*
2481043 TAATATAAACATACCAAGCTAAATAAGTTCATGTTT
1 TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
*
2481079 TAATATAAACATACCAAGTTAAAGAAGTTCATGTTT
1 TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
2481115 TAA
1 TAA
2481118 CTTCCCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (36 bp):
TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
Found at i:2481879 original size:16 final size:16
Alignment explanation
Indices: 2481858--2481890 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2481848 GAATTTTTAA
2481858 TAATTA-TTAAGTAGTT
1 TAATTATTTAA-TAGTT
2481874 TAATTATTTAATAGTT
1 TAATTATTTAATAGTT
2481890 T
1 T
2481891 TATGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
TAATTATTTAATAGTT
Found at i:2482112 original size:26 final size:27
Alignment explanation
Indices: 2482054--2482112 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
2482044 CTCTTTTGAG
* *
2482054 TTAATAAA-TTCTCTTTGAGTTTTTCT
1 TTAAAAAATTTCTCTTTGAGTTTCTCT
2482080 TTAAAAAATTTCTC-TTGAGTTTCT-T
1 TTAAAAAATTTCTCTTTGAGTTTCTCT
*
2482105 TTAGAAAA
1 TTAAAAAA
2482113 GTTTTAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 8 0.28
26 16 0.55
27 5 0.17
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (27 bp):
TTAAAAAATTTCTCTTTGAGTTTCTCT
Found at i:2482341 original size:13 final size:13
Alignment explanation
Indices: 2482325--2482361 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2482315 TTATTCTATT
2482325 TTATTTATCTTAG
1 TTATTTATCTTAG
*
2482338 TTATTTATTTTAG
1 TTATTTATCTTAG
2482351 TTATTTTATCT
1 TTA-TTTATCT
2482362 GACTATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (13 bp):
TTATTTATCTTAG
Found at i:2485293 original size:2 final size:2
Alignment explanation
Indices: 2485286--2485311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2485276 GATTGAATTG
2485286 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2485312 TATGAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2487046 original size:2 final size:2
Alignment explanation
Indices: 2487039--2487075 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2487029 AATCGTAAAC
2487039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2487076 AGAAAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2502168 original size:21 final size:21
Alignment explanation
Indices: 2502142--2502181 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2502132 TTGTACAAAC
2502142 TAAGCCTTTAAGCAAAGAAAT
1 TAAGCCTTTAAGCAAAGAAAT
2502163 TAAGCCTTTAAGCAAAGAA
1 TAAGCCTTTAAGCAAAGAA
2502182 GTTGATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
TAAGCCTTTAAGCAAAGAAAT
Found at i:2516618 original size:19 final size:20
Alignment explanation
Indices: 2516594--2516644 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2516584 TAAAATACAA
* *
2516594 ATTTTGGCATTTTATAAA-T
1 ATTTTGGAATTTTAAAAATT
2516613 ATTTT-GAATTTTAAAAATT
1 ATTTTGGAATTTTAAAAATT
*
2516632 ATTTTGAAATTTT
1 ATTTTGGAATTTT
2516645 GAAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTTTGGAATTTTAAAAATT
Found at i:2516625 original size:18 final size:20
Alignment explanation
Indices: 2516602--2516644 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
2516592 AAATTTTGGC
*
2516602 ATTTTATAAA-TATTTTG-A
1 ATTTTAAAAATTATTTTGAA
2516620 ATTTTAAAAATTATTTTGAA
1 ATTTTAAAAATTATTTTGAA
2516640 ATTTT
1 ATTTT
2516645 GAAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTAAAAATTATTTTGAA
Found at i:2517783 original size:13 final size:14
Alignment explanation
Indices: 2517756--2517784 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2517746 TAAATATTAG
2517756 TATTTTAATAATTT
1 TATTTTAATAATTT
2517770 TATTTTAA-AATTT
1 TATTTTAATAATTT
2517783 TA
1 TA
2517785 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTAATAATTT
Found at i:2517784 original size:8 final size:8
Alignment explanation
Indices: 2517771--2517795 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2517761 TAATAATTTT
2517771 ATTTTAAA
1 ATTTTAAA
2517779 ATTTTAAA
1 ATTTTAAA
2517787 ATTTTAAA
1 ATTTTAAA
2517795 A
1 A
2517796 CAATTCTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:2524272 original size:309 final size:307
Alignment explanation
Indices: 2523414--2524614 Score: 1561
Period size: 309 Copynumber: 3.9 Consensus size: 307
2523404 CTGAACCCAT
* * * * * * *
2523414 ATGATGAAATCACTTTCATGGCAAGACCTTAATAGGAATGCGACAATGGAAAAG-CTCATAATGA
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGG-AAGGCCTCAGAATGA
* *
2523478 ATTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTCGGAC-AGAACATTTGGGGAGAGGTCATG
65 ATTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAG-ACATTTGGGGAGAGGTCATG
* ** * * ** **
2523542 ATGTAAATTGTCAAAAGGTTTTTATGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAGTAGGTA
129 GTGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAAATA
** *
2523607 CTAAAGCTATGTCTTTCATGTACTGAATA-TTTCTTCATATTGAATAAAACCCGTGGTTCCAAAT
194 CTAAAGCTATGTCTTTCATGTACCAAATATTTTC-TCATATTGAATAAAACTCGTGGTTCCAAAT
*
2523671 AAATATTAATTATCTTCTCCCTTTTATTCATTACAAATA-----T-----
258 ATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
* *
2523711 A--ATGAAATCACTCTCATGGCAAGACCTCAACACGAAGGCGACAATGGAGGGCCTCAGAATGAA
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGAA
* * *
2523774 TTCAAGATTCTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTGTGGGGAGAGGTCATGG
66 TTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATT-TGGGGAGAGGTCATGG
**
2523839 TGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAGGTAC
130 TGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAAATAC
* * * *
2523904 TAAAGTTATGTATTTCATATACCAAATGTTTTCTCATATTGAATAAAACTCGTGGTTCCAAATAT
195 TAAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATAT
2523969 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
260 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
* *
2524017 ATGACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAAGGCCTCAGAATGAT
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGA-
* * * * *
2524082 TTTTAAGGTTTTGATTAAAAGGAAAATAAGATTATTTAGGCAAGACATTTGGGGAGAGGTCATCG
65 ATTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGG
* * **
2524147 TGTAAATTATCAAAAAGCTTTTTACGCCATTGTTGGTGGGAGCCGGTAGAAAATAAGAACAAATA
130 TGTAAATTA-CCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAAATA
* * * * *
2524212 CTAAAGTTATGTCTTTTATGTACCAAATATTTCCTTATATTGAATAAAATTCGTGGTTCCAAATA
194 CTAAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATA
* *
2524277 TATATTAATTATCTTATCCCTTTTTAATTCATTACAAATATTGGCTACCAT
259 TATATTAATTATCTTCTCCC-TTTT-ATTCATTACAAATATTGGCTACCAA
* ** * *
2524328 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGTGACCTTGGAGGGCCTTAGAATGAA
1 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGAA
* * * *
2524393 TCCAAGGTTCTGATTAAAAGGAAAATAAGATTGTTTGGGCAAAAAATTTGGGGAGAGGTCATGGT
66 TTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGGT
* ** * ***
2524458 ATAAATTACCAAAAGCTTTTTACGCTGTTGTTGGTGGGAGCTGCTAGAAAATAAGAACAAATACT
131 GTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAAATACT
* * * * *
2524523 AAAGCTATGTCTTTCATGTACCAAATGTTTTCTCGTATTGAACAAAACT-TTGGTTCCAAATAGA
196 AAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATATA
*
2524587 TATTAATTATCTTCTCCCTTTTAATCAT
261 TATTAATTATCTTCTCCCTTTTATTCAT
2524615 CGAGTGAATT
Statistics
Matches: 795, Mismatches: 89, Indels: 31
0.87 0.10 0.03
Matches are distributed among these distances:
294 2 0.00
295 91 0.11
296 165 0.21
297 5 0.01
301 1 0.00
306 6 0.01
307 4 0.01
308 111 0.14
309 261 0.33
310 68 0.09
311 81 0.10
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (307 bp):
ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAAGGCCTCAGAATGAA
TTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGGT
GTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAAATACT
AAAGCTATGTCTTTCATGTACCAAATATTTTCTCATATTGAATAAAACTCGTGGTTCCAAATATA
TATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
Found at i:2525277 original size:80 final size:78
Alignment explanation
Indices: 2525139--2525373 Score: 310
Period size: 80 Copynumber: 3.0 Consensus size: 78
2525129 TTTCACAGTA
* * * *
2525139 TTTTCATGTTGTTGACCATTCTGGACCTCCTCTCTTGTTTCAGACAACATAAAGCATAAGCATAC
1 TTTTCATGTTGTTGACCATCCTGGACCTCCTCCCCTGTTTCAGACTACATAAAGCATAAGCATAC
2525204 TACTTAAAATATG
66 TACTTAAAATATG
* * *
2525217 TTTTCTATGTTGTTGACCATCCTGGACCCTCCTCCCCTGTCTCAGACTACATTAAGCATAAACAT
1 TTTTC-ATGTTGTTGACCATCCTGGA-CCTCCTCCCCTGTTTCAGACTACATAAAGCATAAGCAT
2525282 ACTACTTAAAATATG
64 ACTACTTAAAATATG
* * * * **
2525297 TTTTCCATGTTGTTGACTATCCTGGATCTTC-CCCCTGTTTCAAACTACATAAAGTGTAAGCATA
1 TTTT-CATGTTGTTGACCATCCTGGACCTCCTCCCCTGTTTCAGACTACATAAAGCATAAGCATA
*
2525361 CTACTTCAAATAT
65 CTACTTAAAATAT
2525374 ATTAATGATA
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
78 44 0.32
79 22 0.16
80 70 0.51
81 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (78 bp):
TTTTCATGTTGTTGACCATCCTGGACCTCCTCCCCTGTTTCAGACTACATAAAGCATAAGCATAC
TACTTAAAATATG
Found at i:2526652 original size:11 final size:12
Alignment explanation
Indices: 2526636--2526687 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
2526626 TACTTTACAT
2526636 TTATA-TATTAA
1 TTATATTATTAA
2526647 TTATATTATTATA
1 TTATATTATTA-A
* *
2526660 TTTCTAATTTTTAA
1 -TTAT-ATTATTAA
2526674 TTATATTATTAA
1 TTATATTATTAA
2526686 TT
1 TT
2526688 TTAATTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 5 0.15
12 14 0.42
13 4 0.12
14 4 0.12
15 6 0.18
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATATTATTAA
Found at i:2526660 original size:19 final size:18
Alignment explanation
Indices: 2526636--2526694 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
2526626 TACTTTACAT
2526636 TTATATATTAATTATATT-A
1 TTATATATTAATT-T-TTAA
*
2526655 TTATATTTCTAATTTTTAA
1 TTATATAT-TAATTTTTAA
2526674 TTATATTATTAA-TTTTAA
1 TTATA-TATTAATTTTTAA
2526692 TTA
1 TTA
2526695 ATCATGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 11 0.31
19 17 0.49
20 7 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATATTAATTTTTAA
Found at i:2526673 original size:27 final size:25
Alignment explanation
Indices: 2526643--2526693 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
2526633 CATTTATATA
2526643 TTAATTATATTATTATATTTCTAATTT
1 TTAATTATATTATTA-ATTT-TAATTT
2526670 TTAATTATATTATTAATTTTAATT
1 TTAATTATATTATTAATTTTAATT
2526694 AATCATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 15 0.62
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTAATTATATTATTAATTTTAATTT
Found at i:2527148 original size:84 final size:84
Alignment explanation
Indices: 2527007--2527176 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 84
2526997 ATCAATAACA
2527007 TCCATAAAAAACAAACACCATTCTTGAAACTCGAAAAATGAAGCAACAGACATGAAAGGAAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAACTCGAAAAATGAAGCAACAGACATGAAAGGAAAAAA
*
2527072 TAGTATGCATCATTCTACT
66 CAGTATGCATCATTCTACT
* * * *
2527091 TCCATGAAAAACAAACACTATTCTTGAAACTCGAAAAATGCAGCAACAGACATGAAAGGGAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAACTCGAAAAATGAAGCAACAGACATGAAAGGAAAAAA
* * *
2527156 CGGTATGCATCGTTTTACT
66 CAGTATGCATCATTCTACT
2527175 TC
1 TC
2527177 GCTTTGAATC
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.21
Consensus pattern (84 bp):
TCCATAAAAAACAAACACCATTCTTGAAACTCGAAAAATGAAGCAACAGACATGAAAGGAAAAAA
CAGTATGCATCATTCTACT
Found at i:2533364 original size:308 final size:306
Alignment explanation
Indices: 2532856--2533637 Score: 1022
Period size: 308 Copynumber: 2.5 Consensus size: 306
2532846 AATAGAGAGG
* * * **
2532856 CTCAGAATGAATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTCGTAC-AGA-ATATTTGGG
1 CTCAGAATGAACTCAAGGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACAT-TTTGGG
** * * *
2532919 AAGAGGTCATGGTGTAAATTGTCAAAAGTTGTT-CATGCCATTGTTGGGGGGAGCCATTAGAAAA
65 -AGAGGTCATGGTGTAAATTACCAAAACTTTTTACAT--CATTGTTGGGGGGAGCCACTAGAAAA
** * * * *
2532983 TAAGAGTAGGTACTAAAGTTATGACTTTCATGTACCGAATATTTCTTCATATTGAATAAAACTCG
127 TAAGAACAGGTACTAAAGCTATGTCTTTCATGTACCAAATGTTTCTTCATATTGAATAAAACTCG
*
2533048 TTGTTCCAAATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATGA
192 TGGTTCCAAATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATGA
** ** *
2533113 TGAAATCACTCCCATGGTAAGACCTCAACACGAAGGTGGCAATGGAGGGC
257 TGAAATCACTCCCATGACAAGACCTCAACAAAAAGGCGGCAATGGAGGGC
* * *
2533163 CTCAGAATGAACTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTATGAGG
1 CTCAGAATGAACTCAAGGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTG-GG
*
2533228 AGAGGTCATGGTGTAAATTACCAAAATCTTTTTACATCATTGTTGGGGGGAGCCACTAGAAAGTA
65 AGAGGTCATGGTGTAAATTACCAAAA-CTTTTTACATCATTGTTGGGGGGAGCCACTAGAAAATA
* *
2533293 AGAACAGGTACTAAAGCTATGTCTTTCATATACCAAATGTTT-TATCATATTGAATAAAACTTGT
129 AGAACAGGTACTAAAGCTATGTCTTTCATGTACCAAATGTTTCT-TCATATTGAATAAAACTCGT
*
2533357 GGTTCCAAATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCATATGAT
193 GGTTCCAAATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATGAT
*
2533422 GAAATCACTCTCATGACAAGACCTCAACAAAAAGGCGGCAATGGAGGGC
258 GAAATCACTCCCATGACAAGACCTCAACAAAAAGGCGGCAATGGAGGGC
* * *
2533471 CTCAGAAAGAAGTCAAGGTTCTAATTAAAAAGAAAATAAGATTGTTTGGGCAAGACATTTTGGGA
1 CTCAGAATGAACTCAAGGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGA
* * * * * ***
2533536 GAGATCATGGTGTAAAATACCAAAAAGCTTTTTA-AGCCATTG-TGGTGGTAGGTGCTAGAAAAT
66 GAGGTCATGGTGTAAATTACC-AAAA-CTTTTTACA-TCATTGTTGGGGGGAGCCACTAGAAAAT
** *
2533599 AAGAACAAATATTAAAGC--TGTCTTTCATGTACCAAATGT
128 AAGAACAGGTACTAAAGCTATGTCTTTCATGTACCAAATGT
2533638 GAAATATAAA
Statistics
Matches: 417, Mismatches: 50, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
305 20 0.05
307 98 0.24
308 288 0.69
309 8 0.02
310 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (306 bp):
CTCAGAATGAACTCAAGGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGA
GAGGTCATGGTGTAAATTACCAAAACTTTTTACATCATTGTTGGGGGGAGCCACTAGAAAATAAG
AACAGGTACTAAAGCTATGTCTTTCATGTACCAAATGTTTCTTCATATTGAATAAAACTCGTGGT
TCCAAATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATGATGAA
ATCACTCCCATGACAAGACCTCAACAAAAAGGCGGCAATGGAGGGC
Found at i:2542633 original size:27 final size:25
Alignment explanation
Indices: 2542579--2542634 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2542569 AAGGACAAAA
* *
2542579 AAAACCCATTCTTTATAGGATGGTC
1 AAAACCCATTCTTTATAGGAAGGAC
2542604 AAAACCCATTCTTTATAGGACAAGGAC
1 AAAACCCATTCTTTATAGG--AAGGAC
2542631 AAAA
1 AAAA
2542635 ATTCATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 19 0.70
27 8 0.30
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (25 bp):
AAAACCCATTCTTTATAGGAAGGAC
Found at i:2544414 original size:101 final size:101
Alignment explanation
Indices: 2544224--2544430 Score: 308
Period size: 101 Copynumber: 2.1 Consensus size: 101
2544214 ATTTTCCATA
** * *
2544224 ATAAATTGAATGGCTAAACAAGATTTGAAAGCAGAAGCAACTCAGCTTCTAGCACCTATTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
* * *
2544289 AGTATAGATTAGGACGGAACTATAACTAAAGATGAC
66 AGGATAGACTAAGACGGAACTATAACTAAAGATGAC
* *
2544325 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTTATCTTCTAGCACATACTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
* *
2544390 AGGATAGACTAAGATGGAATTATAACTAAAGATGAC
66 AGGATAGACTAAGACGGAACTATAACTAAAGATGAC
2544426 A-AAAT
1 ATAAAT
2544431 AAAAAGACAA
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 4 0.04
101 91 0.96
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (101 bp):
ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
AGGATAGACTAAGACGGAACTATAACTAAAGATGAC
Found at i:2546126 original size:3 final size:3
Alignment explanation
Indices: 2546120--2546149 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2546110 AAGGGAAAAA
2546120 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2546150 CGAAACCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2549593 original size:56 final size:56
Alignment explanation
Indices: 2549517--2549626 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
2549507 ATGTTATAAT
*
2549517 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTATAAAATGA
1 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAATGA
*
2549573 GTAACTACTTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAAT
1 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAAT
2549627 AAGTGTGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (56 bp):
GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAATGA
Found at i:2550371 original size:23 final size:24
Alignment explanation
Indices: 2550340--2550394 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
2550330 TAGGTTAGAT
2550340 AATT-AAATAATTAGGAATAATTA-
1 AATTAAAATAATTA-GAATAATTAG
2550363 AA-TAAAATAATTAGAATAATTAG
1 AATTAAAATAATTAGAATAATTAG
2550386 AATTAAAAT
1 AATTAAAAT
2550395 TTTGGGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
AATTAAAATAATTAGAATAATTAG
Found at i:2551774 original size:15 final size:14
Alignment explanation
Indices: 2551745--2551792 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2551735 TGTTGTTTTC
*
2551745 TTAAAGCTTTTGATG
1 TTAAAGC-TTAGATG
*
2551760 TTAAATGGTTAGATG
1 TTAAA-GCTTAGATG
2551775 TT-AAGCTTAGATG
1 TTAAAGCTTAGATG
2551788 TTAAA
1 TTAAA
2551793 AATGACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 4 0.14
15 13 0.46
16 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (14 bp):
TTAAAGCTTAGATG
Found at i:2554507 original size:41 final size:41
Alignment explanation
Indices: 2554438--2554610 Score: 220
Period size: 41 Copynumber: 4.2 Consensus size: 41
2554428 TGAATGTAAG
* * * *
2554438 GGGTTGATAAGTGTAGGTTCCCCGAATCATTGATCAAAAAA
1 GGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAAAAA
* * * *
2554479 GAGTTGCTAAGTGCCGATTCCCTAAATCATAGATCAAAAAA
1 GGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAAAAA
* * * *
2554520 TGGTTGCTAAGTGCAAATTCCCCGAATCATTGATCAAAAAG
1 GGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAAAAA
* *
2554561 GGGTTGCTAAGTGCAGATTCCCCAAATTATTGATCAAAAAG
1 GGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAAAAA
2554602 GGGTTGCTA
1 GGGTTGCTA
2554611 TGTGTTGATT
Statistics
Matches: 112, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (41 bp):
GGGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAAAAA
Found at i:2554692 original size:43 final size:43
Alignment explanation
Indices: 2554639--2554836 Score: 225
Period size: 42 Copynumber: 4.7 Consensus size: 43
2554629 CGGTAACTAC
2554639 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATGGTGA-
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCAC-TGAT-GT-AT
* *
2554683 AAGG-GGTTGCTATGTGCTGATTCC-CCGTATCACTGA-ATAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGTAT
*
2554723 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGA-
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTGAT-GT-AT
* * *
2554767 AAGG-GGTTTCTATGTGTTGATTCC-CCGTATCACTGAT-TAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGTAT
*
2554807 AAGGTGGTTGCTAAGTACTGATTCCACCGT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGT
2554837 GTAATGGTTA
Statistics
Matches: 131, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
39 2 0.02
40 10 0.08
41 35 0.27
42 37 0.28
43 37 0.28
44 9 0.07
45 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (43 bp):
AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGTAT
Found at i:2554704 original size:84 final size:83
Alignment explanation
Indices: 2554598--2554836 Score: 361
Period size: 84 Copynumber: 2.8 Consensus size: 83
2554588 TATTGATCAA
* * ** *
2554598 AAAGGGGTTGCTATGTGTTGATTTCCCATATCGGTAACTACAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTAA-TATAAGGTGGTTGCTAAGTGCTGATTC
*
2554663 CACCGTATCCTTGATGGTG
65 CACCGTATCATTGATGGTG
*
2554682 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACT-AATATAAGGTGGTTGCTAAGTGCTGATTC
2554747 CACCGTATCATTGATGGTG
65 CACCGTATCATTGATGGTG
* * *
2554766 AAAGGGGTTTCTATGTGTTGATTCCCCGTATCACTGATTATAAGGTGGTTGCTAAGTACTGATTC
1 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACT-AATATAAGGTGGTTGCTAAGTGCTGATTC
2554831 CACCGT
65 CACCGT
2554837 GTAATGGTTA
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
84 141 0.99
85 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (83 bp):
AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTAATATAAGGTGGTTGCTAAGTGCTGATTCC
ACCGTATCATTGATGGTG
Found at i:2561397 original size:42 final size:42
Alignment explanation
Indices: 2561338--2561422 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
2561328 TCAATCCTCC
2561338 TAACAAAGGAGAGTCTCAATGACAAGAGTGAAGCTTTTATCA
1 TAACAAAGGAGAGTCTCAATGACAAGAGTGAAGCTTTTATCA
2561380 TAACAAAGGAGAGTCTCAATGACAAGAGTGAAGCTTTTATCA
1 TAACAAAGGAGAGTCTCAATGACAAGAGTGAAGCTTTTATCA
2561422 T
1 T
2561423 CGGAGTTGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (42 bp):
TAACAAAGGAGAGTCTCAATGACAAGAGTGAAGCTTTTATCA
Found at i:2563600 original size:101 final size:101
Alignment explanation
Indices: 2563410--2563612 Score: 316
Period size: 101 Copynumber: 2.0 Consensus size: 101
2563400 ATTTTCCATA
* * *
2563410 ATAAATTGAATGGCTAAACAAGATTCGAAAGCAGAAGCAACTCAGCTTCTAGCACCTATTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
* * *
2563475 AGTATAGATTAGGACGGAACTATAACTAAAGATGAC
66 AGGATAGACTAAGACGGAACTATAACTAAAGATGAC
* *
2563511 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTTATCTTCTAGCACATACTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
* *
2563576 AGGATAGACTAAGATGGAATTATAACTAAAGATGAC
66 AGGATAGACTAAGACGGAACTATAACTAAAGATGAC
2563612 A
1 A
2563613 AACTAAAAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (101 bp):
ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
AGGATAGACTAAGACGGAACTATAACTAAAGATGAC
Found at i:2569594 original size:15 final size:15
Alignment explanation
Indices: 2569574--2569617 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
2569564 AAGAAATTGA
2569574 AATTAAGTTTTTGGG
1 AATTAAGTTTTTGGG
2569589 AATTAA---TTTGGG
1 AATTAAGTTTTTGGG
2569601 AATTAAGTTTTTGGG
1 AATTAAGTTTTTGGG
2569616 AA
1 AA
2569618 ATAATTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.46
15 14 0.54
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (15 bp):
AATTAAGTTTTTGGG
Found at i:2569637 original size:27 final size:27
Alignment explanation
Indices: 2569572--2569638 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
2569562 TTAAGAAATT
* * *
2569572 GAAATTAAGTTTTTGGGAATTAATTTG
1 GAAAATAAGTTTTTGGGAAATAATTTA
* *
2569599 GGAATTAAGTTTTTGGGAAATAATTTA
1 GAAAATAAGTTTTTGGGAAATAATTTA
*
2569626 GAAAATATGTTTT
1 GAAAATAAGTTTT
2569639 AATTGAACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (27 bp):
GAAAATAAGTTTTTGGGAAATAATTTA
Found at i:2572407 original size:51 final size:51
Alignment explanation
Indices: 2572350--2572452 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
2572340 AAAATTCTGA
2572350 AAATTTTATGGTAAGAATATATGTGAGTCTAGTTTCAGGGAAAATTAATGG
1 AAATTTTATGGTAAGAATATATGTGAGTCTAGTTTCAGGGAAAATTAATGG
2572401 AAATTTTATGGTAAGAATATATGTGAGTCTAGTTTCAGGGAAAATTAATGG
1 AAATTTTATGGTAAGAATATATGTGAGTCTAGTTTCAGGGAAAATTAATGG
2572452 A
1 A
2572453 TCTCAATTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (51 bp):
AAATTTTATGGTAAGAATATATGTGAGTCTAGTTTCAGGGAAAATTAATGG
Found at i:2580616 original size:22 final size:22
Alignment explanation
Indices: 2580591--2580632 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2580581 ACATCGAAAT
* *
2580591 GAGGCACTGTAGTGCAAATACA
1 GAGGCACTGAAGTGAAAATACA
2580613 GAGGCACTGAAGTGAAAATA
1 GAGGCACTGAAGTGAAAATA
2580633 AAGACACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (22 bp):
GAGGCACTGAAGTGAAAATACA
Found at i:2580665 original size:20 final size:19
Alignment explanation
Indices: 2580591--2580667 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 19
2580581 ACATCGAAAT
*
2580591 GAGGCACTGTAGTGCAAATACA
1 GAGGCAC-GAAGTG-AAA-ACA
*
2580613 GAGGCACTGAAGTGAAAATA
1 GAGGCAC-GAAGTGAAAACA
* * *
2580633 AAGACACCAAAGTGAAAACA
1 GAGGCA-CGAAGTGAAAACA
2580653 GAGGCATCGAAGTGA
1 GAGGCA-CGAAGTGA
2580668 GATCCAGTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 27 0.61
21 4 0.09
22 13 0.30
ACGTcount: A:0.44, C:0.16, G:0.27, T:0.13
Consensus pattern (19 bp):
GAGGCACGAAGTGAAAACA
Found at i:2585418 original size:21 final size:21
Alignment explanation
Indices: 2585370--2585418 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2585360 GTTTCGTTTG
*
2585370 TTATTCTGTTTCTTTTCTTCT
1 TTATTTTGTTTCTTTTCTTCT
* *
2585391 ATCTTTTGTTTC-TTTCTTTCT
1 TTATTTTGTTTCTTTTC-TTCT
2585412 TTATTTT
1 TTATTTT
2585419 ACTTACTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.73
Consensus pattern (21 bp):
TTATTTTGTTTCTTTTCTTCT
Found at i:2590188 original size:23 final size:22
Alignment explanation
Indices: 2590162--2590225 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 22
2590152 CGAAGGGTGT
2590162 TACAATTTATAAGTATTTATTTA
1 TACAATTTATAAGTATTT-TTTA
2590185 TACACATATTA-AA-TATTTTTTA
1 TACA-AT-TTATAAGTATTTTTTA
2590207 T---ATTTATAAGTATTTTTTA
1 TACAATTTATAAGTATTTTTTA
2590226 CATATATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 9 0.24
22 5 0.14
23 9 0.24
24 4 0.11
25 3 0.08
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (22 bp):
TACAATTTATAAGTATTTTTTA
Found at i:2590242 original size:19 final size:19
Alignment explanation
Indices: 2590179--2590244 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
2590169 TATAAGTATT
* *
2590179 TATTTATACACATATTAAA
1 TATTTTTACATATATTAAA
*
2590198 TATTTTT-TATAT-TTATAA
1 TATTTTTACATATATTA-AA
2590216 GTATTTTTTACATATATTAAA
1 -TA-TTTTTACATATATTAAA
2590237 TATTTTTA
1 TATTTTTA
2590245 AAAATATCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.08
18 5 0.13
19 14 0.37
20 7 0.18
21 6 0.16
22 3 0.08
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTTTTACATATATTAAA
Found at i:2590242 original size:39 final size:42
Alignment explanation
Indices: 2590166--2590243 Score: 126
Period size: 39 Copynumber: 1.9 Consensus size: 42
2590156 GGGTGTTACA
2590166 ATTTATAAGTATTTATTTATACACATATTAAATATTTTTTAT
1 ATTTATAAGTATTTATTTATACACATATTAAATATTTTTTAT
*
2590208 ATTTATAAGTA-TT-TTT-TACATATATTAAATATTTTT
1 ATTTATAAGTATTTATTTATACACATATTAAATATTTTT
2590244 AAAAATATCG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 19 0.54
40 3 0.09
41 2 0.06
42 11 0.31
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (42 bp):
ATTTATAAGTATTTATTTATACACATATTAAATATTTTTTAT
Found at i:2590251 original size:19 final size:19
Alignment explanation
Indices: 2590190--2590251 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
2590180 ATTTATACAC
*
2590190 ATATTAAATATTTTT-TAT
1 ATATTAAATATTTTTAAAT
*
2590208 AT-TTATAAGTATTTTTTACAT
1 ATATTA-AA-TA-TTTTTAAAT
*
2590229 ATATTAAATATTTTTAAAA
1 ATATTAAATATTTTTAAAT
2590248 ATAT
1 ATAT
2590252 CGGTTAGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 13 0.36
20 7 0.19
21 6 0.17
22 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
ATATTAAATATTTTTAAAT
Found at i:2592375 original size:16 final size:17
Alignment explanation
Indices: 2592344--2592381 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2592334 GCGTTTCTTC
*
2592344 TTCTTCCATTTCTTTGT
1 TTCTTCCATCTCTTTGT
2592361 TTCTTCCA-CTCTTTGT
1 TTCTTCCATCTCTTTGT
2592377 TTCTT
1 TTCTT
2592382 TCCGACGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.05, C:0.26, G:0.05, T:0.63
Consensus pattern (17 bp):
TTCTTCCATCTCTTTGT
Found at i:2600627 original size:5 final size:5
Alignment explanation
Indices: 2600608--2600642 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
2600598 TCATATTATT
*
2600608 GTATCC GTATT GTATC GTATC GTATC GTATC GTAT
1 GTAT-C GTATC GTATC GTATC GTATC GTATC GTAT
2600643 ATTTATTACG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (5 bp):
GTATC
Found at i:2603800 original size:18 final size:18
Alignment explanation
Indices: 2603779--2603821 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2603769 TATTCATCTA
**
2603779 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
2603797 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
2603815 AACCCAA
1 AACCCAA
2603822 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:2604001 original size:9 final size:9
Alignment explanation
Indices: 2603925--2604000 Score: 109
Period size: 9 Copynumber: 8.4 Consensus size: 9
2603915 GTAGTGATTC
*
2603925 AATTTGGTT
1 AATTCGGTT
2603934 AATTCGGTT
1 AATTCGGTT
*
2603943 AATTCGGGT
1 AATTCGGTT
2603952 AATTCGGTT
1 AATTCGGTT
2603961 AATTCGAG-T
1 AATTCG-GTT
2603970 AATTCGGTT
1 AATTCGGTT
2603979 AATTCGGTT
1 AATTCGGTT
*
2603988 AATTTGGTT
1 AATTCGGTT
2603997 AATT
1 AATT
2604001 TTCAACCAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
8 1 0.02
9 59 0.97
10 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:2606046 original size:18 final size:19
Alignment explanation
Indices: 2606023--2606059 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2606013 ATTGAATTTT
*
2606023 AATT-AATATAAATAAACA
1 AATTAAATATAAAAAAACA
2606041 AATTAAATATAAAAAAACA
1 AATTAAATATAAAAAAACA
2606060 TATAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AATTAAATATAAAAAAACA
Found at i:2606067 original size:19 final size:19
Alignment explanation
Indices: 2606027--2606067 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2606017 AATTTTAATT
* *
2606027 AATATAAATAAACAAATTA
1 AATATAAAAAAACAAATAA
*
2606046 AATATAAAAAAACATATAA
1 AATATAAAAAAACAAATAA
2606065 AAT
1 AAT
2606068 GATTTTGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AATATAAAAAAACAAATAA
Found at i:2606427 original size:113 final size:112
Alignment explanation
Indices: 2606166--2606815 Score: 527
Period size: 113 Copynumber: 5.8 Consensus size: 112
2606156 TCGGGAAAAG
* * * ** * *
2606166 CGCCGCTAATACTATGCTTTAGCGGCATTTTCCCGTGTGCGCCACTAATTCCAGTATACATCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATCAAG
* * * * * * * *
2606231 AACTAAACGCTGTGTTTTCGTTAATAT-CTTTTGGCGGCACTTACCAAAAA
65 ATC-AAACTCTGCGTTTTGGTTAAGATAC-TTT-GCGGCGCTTTCCACAAA
* ** * *
2606281 GCGCCGC-AA-GC---A--TTAGCGGCGTTTTGAAATAAGCGCCACTAACTCTAATATACCTCAA
1 -CGCCGCTAATACTATACTTTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATCAA
2606339 GGA-CAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCACAAA
64 -GATCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCACAAA
* * * *
2606388 TGCCGCTACTACTGTACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAAG
* * *
2606453 ATCAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
65 ATCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCA-CAAA
* * * * * * * *
2606502 CGCTGCTATTACTATGCTTTAGCGGCGTTTTCCTTAAACGCCACTGATTATAGTATACATCAAGA
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
* * * *
2606567 TCAAAACGT-TGCGTTTTGGTTAAGATATTTTGCTGCG-TTTAACGCTC-AG
66 TC-AAAC-TCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTT--C-CACAAA
* * ** *
2606616 CGCCGCTAATACTATACATTAGCGGCATTTTCTTTGCAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCCAT--AAGCGCCACTAATTCTAATATACATCAA
* * * *
2606681 GACCAAACTCTGCGTTTTGGTTAACAT-CTTTTGCAGCGC-TTCCGCTAAA
64 GATCAAACTCTGCGTTTTGGTTAAGATAC-TTTGCGGCGCTTTCCAC-AAA
* * * *
2606730 CGCCGCTAATACTATGCGTTAGCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTT-TCCATAAGCGCCACTAATTCTAATATACATCAAG
* * *
2606795 ACCAGAACGCTGCGTGTTGGT
65 ATCA-AACTCTGCGTTTTGGT
2606816 CTTGAGATTT
Statistics
Matches: 438, Mismatches: 70, Indels: 54
0.78 0.12 0.10
Matches are distributed among these distances:
106 5 0.01
107 15 0.03
108 23 0.05
109 37 0.08
110 2 0.00
111 1 0.00
112 4 0.01
113 144 0.33
114 136 0.31
115 37 0.08
116 34 0.08
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (112 bp):
CGCCGCTAATACTATACTTTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
TCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCACAAA
Found at i:2606592 original size:114 final size:114
Alignment explanation
Indices: 2606166--2606815 Score: 524
Period size: 114 Copynumber: 5.7 Consensus size: 114
2606156 TCGGGAAAAG
* * * ** * *
2606166 CGCCGCTAATACTATGCTTTAGCGGCATTTTCCCGTGTGCGCCACTAATTCCAGTATACATCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTTT-CCTTAAGCGCCACTAATTCTAATATACATCAAG
* * * * * * * * * *
2606231 AACTAAACGCTGTGTTTTCGTTAATATCTTTTGGCGGCACTTACCA-AAAA
65 ATCAAAACTCTGCGTTTTGGTTAAGATATTTT-GAGGCGCTTACCACCAAA
* *** * *
2606281 GCGCCGC-AA-GC---A--TTAGCGGCGTTTTGAAATAAGCGCCACTAACTCTAATATACCTCAA
1 -CGCCGCTAATACTATACTTTAGCGGCGTTTT-CCTTAAGCGCCACTAATTCTAATATACATCAA
* * *
2606339 GGA-C-AAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCA-CAAA
64 -GATCAAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
* * * * *
2606388 TGCCGCTACTACTGTACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCC-TTAAGCGCCACTAATTCTAATATACATCAAG
2606453 ATC-AAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
65 ATCAAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
* * * * * * *
2606502 CGCTGCTATTACTATGCTTTAGCGGCGTTTTCCTTAAACGCCACTGATTATAGTATACATCAAGA
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCCTTAAGCGCCACTAATTCTAATATACATCAAGA
** * * * *
2606567 TCAAAACGT-TGCGTTTTGGTTAAGATATTTTGCTGCGTTTAACGCTC-AG
66 TCAAAAC-TCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCAC-CAAA
* * * *
2606616 CGCCGCTAATACTATACATTAGCGGCATTTTCTTTGCAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCCTT--AAGCGCCACTAATTCTAATATACATCAA
* * * * *
2606681 GA-CCAAACTCTGCGTTTTGGTTAACATCTTTTGCA-GCGCTT-CCGCTAAA
64 GATCAAAACTCTGCGTTTTGGTTAAGATATTTTG-AGGCGCTTACCACCAAA
* * * *
2606730 CGCCGCTAATACTATGCGTTAGCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTT-TCCTTAAGCGCCACTAATTCTAATATACATCAAG
* * * *
2606795 ACCAGAACGCTGCGTGTTGGT
65 ATCAAAACTCTGCGTTTTGGT
2606816 CTTGAGATTT
Statistics
Matches: 436, Mismatches: 77, Indels: 44
0.78 0.14 0.08
Matches are distributed among these distances:
106 5 0.01
107 15 0.03
108 23 0.05
109 36 0.08
110 2 0.00
111 1 0.00
112 2 0.00
113 138 0.32
114 145 0.33
115 37 0.08
116 32 0.07
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (114 bp):
CGCCGCTAATACTATACTTTAGCGGCGTTTTCCTTAAGCGCCACTAATTCTAATATACATCAAGA
TCAAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAA
Found at i:2606891 original size:229 final size:229
Alignment explanation
Indices: 2606389--2606815 Score: 502
Period size: 229 Copynumber: 1.9 Consensus size: 229
2606379 TTCCACAAAT
* * * * * *
2606389 GCCGCTACTACTGTACTTTAGCGGCGTTTTC-CA-ATAAGCGCCACTAATTCTAATATACCTCAA
1 GCCGCTAATACTATACATTAGCGGCATTTTCTCAGA-AAACGCCACTAATTCTAATATACATCAA
* * * *
2606452 GATCAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAACGCTGCTATTACTAT
65 GACCAAACTCTGCGTTTTGGTTAACATATTTTGAGGCGCTTACCACCAAACGCCGCTAATACTAT
* * * * * * *
2606517 GCTTTAGCGGCGTTTTCCTTAAACGCCACTGATTATAGTATACATCAAGATCAAAACGTTGCGTT
130 GCGTTAGCGGCGTTTTCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTGCGTG
* * * *
2606582 TTGGTTAAGATATTTTGCTGCGTTTAACGCTCAGC
195 TTGGTTAAGAGATTTTGCTGCGTGTAACGCTAAAC
** * * *
2606617 GCCGCTAATACTATACATTAGCGGCATTTTCTTTGCAAGCGCCACTAATTGTAATATACATCAAG
1 GCCGCTAATACTATACATTAGCGGCATTTTCTCAGAAAACGCCACTAATTCTAATATACATCAAG
* * *
2606682 ACCAAACTCTGCGTTTTGGTTAACATCTTTTGCA-GCGCTT-CCGCTAAACGCCGCTAATACTAT
66 ACCAAACTCTGCGTTTTGGTTAACATATTTTG-AGGCGCTTACCACCAAACGCCGCTAATACTAT
* * * *
2606745 GCGTTAGCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAGACCAGAACGCTGCGT
130 GCGTTAGCGGCGTTT-TCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTGCGT
2606810 GTTGGT
194 GTTGGT
2606816 CTTGAGATTT
Statistics
Matches: 168, Mismatches: 27, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
228 60 0.36
229 107 0.64
230 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (229 bp):
GCCGCTAATACTATACATTAGCGGCATTTTCTCAGAAAACGCCACTAATTCTAATATACATCAAG
ACCAAACTCTGCGTTTTGGTTAACATATTTTGAGGCGCTTACCACCAAACGCCGCTAATACTATG
CGTTAGCGGCGTTTTCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTGCGTGT
TGGTTAAGAGATTTTGCTGCGTGTAACGCTAAAC
Found at i:2606955 original size:40 final size:40
Alignment explanation
Indices: 2606908--2606996 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
2606898 CCAGCTTTTT
2606908 GCGGCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTA
1 GCGGCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTA
***** * * *
2606948 GCGGCGTTTTATTCTTAGCGTCGCTAATGCTCGATTTTTA
1 GCGGCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTA
2606988 GCGGCGTTT
1 GCGGCGTTT
2606997 GTAATCCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (40 bp):
GCGGCGTTTTAAAAGAAGCGCCGCTAATGCTAGATCTTTA
Found at i:2608759 original size:14 final size:15
Alignment explanation
Indices: 2608740--2608782 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2608730 TTAGCCCAAT
2608740 ATTTTATTTATTAA-
1 ATTTTATTTATTAAC
*
2608754 ATTTTATATTTTTAAC
1 ATTTTAT-TTATTAAC
2608770 A-TTTATTTATTAA
1 ATTTTATTTATTAA
2608783 GTTTAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.52
15 11 0.44
16 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTATTTATTAAC
Found at i:2610532 original size:26 final size:27
Alignment explanation
Indices: 2610496--2610550 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
2610486 ATAAAAATTA
2610496 ACCAAAATATTA-TATTTTTT-TTATTT
1 ACCAAAATATTACT-TTTTTTATTATTT
2610522 ACCAAAATATTACTTTTTTTATTATTT
1 ACCAAAATATTACTTTTTTTATTATTT
2610549 AC
1 AC
2610551 GATAATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.55
Consensus pattern (27 bp):
ACCAAAATATTACTTTTTTTATTATTT
Found at i:2610543 original size:24 final size:26
Alignment explanation
Indices: 2610496--2610544 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
2610486 ATAAAAATTA
*
2610496 ACCAAAATATTATATTTTTTTTATTT
1 ACCAAAATATTATACTTTTTTTATTT
2610522 ACCAAAATA-T-TACTTTTTTTATT
1 ACCAAAATATTATACTTTTTTTATT
2610545 ATTTACGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 1 0.05
26 9 0.41
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (26 bp):
ACCAAAATATTATACTTTTTTTATTT
Found at i:2610648 original size:27 final size:27
Alignment explanation
Indices: 2610618--2610669 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2610608 GGCCAATCAC
* *
2610618 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGCCACCAAAGGGGCCAAAGAG
* *
2610645 ATTGGTGCCACCAATGGGGCCAAAG
1 ATTGGCGCCACCAAAGGGGCCAAAG
2610670 GACTAAAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (27 bp):
ATTGGCGCCACCAAAGGGGCCAAAGAG
Found at i:2610770 original size:19 final size:19
Alignment explanation
Indices: 2610743--2610812 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2610733 TCAACTCATT
*
2610743 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2610762 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2610780 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2610799 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2610813 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2610793 original size:37 final size:37
Alignment explanation
Indices: 2610748--2610818 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2610738 TCATTTTTTT
2610748 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2610785 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2610819 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2611173 original size:37 final size:37
Alignment explanation
Indices: 2611126--2611196 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
2611116 AGTATTACTT
*
2611126 AATATTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
2611163 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
2611197 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:2611201 original size:19 final size:19
Alignment explanation
Indices: 2611132--2611200 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2611122 ACTTAATATT
2611132 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
2611151 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
2611169 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
2611188 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
2611201 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:2611305 original size:27 final size:27
Alignment explanation
Indices: 2611275--2611326 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2611265 CATTTTAGTC
2611275 CTTTGGCACCATTGGTGCCACCAATCT
1 CTTTGGCACCATTGGTGCCACCAATCT
* *
2611302 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCACCAAT
2611327 GTGATTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCACCAATCT
Found at i:2611334 original size:27 final size:27
Alignment explanation
Indices: 2611277--2611335 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
2611267 TTTTAGTCCT
*
2611277 TTGGCACCATTGGTGCCACCAATCTCT
1 TTGGCACCATTGGTGCCACCAATCTCA
* * * *
2611304 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCACCAATCTCA
2611331 TTGGC
1 TTGGC
2611336 CTGATCAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCACCAATCTCA
Found at i:2611378 original size:10 final size:10
Alignment explanation
Indices: 2611364--2611394 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2611354 GCTTTTTACA
2611364 GGTTTTTTTT
1 GGTTTTTTTT
*
2611374 TGTTTTTTTT
1 GGTTTTTTTT
2611384 GGTTTTTTTT
1 GGTTTTTTTT
2611394 G
1 G
2611395 TATATTTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (10 bp):
GGTTTTTTTT
Found at i:2611455 original size:26 final size:26
Alignment explanation
Indices: 2611396--2611457 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
2611386 TTTTTTTTGT
*
2611396 ATATTTTCGTAAATAATAAAAAAATA
1 ATATTTTGGTAAATAATAAAAAAATA
*
2611422 ATATTTTGGTAAATAA-AAAAATTATA
1 ATATTTTGGTAAATAATAAAAA-AATA
2611448 ATATTTTGGT
1 ATATTTTGGT
2611458 TAATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (26 bp):
ATATTTTGGTAAATAATAAAAAAATA
Found at i:2617065 original size:18 final size:19
Alignment explanation
Indices: 2617039--2617078 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
2617029 ACATTTAATT
*
2617039 AATTTAAAAAAAAT-TAAA
1 AATTCAAAAAAAATATAAA
2617057 AATTCAAAAAAAATATAAA
1 AATTCAAAAAAAATATAAA
2617076 AAT
1 AAT
2617079 CATTAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AATTCAAAAAAAATATAAA
Found at i:2623577 original size:31 final size:31
Alignment explanation
Indices: 2623542--2623600 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
2623532 AGGTGTATAA
*
2623542 TTAAATCAAAATTAAAATTTTAAGTATACAT
1 TTAAACCAAAATTAAAATTTTAAGTATACAT
* * * *
2623573 TTAAACCACAATTAGAGTTTTATGTATA
1 TTAAACCAAAATTAAAATTTTAAGTATA
2623601 TAATTGAACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (31 bp):
TTAAACCAAAATTAAAATTTTAAGTATACAT
Found at i:2632036 original size:90 final size:90
Alignment explanation
Indices: 2631883--2632058 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 90
2631873 GAGTTGAGGT
* * * *
2631883 TACAAAATTAATGCGACGAATAACATGTAACTCATAAATGATAAGTTTTGAATGGTCGTTTCCAT
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
2631948 CCAACATACGTTGCTTTTGTAGTCC
66 CCAACATACGTTGCTTTTGTAGTCC
* *
2631973 TACAAAATTAATGCAACAAATAACATATAACTCGTAAATGATAAGTTCTGAATGGTCTTTTCCAT
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
*
2632038 CCAACATATGTTGCTTTTGTA
66 CCAACATACGTTGCTTTTGTA
2632059 ATCCAGGTAC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (90 bp):
TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
CCAACATACGTTGCTTTTGTAGTCC
Found at i:2632221 original size:10 final size:10
Alignment explanation
Indices: 2632206--2632241 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2632196 TGTTTATCAA
2632206 TCTCTCCCTC
1 TCTCTCCCTC
2632216 TCTCTCCCTC
1 TCTCTCCCTC
2632226 TCTC-CCTCTC
1 TCTCTCC-CTC
2632236 TCTCTC
1 TCTCTC
2632242 ACTTACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 2 0.08
10 21 0.88
11 1 0.04
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (10 bp):
TCTCTCCCTC
Found at i:2633148 original size:33 final size:34
Alignment explanation
Indices: 2633053--2633149 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 34
2633043 TTAATATTTT
*
2633053 AATATATGAAATATAAATTTTAAATACTTT--TTAGC
1 AATATAT-AAAT-TATATTTTAAATA-TTTAATTAGC
* *
2633088 AATAAATATTAATTAT-TTATAAA-ATTTAATTAG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAGC
2633121 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
2633150 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 9 0.18
33 10 0.20
34 10 0.20
35 5 0.10
36 3 0.06
37 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (34 bp):
AATATATAAATTATATTTTAAATATTTAATTAGC
Found at i:2636279 original size:48 final size:48
Alignment explanation
Indices: 2636203--2636618 Score: 226
Period size: 49 Copynumber: 8.6 Consensus size: 48
2636193 CAAAAAAATT
* * *
2636203 AAAAAAAA-TTTGGGTGCTGGCC-TGTCAATGGCCAGTACCAGTATACG
1 AAAAAAAATTTTGGGTG-TTGCCTTGTCAATGGCCGGAACCAGTATACG
*
2636250 AAAAAAAATTTTGGGTGTTGCCTTCTCAATGGCCGGAACCAGTATACG
1 AAAAAAAATTTTGGGTGTTGCCTTGTCAATGGCCGGAACCAGTATACG
* * * * **
2636298 -AAAAAAATTTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCAATACG
1 AAAAAAAATTTTGGGTGTTGCCTTGTCAATGGCCGGAACCA-GTATACG
* * * * * * **
2636346 AAAAAAAAATTTGGGTGCTGGAC-TATCAATAGCCGGCACCAACAGTACG
1 AAAAAAAATTTTGGGTG-TTGCCTTGTCAATGGCCGGAACCAGTA-TACG
* * **
2636395 AAAAAAAA-TTT-GCTG--GCC-TGTCAATGGCCGGCACCACCAGTACG
1 AAAAAAAATTTTGGGTGTTGCCTTGTCAATGGCCGGAACCAGTA-TACG
* * * * * *
2636439 AAAAAAAATTTTGGGTGCTGGCC-TGTCAATGGTCGGCACCAGCAGTGCA
1 AAAAAAAATTTTGGGTG-TTGCCTTGTCAATGGCCGGAACCAGTA-TACG
* * * ** * * *
2636488 AAAAAAAATGTTGGGGTGCTGGCTTGTCAATGGTAGGCACCAGCAATACAAA
1 AAAAAAAAT-TTTGGGTGTTGCCTTGTCAATGGCCGGAACCAG-TATAC--G
* * * * * *
2636540 AAATAAAAATTTTGGGTGCTGGCC-TGTCAATGGCTGGCACTAGTAGATG
1 AAA-AAAAATTTTGGGTG-TTGCCTTGTCAATGGCCGGAACCAGTATACG
* *
2636589 AAAAAAAAATTTGGGTGCTGGCC-TGTCAAT
1 AAAAAAAATTTTGGGTG-TTGCCTTGTCAAT
2636619 AGTCAGCACC
Statistics
Matches: 302, Mismatches: 49, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
44 33 0.11
45 3 0.01
46 3 0.01
47 50 0.17
48 65 0.22
49 81 0.27
50 29 0.10
51 3 0.01
52 27 0.09
53 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (48 bp):
AAAAAAAATTTTGGGTGTTGCCTTGTCAATGGCCGGAACCAGTATACG
Found at i:2636361 original size:49 final size:49
Alignment explanation
Indices: 2636203--2636657 Score: 404
Period size: 48 Copynumber: 9.4 Consensus size: 49
2636193 CAAAAAAATT
** * *
2636203 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCAGTACCAG-TATACGA
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCTGGCACCAGCAATACGA
* * * * * *
2636251 AAAAAAATTTTGGGTG-TTGCCTTCTCAATGGCCGGAACCAG-TATACG-
1 AAAAAAAATTTGGGTGCTGGCC-TGTCAATGGCTGGCACCAGCAATACGA
* * *
2636298 AAAAAAATTTTGGGTGCTGGCTTGTCAATGGCTGGCACCACCAATACGA
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCTGGCACCAGCAATACGA
* * * * * *
2636347 AAAAAAAATTTGGGTGCTGGACTATCAATAGCCGGCACCAACAGTACG-
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCTGGCACCAGCAATACGA
* * *
2636395 AAAAAAAA-TT---TGCTGGCCTGTCAATGGCCGGCACCACCAGTACGA
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCTGGCACCAGCAATACGA
* * *
2636440 AAAAAAATTTTGGGTGCTGGCCTGTCAATGG-TCGGCACCAGCAGTGC-A
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCT-GGCACCAGCAATACGA
* *
2636488 AAAAAAAATGTTGGGGTGCTGGCTTGTCAATGG-TAGGCACCAGCAATACAAA
1 AAAAAAAAT-TT-GGGTGCTGGCCTGTCAATGGCT-GGCACCAGCAATAC-GA
* *
2636540 AAATAAAAATTTTGGGTGCTGGCCTGTCAATGGCTGGCACTAGTAGAT--GA
1 AAA-AAAAA-TTTGGGTGCTGGCCTGTCAATGGCTGGCACCAGCA-ATACGA
* * * *
2636590 AAAAAAAATTTGGGTGCTGGCCTGTCAATAG-TCAGCACCAGC-GTA-TA
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCT-GGCACCAGCAATACGA
2636637 AAAAAAAATTTGGGTGCTGGC
1 AAAAAAAATTTGGGTGCTGGC
2636658 AATTTATCAA
Statistics
Matches: 344, Mismatches: 43, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
44 30 0.09
45 7 0.02
46 3 0.01
47 60 0.17
48 90 0.26
49 76 0.22
50 36 0.10
52 31 0.09
53 10 0.03
54 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (49 bp):
AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCTGGCACCAGCAATACGA
Found at i:2636645 original size:102 final size:102
Alignment explanation
Indices: 2636298--2636643 Score: 280
Period size: 93 Copynumber: 3.5 Consensus size: 102
2636288 CCAGTATACG
* * * * **
2636298 AAAAAAAT-TTTGGGTGCTGGCTTGTCAATGGCT-GGCACCACCAAT-ACGAAAA-AAAAA-TTT
1 AAAAAAATGTTGGGGTGCTGGCCTGTCAATAG-TAGGCACCAGCAATAAAAAAAATAAAAATTTT
* * * * * * *
2636358 GGGTGCTGGACTATCAATAGCCGGCACCAACAGTACGA
65 GGGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTGCAA
* ** * * **
2636396 AAAAAAA--TT----TGCTGGCCTGTCAATGGCCGGCACCACCAGT--ACGAAA-AAAAATTTTG
1 AAAAAAATGTTGGGGTGCTGGCCTGTCAATAGTAGGCACCAGCAATAAAAAAAATAAAAATTTTG
2636452 GGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTGCAA
66 GGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTGCAA
* * *
2636489 AAAAAAATGTTGGGGTGCTGGCTTGTCAATGGTAGGCACCAGCAATACAAAAAATAAAAATTTTG
1 AAAAAAATGTTGGGGTGCTGGCCTGTCAATAGTAGGCACCAGCAATAAAAAAAATAAAAATTTTG
* *
2636554 GGTGCTGGCCTGTCAATGG-CTGGCACTAGTAGATG-AA
66 GGTGCTGGCCTGTCAATGGTC-GGCACCAGCAG-TGCAA
*
2636591 AAAAAAAT-TT-GGGTGCTGGCCTGTCAATAGTCA-GCACCAGCGTATAAAAAAAA
1 AAAAAAATGTTGGGGTGCTGGCCTGTCAATAGT-AGGCACCAGC-AATAAAAAAAA
2636644 ATTTGGGTGC
Statistics
Matches: 207, Mismatches: 26, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
92 8 0.04
93 68 0.33
95 2 0.01
97 2 0.01
98 7 0.03
99 26 0.13
100 27 0.13
101 17 0.08
102 48 0.23
103 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (102 bp):
AAAAAAATGTTGGGGTGCTGGCCTGTCAATAGTAGGCACCAGCAATAAAAAAAATAAAAATTTTG
GGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTGCAA
Found at i:2639615 original size:27 final size:26
Alignment explanation
Indices: 2639588--2639667 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
2639578 AGAGAAAAAT
2639588 TTTTGAATTGAAAATAGAAAATTTAA
1 TTTTGAATTGAAAATAGAAAATTTAA
* * * **
2639614 TTATAAAATG-AAATGAGAAAAAAATAA
1 TTTTGAATTGAAAAT-AG-AAAATTTAA
* *
2639641 ATTTGCATTGAAAATAGAAAATTTAA
1 TTTTGAATTGAAAATAGAAAATTTAA
2639667 T
1 T
2639668 GAAATACGGA
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
25 4 0.11
26 16 0.42
27 14 0.37
28 4 0.11
ACGTcount: A:0.55, C:0.01, G:0.11, T:0.33
Consensus pattern (26 bp):
TTTTGAATTGAAAATAGAAAATTTAA
Found at i:2639717 original size:16 final size:16
Alignment explanation
Indices: 2639696--2639726 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2639686 AATTTAAATT
2639696 AAAAAAATAAATTGAG
1 AAAAAAATAAATTGAG
2639712 AAAAAAATAAATTGA
1 AAAAAAATAAATTGA
2639727 AATTGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAAAAAATAAATTGAG
Found at i:2640064 original size:14 final size:14
Alignment explanation
Indices: 2640028--2640063 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
2640018 AAATAATAAA
2640028 TAAATGAAAATATT
1 TAAATGAAAATATT
2640042 TAAAT-AAAATA-T
1 TAAATGAAAATATT
2640054 TAAATGAAAA
1 TAAATGAAAA
2640064 AAAGTGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (14 bp):
TAAATGAAAATATT
Found at i:2643653 original size:54 final size:48
Alignment explanation
Indices: 2643576--2643829 Score: 280
Period size: 49 Copynumber: 5.1 Consensus size: 48
2643566 TCAGCACCTA
*
2643576 TTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCTA-CACCCAAAAATTT
1 TTTTTTTTCGTA-TACTGGTGCCGGCCATTGACAGGCC-AGCACCC--AAA--T
*
2643629 TTTGTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCTAGCACCCAAAT
1 TTT-TTTTTCGTA-TACTGGTGCCGGCCATTGACAGGCCAGCACCCAAAT
** * * *
2643679 TTTTTTTTCGTATTGGTGGTGCCAGCTATTGACAGGCCAGCACCTAAATT
1 TTTTTTTTCGTA-TACTGGTGCCGGCCATTGACAGGCCAGCACCCAAA-T
* * *
2643729 TTTTTTTTCGTATACTGCTGCCGGCCATTGACAAGACAGCACCCAAAT
1 TTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAGCACCCAAAT
* * *
2643777 TTTTTTTT-GTATACTGGTGCTGGCCATTGACAGGCTAGCA-CCTAAT
1 TTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAGCACCCAAAT
2643823 TTTTTTT
1 TTTTTTT
2643830 ATTTTTTTTT
Statistics
Matches: 175, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
46 12 0.07
47 27 0.15
48 9 0.05
49 65 0.37
50 17 0.10
52 3 0.02
53 4 0.02
54 38 0.22
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (48 bp):
TTTTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAGCACCCAAAT
Found at i:2643781 original size:98 final size:98
Alignment explanation
Indices: 2643576--2643829 Score: 320
Period size: 98 Copynumber: 2.6 Consensus size: 98
2643566 TCAGCACCTA
*
2643576 TTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCTA-CACCCAAAAATTTTTTGTTTTTCG
1 TTTTTTTTCGTA-TGCTGGTGCCGGCCATTGACAGGCC-AGCA-CC-TAAA-TTTTT-TTTTTCG
* *
2643640 TACTACTGGTGCCGGCCATTGACAGGCTAGCACCCAAAT
60 TACTACTGCTGCCGGCCATTGACAGACTAGCACCCAAAT
* * *
2643679 TTTTTTTTCGTATTGGTGGTGCCAGCTATTGACAGGCCAGCACCTAAATTTTTTTTTTCGTA-TA
1 TTTTTTTTCGTA-TGCTGGTGCCGGCCATTGACAGGCCAGCACCTAAATTTTTTTTTTCGTACTA
2643743 CTGCTGCCGGCCATTGACAAGAC-AGCACCCAAAT
65 CTGCTGCCGGCCATTGAC-AGACTAGCACCCAAAT
* * *
2643777 TTTTTTTT-GTATACTGGTGCTGGCCATTGACAGGCTAGCACCT-AATTTTTTTT
1 TTTTTTTTCGTATGCTGGTGCCGGCCATTGACAGGCCAGCACCTAAATTTTTTTT
2643830 ATTTTTTTTT
Statistics
Matches: 136, Mismatches: 13, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
95 10 0.07
96 26 0.19
97 3 0.02
98 38 0.28
99 12 0.09
100 5 0.04
101 3 0.02
102 3 0.02
103 36 0.26
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (98 bp):
TTTTTTTTCGTATGCTGGTGCCGGCCATTGACAGGCCAGCACCTAAATTTTTTTTTTCGTACTAC
TGCTGCCGGCCATTGACAGACTAGCACCCAAAT
Found at i:2650449 original size:31 final size:33
Alignment explanation
Indices: 2650414--2650484 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 33
2650404 ATTTGATTTT
2650414 TTTTAGATAATATTTAATTATTT-A-A-TTATTA
1 TTTTAGATAATA-TTAATTATTTAATATTTATTA
* * *
2650445 TTTTATGTTGATATTAATTCTTTAATATTTATTA
1 TTTTA-GATAATATTAATTATTTAATATTTATTA
2650479 TTTTAG
1 TTTTAG
2650485 TTTTGTGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 14 0.42
32 6 0.18
33 2 0.06
34 11 0.33
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (33 bp):
TTTTAGATAATATTAATTATTTAATATTTATTA
Found at i:2651650 original size:60 final size:59
Alignment explanation
Indices: 2651505--2651651 Score: 170
Period size: 60 Copynumber: 2.5 Consensus size: 59
2651495 ATAAAGACAA
* * * * *
2651505 CATTGGAGAGTTCATTGTATATCTACCCTTATGGAGTTCACTCACTGATACGAACCCCTT
1 CATTGGAGAGTTCATTATATATCTATCATTACGGAGTTAACTCACTGATAC-AACCCCTT
** * *
2651565 CATTGGAGAGTTCATTATGCATCTATTATTACGGAGTTAACTCACTCAGGTA-AACCCCTT
1 CATTGGAGAGTTCATTATATATCTATCATTACGGAGTTAACTCACT--GATACAACCCCTT
*
2651625 CATTGAAGAGTTCATTATATATCTATC
1 CATTGGAGAGTTCATTATATATCTATC
2651652 TCATTTATTC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
60 69 0.96
62 3 0.04
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (59 bp):
CATTGGAGAGTTCATTATATATCTATCATTACGGAGTTAACTCACTGATACAACCCCTT
Found at i:2654361 original size:23 final size:23
Alignment explanation
Indices: 2654319--2654364 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2654309 CTTTCTTAAT
*
2654319 GTAGTAATTTTCGAGGTATTACA
1 GTAGTAATTTTCGAGATATTACA
2654342 GTAGTAATTTTCG-GAATATTACA
1 GTAGTAATTTTCGAG-ATATTACA
2654365 ATATATATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (23 bp):
GTAGTAATTTTCGAGATATTACA
Found at i:2658756 original size:20 final size:20
Alignment explanation
Indices: 2658728--2658765 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2658718 TATTTTCCAA
*
2658728 TAAATCATTTTACAGAAAAG
1 TAAAACATTTTACAGAAAAG
*
2658748 TAAAACATTTTCCAGAAA
1 TAAAACATTTTACAGAAA
2658766 TCATTTTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (20 bp):
TAAAACATTTTACAGAAAAG
Found at i:2658770 original size:34 final size:35
Alignment explanation
Indices: 2658714--2658780 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2658704 CAAACACCAG
* *
2658714 AAAATATTTTCCAATAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAAGAAATCATTTTACAGAAAAGT
*
2658749 AAAACATTTTCC-AGAAATCATTTTACGGAAAA
1 AAAACATTTTCCAAGAAATCATTTTACAGAAAA
2658781 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAAGAAATCATTTTACAGAAAAGT
Found at i:2660210 original size:11 final size:11
Alignment explanation
Indices: 2660194--2660236 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
2660184 ATTATATTTT
2660194 TAAAAATTATA
1 TAAAAATTATA
2660205 TAAAAATAATAATA
1 TAAAAAT--T-ATA
2660219 TTAAAAATTATA
1 -TAAAAATTATA
2660231 TAAAAA
1 TAAAAA
2660237 CTAATACGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 13 0.46
12 3 0.11
13 2 0.07
14 3 0.11
15 7 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:2669878 original size:43 final size:42
Alignment explanation
Indices: 2669829--2669946 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 42
2669819 ATAATTTCGT
*
2669829 TGAACTTGAGTGATTCAGATTGTGATTAATATATATTTTCGGA
1 TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTT-GGA
* * *
2669872 TGAACTTAAGTGATTCAGATTGTGATCAAATATGTATTTTTGA
1 TGAACTTAAGTGATTCAGATTGTGAT-TAATATATATTTTGGA
* *
2669915 TGAACTTTTAAGTGACTCAAATTGTGATTAAT
1 TGAAC--TTAAGTGATTCAGATTGTGATTAAT
2669947 TTTGGGGTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
43 32 0.49
44 14 0.22
45 19 0.29
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (42 bp):
TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTTGGA
Found at i:2674426 original size:19 final size:19
Alignment explanation
Indices: 2674402--2674440 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2674392 ATTACGGGCC
2674402 TAAAATTATCTGATTTCTA
1 TAAAATTATCTGATTTCTA
* *
2674421 TAAAATTGTTTGATTTCTA
1 TAAAATTATCTGATTTCTA
2674440 T
1 T
2674441 TCTGTTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (19 bp):
TAAAATTATCTGATTTCTA
Found at i:2677831 original size:16 final size:15
Alignment explanation
Indices: 2677815--2677856 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
2677805 ACAGTTTTAT
2677815 TTCATTACAGCTCTA
1 TTCATTACAGCTCTA
2677830 TTCAGTTACAGCTCTA
1 TTCA-TTACAGCTCTA
2677846 TTCTATTACAG
1 TTC-ATTACAG
2677857 TAAATCATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.16
16 20 0.80
17 1 0.04
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (15 bp):
TTCATTACAGCTCTA
Found at i:2688870 original size:52 final size:52
Alignment explanation
Indices: 2688808--2688912 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
2688798 TTTGCTAACT
2688808 GCTCTGACTACATATGATAAATCTGGACGTGAACAAACCATAGCATACATGA
1 GCTCTGACTACATATGATAAATCTGGACGTGAACAAACCATAGCATACATGA
2688860 GCTCTGACTACATATGATAAATCTGGACGTGAACAAACCATAGCATACATGA
1 GCTCTGACTACATATGATAAATCTGGACGTGAACAAACCATAGCATACATGA
2688912 G
1 G
2688913 AGATCCCACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (52 bp):
GCTCTGACTACATATGATAAATCTGGACGTGAACAAACCATAGCATACATGA
Found at i:2689084 original size:23 final size:22
Alignment explanation
Indices: 2689057--2689104 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
2689047 ACCTGCAAAG
*
2689057 AACTTTCTCGATGTACCCCTTCT
1 AACTTT-TAGATGTACCCCTTCT
*
2689080 AAC--TTAGGTGTACCCCTTCT
1 AACTTTTAGATGTACCCCTTCT
2689100 AACTT
1 AACTT
2689105 AGGTACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
20 17 0.81
21 1 0.05
23 3 0.14
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (22 bp):
AACTTTTAGATGTACCCCTTCT
Found at i:2689093 original size:20 final size:20
Alignment explanation
Indices: 2689068--2689108 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2689058 ACTTTCTCGA
2689068 TGTACCCCTTCTAACTTAGG
1 TGTACCCCTTCTAACTTAGG
2689088 TGTACCCCTTCTAACTTAGG
1 TGTACCCCTTCTAACTTAGG
2689108 T
1 T
2689109 ACAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTACCCCTTCTAACTTAGG
Found at i:2696021 original size:19 final size:19
Alignment explanation
Indices: 2695992--2696056 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
2695982 CAAAATTGAA
*
2695992 AAATGAATATGAGATGA-G
1 AAATGAATATGAAATGATG
2696010 AAATGTAATATGAAATGATG
1 AAATG-AATATGAAATGATG
*
2696030 AAATGAGATGTGAAACT--TG
1 AAATGA-ATATGAAA-TGATG
2696049 AAATGAAT
1 AAATGAAT
2696057 TCAAGTATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 7 0.17
19 20 0.49
20 13 0.32
21 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.26
Consensus pattern (19 bp):
AAATGAATATGAAATGATG
Found at i:2699524 original size:44 final size:44
Alignment explanation
Indices: 2699461--2699551 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
2699451 AACTTTGTTT
* *
2699461 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
2699505 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
2699549 TTA
1 TTA
2699552 TTTGACCTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
Found at i:2700615 original size:49 final size:48
Alignment explanation
Indices: 2700559--2700713 Score: 138
Period size: 49 Copynumber: 3.2 Consensus size: 48
2700549 TACCACAAAG
2700559 GCATCTAAGTAAAAAATCATAATTGATGCAATTCAAATGTTCAATACAA
1 GCATCTAAGTAAAAAA-CATAATTGATGCAATTCAAATGTTCAATACAA
* * * ** * * **
2700608 GCATCTAAGCATAATACGATAATCAATGCAAAT--GA-GTT-ACCACAAA
1 GCATCTAAGTAAAAAAC-ATAATTGATGCAATTCAAATGTTCAATAC-AA
*
2700654 GGCATCTAAGTAAAGAAAACATAATTGATGCAGTTCAAATGTTCAATACAA
1 -GCATCTAAGT-AA-AAAACATAATTGATGCAATTCAAATGTTCAATACAA
2700705 GCATCTAAG
1 GCATCTAAG
2700714 CATAATACCA
Statistics
Matches: 78, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
45 3 0.04
46 5 0.06
47 10 0.13
48 13 0.17
49 29 0.37
50 10 0.13
51 5 0.06
52 3 0.04
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (48 bp):
GCATCTAAGTAAAAAACATAATTGATGCAATTCAAATGTTCAATACAA
Found at i:2700818 original size:99 final size:97
Alignment explanation
Indices: 2700539--2700823 Score: 466
Period size: 97 Copynumber: 2.9 Consensus size: 97
2700529 TTAAAAAGAG
* *
2700539 GCAAATGAATTACCACAAAGGCATCTAAGT-AAAAAATCATAATTGATGCAATTCAAATGTTCAA
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAA
*
2700603 TACAAGCATCTAAGCATAATACGATAATCAAT
66 TACAAGCATCTAAGCATAATACCATAATCAAT
* *
2700635 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAGAAAACATAATTGATGCAGTTCAAATGTTCAA
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAA
2700700 TACAAGCATCTAAGCATAATACCATAATCAAT
66 TACAAGCATCTAAGCATAATACCATAATCAAT
*
2700732 GCAAATGAGTTACCACAAAGG-ATTTAAGTAAAAAAAAAAACATAATTGATGCAATTCAAATGTT
1 GCAAATGAGTTACCACAAAGGCATCTAAGT---AAAAAAAACATAATTGATGCAATTCAAATGTT
*
2700796 TAATACAAGCATCTAAGCATAATACCAT
63 CAATACAAGCATCTAAGCATAATACCAT
2700824 GATTGATGTA
Statistics
Matches: 176, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
96 36 0.20
97 83 0.47
99 57 0.32
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (97 bp):
GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAA
TACAAGCATCTAAGCATAATACCATAATCAAT
Found at i:2701290 original size:22 final size:22
Alignment explanation
Indices: 2701246--2701289 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2701236 TAGAAGGAGG
2701246 AGAAGCAAGAAACAAGCAAAAA
1 AGAAGCAAGAAACAAGCAAAAA
*
2701268 AGAAGCAAGAAGCAA-CAAAAA
1 AGAAGCAAGAAACAAGCAAAAA
2701289 A
1 A
2701290 AAATTTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.68, C:0.14, G:0.18, T:0.00
Consensus pattern (22 bp):
AGAAGCAAGAAACAAGCAAAAA
Found at i:2701960 original size:28 final size:27
Alignment explanation
Indices: 2701928--2701990 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
2701918 TTTAATATTA
*
2701928 AAATAATACA-AAAATTCATTTATAATTT
1 AAATAATA-ATAAAATTCA-GTATAATTT
* *
2701956 GAATAATAATATAATTCAGTATAATTT
1 AAATAATAATAAAATTCAGTATAATTT
2701983 AAATAATA
1 AAATAATA
2701991 TTACTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (27 bp):
AAATAATAATAAAATTCAGTATAATTT
Found at i:2704105 original size:57 final size:59
Alignment explanation
Indices: 2703968--2704365 Score: 495
Period size: 57 Copynumber: 6.8 Consensus size: 59
2703958 GACATCTCTT
** * *
2703968 TTTTTCTGGCAACTTTTTTGCTGCCTCTTCACG-ATCTCTTTGCCACCCCTGCTACTATTAT
1 TTTTT-TGGCAACTGCTTTGCTGCCTCTTCACGTATCTC--TGCAACCCCTGCTACTATTAG
* * *
2704029 TTTTTTCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTA-T-G
1 TTTTTT-GGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCTACTATTAG
* * *
2704087 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTAT
1 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCTACTATTAG
* * *
2704146 TTTTTTCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTA-T-G
1 TTTTTT-GGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCTACTATTAG
* * *
2704204 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTAT
1 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCTACTATTAG
* * * *
2704263 TTTTTTCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTACAACCCTTGCTGCTA-T-G
1 TTTTTT-GGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCTACTATTAG
* *
2704321 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACC
1 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACC
2704366 TCTACTGATT
Statistics
Matches: 293, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
57 123 0.42
58 20 0.07
59 15 0.05
60 102 0.35
61 28 0.10
62 5 0.02
ACGTcount: A:0.13, C:0.31, G:0.14, T:0.42
Consensus pattern (59 bp):
TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCTACTATTAG
Found at i:2704181 original size:117 final size:117
Alignment explanation
Indices: 2703968--2704365 Score: 742
Period size: 117 Copynumber: 3.4 Consensus size: 117
2703958 GACATCTCTT
** *
2703968 TTTTTCTGGCAACTTTTTTGCTGCCTCTTCACGATCTCTTTGCCACCCCTGCTACTATTATTTTT
1 TTTTT-TGGCAACTGCTTTGCTGCCTCTTCACG-TCTCTTTGCAACCCCTGCTACTATTATTTTT
2704033 TTCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTATG
64 TTCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTATG
2704087 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTTT
1 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTTT
2704152 CTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTATG
66 CTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTATG
2704204 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTTT
1 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTTT
*
2704269 CTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTACAACCCTTGCTGCTATG
66 CTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTATG
2704321 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACC
1 TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACC
2704366 TCTACTGATT
Statistics
Matches: 275, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
117 245 0.89
118 25 0.09
119 5 0.02
ACGTcount: A:0.13, C:0.31, G:0.14, T:0.42
Consensus pattern (117 bp):
TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTTT
CTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTATG
Found at i:2710997 original size:18 final size:18
Alignment explanation
Indices: 2710982--2711016 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2710972 CAGCCCAATA
*
2710982 CCATCATTTGGCCCAAAG
1 CCATCAATTGGCCCAAAG
2711000 CCATCAATTGGCCCAAA
1 CCATCAATTGGCCCAAA
2711017 ATTGCGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.20
Consensus pattern (18 bp):
CCATCAATTGGCCCAAAG
Found at i:2714764 original size:30 final size:31
Alignment explanation
Indices: 2714721--2714780 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2714711 GGAGGTGGGA
*
2714721 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGAGAATAAAAATTTTAGGGGAAAAG
* *
2714752 TGGGAGGA-AATAAAAATTTTGGGGGAAAA
1 TGGGAAGAGAATAAAAATTTTAGGGGAAAA
2714781 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (31 bp):
TGGGAAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:2714800 original size:9 final size:9
Alignment explanation
Indices: 2714786--2714810 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2714776 GAAAATAAAA
2714786 GGTTTTGAG
1 GGTTTTGAG
2714795 GGTTTTGAG
1 GGTTTTGAG
2714804 GGTTTTG
1 GGTTTTG
2714811 GGGAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.44, T:0.48
Consensus pattern (9 bp):
GGTTTTGAG
Found at i:2715000 original size:9 final size:9
Alignment explanation
Indices: 2714986--2715022 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2714976 TATAGTTTGA
2714986 TATTCGAAT
1 TATTCGAAT
2714995 TATTCGAAT
1 TATTCGAAT
*
2715004 TATTCGAGT
1 TATTCGAAT
2715013 TATTCGAAT
1 TATTCGAAT
2715022 T
1 T
2715023 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:2717603 original size:44 final size:44
Alignment explanation
Indices: 2717540--2717674 Score: 243
Period size: 44 Copynumber: 3.1 Consensus size: 44
2717530 AACTCTATTT
* * *
2717540 TTAGTTTCTCACTTAAACTCTGATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACATAAACTCTAATTAATGTAGGTTATTTTAATA
2717584 TTAGTTTCCCACATAAACTCTAATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACATAAACTCTAATTAATGTAGGTTATTTTAATA
2717628 TTAGTTTCCCACATAAACTCTAATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACATAAACTCTAATTAATGTAGGTTATTTTAATA
2717672 TTA
1 TTA
2717675 TTTGACCTAC
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 88 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.45
Consensus pattern (44 bp):
TTAGTTTCCCACATAAACTCTAATTAATGTAGGTTATTTTAATA
Found at i:2718939 original size:101 final size:100
Alignment explanation
Indices: 2718666--2718953 Score: 449
Period size: 97 Copynumber: 2.9 Consensus size: 100
2718656 TTAAAAAGAG
*
2718666 GCAAATGAATTACCACAAAGGCATCTAAGTAAAAAAAAAACATAATTGATGCAGTTCAAATGTTC
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAAACATAATTGATGCAGTTCAAATGTTC
* * *
2718731 AATACAAGCATTTAAGCATAATA-CGATAATCGAT
66 AATACAAGCATCTAAGCATAATACCCATAATCAAT
*
2718765 GCAAATGAGTTACCACAAAGGCATCTAAGT--AAAGAAAACATAATTGATGCAGTTCAAATGTTC
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAAACATAATTGATGCAGTTCAAATGTTC
2718828 AATACAAGCATCTAAGCATAATACCCATAATCAAT
66 AATACAAGCATCTAAGCATAATACCCATAATCAAT
* * *
2718863 GCAAATGAGTTACCACAAAGG-ATTTAAGTAAAAAAAAAAACCATAATTGTTGCAATTCAAATGT
1 GCAAATGAGTTACCACAAAGGCATCTAAGT-AAAAAAAAAA-CATAATTGATGCAGTTCAAATGT
*
2718927 TTAATACAAGCATCTAAGCATAATACC
64 TCAATACAAGCATCTAAGCATAATACC
2718954 ATGATTGACG
Statistics
Matches: 174, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
97 61 0.35
98 30 0.17
99 29 0.17
100 7 0.04
101 47 0.27
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (100 bp):
GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAAACATAATTGATGCAGTTCAAATGTTC
AATACAAGCATCTAAGCATAATACCCATAATCAAT
Found at i:2720105 original size:27 final size:29
Alignment explanation
Indices: 2720074--2720135 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 29
2720064 TTTAATATTA
*
2720074 AAATAATACAA-A-AATTCATTATAATTT
1 AAATAATACAATATAATTCAGTATAATTT
*
2720101 GAAT-A-ACAATATAATTCAGTATAATTT
1 AAATAATACAATATAATTCAGTATAATTT
2720128 AAATAATA
1 AAATAATA
2720136 TTACTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 4 0.14
26 2 0.07
27 20 0.71
28 1 0.04
29 1 0.04
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAATACAATATAATTCAGTATAATTT
Found at i:2720564 original size:10 final size:11
Alignment explanation
Indices: 2720552--2720607 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
2720542 ATTTTTTTAA
*
2720552 TTTTAAAATAT
1 TTTTAAAATAC
2720563 TTTTAAAATAC
1 TTTTAAAATAC
** *
2720574 TTTT--TTTAA
1 TTTTAAAATAC
2720583 TTTTAAAATA-
1 TTTTAAAATAC
2720593 TTTTAAAATAC
1 TTTTAAAATAC
2720604 TTTT
1 TTTT
2720608 TTTAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 6 0.17
10 10 0.28
11 20 0.56
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:2720597 original size:30 final size:31
Alignment explanation
Indices: 2720543--2720623 Score: 146
Period size: 31 Copynumber: 2.6 Consensus size: 31
2720533 ATTTTTTTAA
2720543 TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
2720574 TTTTTTTAATTTTAAAATA-TTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
2720604 TTTTTTTAATTTTTAAAATA
1 TTTTTTTAA-TTTTAAAATA
2720624 AATTTTTGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 20 0.41
31 29 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:2723588 original size:17 final size:14
Alignment explanation
Indices: 2723556--2723585 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2723546 TCATTCCATT
2723556 CAACAAAATAATAG
1 CAACAAAATAATAG
2723570 CAACAAAATAATAG
1 CAACAAAATAATAG
2723584 CA
1 CA
2723586 GCAGGGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.17, G:0.07, T:0.13
Consensus pattern (14 bp):
CAACAAAATAATAG
Found at i:2727360 original size:13 final size:13
Alignment explanation
Indices: 2727290--2727362 Score: 55
Period size: 13 Copynumber: 5.7 Consensus size: 13
2727280 ACAAATAATA
*
2727290 TTAAATAATATAT
1 TTAAATATTATAT
*
2727303 TCTAAATACTATA-
1 T-TAAATATTATAT
*
2727316 TAAAATATTATA-
1 TTAAATATTATAT
2727328 --AAATATGTACTAT
1 TTAAATAT-TA-TAT
2727341 TTAAATATTATAT
1 TTAAATATTATAT
*
2727354 TTTAATATT
1 TTAAATATT
2727363 GTAAAATACT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.12
11 2 0.04
12 11 0.22
13 13 0.26
14 12 0.24
15 6 0.12
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (13 bp):
TTAAATATTATAT
Found at i:2730713 original size:22 final size:21
Alignment explanation
Indices: 2730688--2730728 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
2730678 AATTAAATAA
2730688 AAAATTACGTGCAACTATTATG
1 AAAATTACGTGCAAC-ATTATG
2730710 AAAATTACGTGCAACATTA
1 AAAATTACGTGCAACATTA
2730729 GAACATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAATTACGTGCAACATTATG
Found at i:2732395 original size:9 final size:9
Alignment explanation
Indices: 2732381--2732415 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2732371 TAGTTTGATG
2732381 TTCGAATTA
1 TTCGAATTA
2732390 TTCGAATTA
1 TTCGAATTA
*
2732399 TTCGAGTTA
1 TTCGAATTA
2732408 TTCGAATT
1 TTCGAATT
2732416 CGAAAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TTCGAATTA
Found at i:2732486 original size:9 final size:9
Alignment explanation
Indices: 2732469--2732499 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2732459 TCGAGTTGAT
2732469 TCGAATAAC
1 TCGAATAAC
*
2732478 TCGATTAAC
1 TCGAATAAC
2732487 TCGAATAAC
1 TCGAATAAC
2732496 TCGA
1 TCGA
2732500 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:2733113 original size:18 final size:18
Alignment explanation
Indices: 2733090--2733124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2733080 AAGGTTTTGC
* *
2733090 TTTTTTTATTTTATTTTA
1 TTTTTTAATGTTATTTTA
2733108 TTTTTTAATGTTATTTT
1 TTTTTTAATGTTATTTT
2733125 CTTGTTGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTTAATGTTATTTTA
Found at i:2733157 original size:22 final size:23
Alignment explanation
Indices: 2733132--2733181 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
2733122 TTTCTTGTTG
*
2733132 TTTTATCT-CTATTTTGCTACTA
1 TTTTATCTACTATGTTGCTACTA
*
2733154 TTTTA-CTATTATGTTGCTACTA
1 TTTTATCTACTATGTTGCTACTA
*
2733176 TCTTAT
1 TTTTAT
2733182 TGTTATTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.58
Consensus pattern (23 bp):
TTTTATCTACTATGTTGCTACTA
Found at i:2734578 original size:17 final size:17
Alignment explanation
Indices: 2734558--2734591 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2734548 TACCTATTTC
*
2734558 ATTATGTATTATATTAT
1 ATTATATATTATATTAT
*
2734575 ATTATATTTTATATTAT
1 ATTATATATTATATTAT
2734592 TTGGTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTATATATTATATTAT
Found at i:2735258 original size:11 final size:11
Alignment explanation
Indices: 2735242--2735281 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
2735232 ATTAAAGTAG
2735242 ATTTTAATGTA
1 ATTTTAATGTA
*
2735253 ATTTTAAAGTA
1 ATTTTAATGTA
2735264 GATTTTAATGTA
1 -ATTTTAATGTA
2735276 ATTTTA
1 ATTTTA
2735282 TTGTCCCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (11 bp):
ATTTTAATGTA
Found at i:2735260 original size:23 final size:23
Alignment explanation
Indices: 2735233--2735281 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2735223 AAACTTTATA
2735233 TTAAAGTAGATTTTAATGTAATT
1 TTAAAGTAGATTTTAATGTAATT
2735256 TTAAAGTAGATTTTAATGTAATT
1 TTAAAGTAGATTTTAATGTAATT
2735279 TTA
1 TTA
2735282 TTGTCCCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (23 bp):
TTAAAGTAGATTTTAATGTAATT
Found at i:2735270 original size:12 final size:11
Alignment explanation
Indices: 2735233--2735281 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
2735223 AAACTTTATA
2735233 TTAAAGTAGATT
1 TTAAAGTA-ATT
*
2735245 TTAATGTAATT
1 TTAAAGTAATT
2735256 TTAAAGTAGATT
1 TTAAAGTA-ATT
*
2735268 TTAATGTAATT
1 TTAAAGTAATT
2735279 TTA
1 TTA
2735282 TTGTCCCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (11 bp):
TTAAAGTAATT
Done.