Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 34 of 322
Found at i:10100279 original size:45 final size:45
Alignment explanation
Indices: 10100215--10100325 Score: 152
Period size: 45 Copynumber: 2.5 Consensus size: 45
10100205 AATGGTAGCA
* *
10100215 GTAACAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGAATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATC-GAATCG
* * * *
10100260 GTAACTGTAACGGTAACAGTATTCGACACATAAAGTATCGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCG
10100305 GTAACAGTAACAGTAACAGTA
1 GTAACAGTAACAGTAACAGTA
10100326 ACAATAGTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 56 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCG
Found at i:10101437 original size:3 final size:3
Alignment explanation
Indices: 10101429--10101471 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
10101419 TATTAACTTT
*
10101429 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10101472 ATATCTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:10101745 original size:26 final size:26
Alignment explanation
Indices: 10101716--10101787 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
10101706 TTAATTTATT
10101716 TTTAATAATAAT-AATAATAATCATAA
1 TTTAATAATAATAAATAATAAT-ATAA
* *
10101742 TTTAATAAT-ATAAATTATAATTTAA
1 TTTAATAATAATAAATAATAATATAA
**
10101767 TAGAATAATAATAAATAATAA
1 TTTAATAATAATAAATAATAA
10101788 ATATCTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 12 0.31
26 27 0.69
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (26 bp):
TTTAATAATAATAAATAATAATATAA
Found at i:10101747 original size:20 final size:20
Alignment explanation
Indices: 10101724--10101778 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
10101714 TTTTTAATAA
10101724 TAATAATAATAATCATAATT
1 TAATAATAATAATCATAATT
*
10101744 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATCATAATT
10101764 TAATAGAATAATAAT
1 TAAT--AATAATAAT
10101779 AAATAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 20 0.67
22 6 0.20
23 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATAATAATAATCATAATT
Found at i:10121816 original size:20 final size:20
Alignment explanation
Indices: 10121793--10121849 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
10121783 TTAATTTATT
10121793 TTTAATAATAATAATCATAA
1 TTTAATAATAATAATCATAA
*
10121813 TTTAATAAT-ATAAATTATAA
1 TTTAATAATAAT-AATCATAA
10121833 TTTAATAGAATAATAAT
1 TTTAAT--AATAATAAT
10121850 AAATAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.06
20 22 0.69
22 6 0.19
23 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
TTTAATAATAATAATCATAA
Found at i:10128036 original size:45 final size:45
Alignment explanation
Indices: 10127972--10128082 Score: 179
Period size: 45 Copynumber: 2.5 Consensus size: 45
10127962 AGCAGTAGCA
* *
10127972 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAATCT
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTC-GAATCG
*
10128017 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCG
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATCG
10128062 GTAACAGTAACGGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
10128083 ACAGTAGTCG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 61 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATCG
Found at i:10128077 original size:12 final size:12
Alignment explanation
Indices: 10128060--10128084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10128050 AGTGTCGAAT
10128060 CGGTAACAGTAA
1 CGGTAACAGTAA
10128072 CGGTAACAGTAA
1 CGGTAACAGTAA
10128084 C
1 C
10128085 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:10128084 original size:51 final size:50
Alignment explanation
Indices: 10127970--10128097 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 50
10127960 GTAGCAGTAG
* *
10127970 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAA
1 CAGTAAC-GTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCGGTAA
10128021 CAGTAACG-----GTAACAGTATTCGACACACAAAGTG-TCGAATCGGTAA
1 CAGTAACGTAACAGTAACAGTATTCGACACACAAAGTGCT-GAATCGGTAA
* *
10128066 CAGTAACGGTAACAGTAACAGTAGTCGGCACA
1 CAGTAAC-GTAACAGTAACAGTATTCGACACA
10128098 TAAGTGCCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
44 1 0.02
45 40 0.61
46 1 0.02
50 1 0.02
51 23 0.35
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (50 bp):
CAGTAACGTAACAGTAACAGTATTCGACACACAAAGTGCTGAATCGGTAA
Found at i:10129050 original size:13 final size:13
Alignment explanation
Indices: 10129032--10129066 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
10129022 AAAGGACTTG
10129032 ATTAAACTTACCA
1 ATTAAACTTACCA
10129045 ATTAAACTTACCA
1 ATTAAACTTACCA
10129058 ATTAAACTT
1 ATTAAACTT
10129067 CAAGCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (13 bp):
ATTAAACTTACCA
Found at i:10129108 original size:16 final size:15
Alignment explanation
Indices: 10129087--10129117 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
10129077 AACCTAAATT
10129087 TTTCCTTTCTTCTTTC
1 TTTCCTTT-TTCTTTC
10129103 TTTCCTTTTTCTTTC
1 TTTCCTTTTTCTTTC
10129118 CTGTTCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCCTTTTTCTTTC
Found at i:10129491 original size:20 final size:20
Alignment explanation
Indices: 10129468--10129522 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
10129458 TTATTTTTAA
10129468 TAATAATAATAATCATAATT
1 TAATAATAATAATCATAATT
* *
10129488 TAATAAT-ATAAATTATGATT
1 TAATAATAAT-AATCATAATT
10129508 TAATAGAATAATAAT
1 TAAT--AATAATAAT
10129523 AAATAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 19 0.66
22 6 0.21
23 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
TAATAATAATAATCATAATT
Found at i:10130685 original size:20 final size:20
Alignment explanation
Indices: 10130660--10130699 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10130650 AAATGTTAGG
10130660 TCTAGCCTCTAATATGCTTA
1 TCTAGCCTCTAATATGCTTA
10130680 TCTAGCCTCTAATATGCTTA
1 TCTAGCCTCTAATATGCTTA
10130700 CTTCACCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (20 bp):
TCTAGCCTCTAATATGCTTA
Found at i:10138464 original size:16 final size:17
Alignment explanation
Indices: 10138443--10138479 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10138433 GTTCCAAGAT
10138443 TTTGAAC-TTTCG-GAAA
1 TTTGAACATTT-GTGAAA
10138459 TTTGAACATTTGTGAAA
1 TTTGAACATTTGTGAAA
10138476 TTTG
1 TTTG
10138480 GTTATGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (17 bp):
TTTGAACATTTGTGAAA
Found at i:10142366 original size:38 final size:38
Alignment explanation
Indices: 10142315--10142391 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
10142305 TTATAAACCA
10142315 AACCATTATGTCAAGCTTCAATCGAATACACAACATGT
1 AACCATTATGTCAAGCTTCAATCGAATACACAACATGT
*
10142353 AACCATTATGTCAAGCTTCAATCGAATACACTACATGT
1 AACCATTATGTCAAGCTTCAATCGAATACACAACATGT
10142391 A
1 A
10142392 CATGTATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.27
Consensus pattern (38 bp):
AACCATTATGTCAAGCTTCAATCGAATACACAACATGT
Found at i:10143316 original size:50 final size:51
Alignment explanation
Indices: 10143214--10143319 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 51
10143204 AATAACACCA
* * *
10143214 CATAAATACTTACCTATATAACCGAAAATATATAAGATCCAATATATCATCT
1 CATAAAAACTTACCTATATAACC-AAAATACACAAGATCCAATATATCATCT
* * * *
10143266 CATAAAAACTTACCTATATAACC-AAATACACAAGGTTCATTATATTATCT
1 CATAAAAACTTACCTATATAACCAAAATACACAAGATCCAATATATCATCT
10143316 CATA
1 CATA
10143320 TGGCTGAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 25 0.53
52 22 0.47
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (51 bp):
CATAAAAACTTACCTATATAACCAAAATACACAAGATCCAATATATCATCT
Found at i:10143433 original size:35 final size:35
Alignment explanation
Indices: 10143393--10143492 Score: 110
Period size: 35 Copynumber: 2.9 Consensus size: 35
10143383 TCTCATATGG
* *
10143393 CCGAATATACAAATTCAATATAACCTCATATGAAA
1 CCGAATATACAAATTCAATATAACCTCACAAGAAA
* * * * * *
10143428 TCGAATATACAAGTTTAATATAACTTCACAAGTAG
1 CCGAATATACAAATTCAATATAACCTCACAAGAAA
* *
10143463 CCGAATATACAAACTCAATATGACCTCACA
1 CCGAATATACAAATTCAATATAACCTCACA
10143493 TCTACATACT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (35 bp):
CCGAATATACAAATTCAATATAACCTCACAAGAAA
Found at i:10171548 original size:13 final size:13
Alignment explanation
Indices: 10171530--10171560 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
10171520 CAAGCTGGTT
10171530 TTCATACTCTAGC
1 TTCATACTCTAGC
10171543 TTCATACTCTAGC
1 TTCATACTCTAGC
10171556 TTCAT
1 TTCAT
10171561 GTAAGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (13 bp):
TTCATACTCTAGC
Found at i:10172986 original size:35 final size:35
Alignment explanation
Indices: 10172947--10173247 Score: 325
Period size: 35 Copynumber: 8.6 Consensus size: 35
10172937 CATGGCAAAG
* * * *
10172947 TGTGAAATGGAGGTATGGTATCATCCATAATAAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
10172982 TGTGAAACGTAGGTATGATATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
** * * *
10173017 TGCAAAACTTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
10173052 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * *
10173087 TGTGAAACGTAGGTATGGTATTAACCATACCGATT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * *
10173122 TGTGAAACGTACGTATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
10173157 TGTGAAAAGTAGGCATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
** * * * *
10173192 TAAGAAACATAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCAT-CCATACTGAGT
*
10173227 TGTGAAATGTAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
10173248 TTCAATGAGG
Statistics
Matches: 225, Mismatches: 40, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
34 1 0.00
35 224 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
Found at i:10173138 original size:105 final size:105
Alignment explanation
Indices: 10172947--10173248 Score: 397
Period size: 105 Copynumber: 2.9 Consensus size: 105
10172937 CATGGCAAAG
* * * * * *
10172947 TGTGAAATGGAGGTATGGTATCATCCATAATAAGTTGTGAAACGTAGGTATGATATTATCCATAC
1 TGTGAAAAGTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
* ** * *
10173012 TGAGTTGCAAAACTTAGGTATGGTATTAACCATACTGAGT
66 CGAGTTGTGAAACGTAGGTATGGTATTAACCATACCGAGT
*
10173052 TGTGAAACGTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
1 TGTGAAAAGTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
* *
10173117 CGATTTGTGAAACGTACGTATGGTATTAACCATACCGAGT
66 CGAGTTGTGAAACGTAGGTATGGTATTAACCATACCGAGT
* * ** * * **
10173157 TGTGAAAAGTAGGCATGGTATTATCCATACTGAGTTAAGAAACATAGGTATGGCATTTCCCATAC
1 TGTGAAAAGTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
*
10173222 CGAGTTGTGAAATGTAGGTATGGTATT
66 CGAGTTGTGAAACGTAGGTATGGTATT
10173249 TCAATGAGGA
Statistics
Matches: 172, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 172 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (105 bp):
TGTGAAAAGTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGGTATGGTATTAACCATAC
CGAGTTGTGAAACGTAGGTATGGTATTAACCATACCGAGT
Found at i:10179801 original size:33 final size:33
Alignment explanation
Indices: 10179764--10179829 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
10179754 AACAATTCAT
10179764 GATAATAATAAGCATCATATCATATAAACAACA
1 GATAATAATAAGCATCATATCATATAAACAACA
*
10179797 GATAATAATCAGCATCATATCATATAAACAACA
1 GATAATAATAAGCATCATATCATATAAACAACA
10179830 TTAAATTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.24
Consensus pattern (33 bp):
GATAATAATAAGCATCATATCATATAAACAACA
Found at i:10180072 original size:30 final size:30
Alignment explanation
Indices: 10180027--10180086 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
10180017 ATTTAATACG
*
10180027 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
10180057 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
10180087 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:10186661 original size:32 final size:32
Alignment explanation
Indices: 10186620--10186683 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
10186610 GGCTGTTATG
*
10186620 AGTATGAAAATGGTTCTGCTAGGCTTGGGTGT
1 AGTATGAAAATGGTTCGGCTAGGCTTGGGTGT
10186652 AGTATGAAAATGGTTCGGCTAGGCTTGGGTGT
1 AGTATGAAAATGGTTCGGCTAGGCTTGGGTGT
10186684 TGAAGAAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.36, T:0.33
Consensus pattern (32 bp):
AGTATGAAAATGGTTCGGCTAGGCTTGGGTGT
Found at i:10192442 original size:19 final size:18
Alignment explanation
Indices: 10192418--10192489 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
10192408 AATTAGATTT
10192418 ATTTAAATAAAATTATTAA
1 ATTTAAATAAAA-TATTAA
*
10192437 ATTTAAATTAAAATATAAA
1 ATTTAAA-TAAAATATTAA
*
10192456 ATTAAAATATTAAATATTTAA
1 ATTTAAATA--AAATA-TTAA
10192477 ATATTAAA-AAAAT
1 AT-TTAAATAAAAT
10192490 TATTGGCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.05
19 22 0.50
20 10 0.23
21 6 0.14
22 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTAAATAAAATATTAA
Found at i:10192473 original size:7 final size:7
Alignment explanation
Indices: 10192431--10192484 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 7
10192421 TAAATAAAAT
10192431 TATTAAA
1 TATTAAA
10192438 T-TTAAA
1 TATTAAA
*
10192444 T-TAAAA
1 TATTAAA
10192450 TA-TAAA
1 TATTAAA
10192456 -ATTAAAA
1 TATT-AAA
10192463 TATTAAA
1 TATTAAA
10192470 TATTTAAA
1 TA-TTAAA
10192478 TATTAAA
1 TATTAAA
10192485 AAAATTATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 1 0.03
6 15 0.38
7 14 0.35
8 10 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TATTAAA
Found at i:10192480 original size:15 final size:14
Alignment explanation
Indices: 10192441--10192485 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 14
10192431 TATTAAATTT
10192441 AAATTAAAATA-TA
1 AAATTAAAATATTA
10192454 AAATTAAAATATTA
1 AAATTAAAATATTA
*
10192468 AATATTTAAATATTA
1 AA-ATTAAAATATTA
10192483 AAA
1 AAA
10192486 AAATTATTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.38
14 5 0.17
15 13 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTAAAATATTA
Found at i:10192851 original size:8 final size:8
Alignment explanation
Indices: 10192838--10192871 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
10192828 TTTTAAAAAA
10192838 ATATTTTT
1 ATATTTTT
10192846 ATATTTTT
1 ATATTTTT
10192854 ATAATTTTTT
1 AT-A-TTTTT
10192864 ATATTTTT
1 ATATTTTT
10192872 TTGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATATTTTT
Found at i:10192853 original size:24 final size:24
Alignment explanation
Indices: 10192788--10192857 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
10192778 TTAGAAATTT
*
10192788 AAATACTTTTTAGAATTTTATAAAA
1 AAATA-TTTTTAAAATTTTATAAAA
* * *
10192813 AAA-ATCTTTAAACTTTTTTAAAA
1 AAATATTTTTAAAATTTTATAAAA
* *
10192836 AAATATTTTTATATTTTTATAA
1 AAATATTTTTAAAATTTTATAA
10192858 TTTTTTATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 18 0.50
24 15 0.42
25 3 0.08
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (24 bp):
AAATATTTTTAAAATTTTATAAAA
Found at i:10192949 original size:28 final size:26
Alignment explanation
Indices: 10192918--10192977 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
10192908 ATTATCGTAT
* *
10192918 TTTTTGTAAATTTTATTTTTATATATAA
1 TTTTTG-AAATTTTATATATATATAT-A
*
10192946 TTTTCTGAATTTTTATATATATATATA
1 TTTT-TGAAATTTTATATATATATATA
10192973 TTTTT
1 TTTTT
10192978 ATTTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 5 0.18
28 20 0.71
29 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (26 bp):
TTTTTGAAATTTTATATATATATATA
Found at i:10196271 original size:16 final size:16
Alignment explanation
Indices: 10196250--10196280 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10196240 TTTTACAAAT
10196250 AAAAGAATAATTATAA
1 AAAAGAATAATTATAA
10196266 AAAAGAATAATTATA
1 AAAAGAATAATTATA
10196281 TTAATAATAA
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:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAAGAATAATTATAA
Found at i:10196363 original size:28 final size:29
Alignment explanation
Indices: 10196331--10196393 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 29
10196321 CTTATATTTG
10196331 TAAAAATTTATAAATAGT-T-TTA-ATAAAA
1 TAAAAATTT-TAAAT-GTATATTATATAAAA
*
10196359 T-AAAATTTTAAATGTATATTATATTAAA
1 TAAAAATTTTAAATGTATATTATATAAAA
10196387 TAAAAAT
1 TAAAAAT
10196394 AAATTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
27 10 0.33
28 7 0.23
29 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
TAAAAATTTTAAATGTATATTATATAAAA
Found at i:10205438 original size:15 final size:15
Alignment explanation
Indices: 10205418--10205450 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10205408 AAAGTAACTT
*
10205418 TAATAATAATGATAA
1 TAATAATAAAGATAA
10205433 TAATAATAAAGATAA
1 TAATAATAAAGATAA
10205448 TAA
1 TAA
10205451 AATGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (15 bp):
TAATAATAAAGATAA
Found at i:10209711 original size:34 final size:34
Alignment explanation
Indices: 10209673--10209739 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
10209663 AGTAACAATC
10209673 CAGTATCAGT-TAGGGCCTTAGCCCATTACAATAT
1 CAGTATCAGTGTA-GGCCTTAGCCCATTACAATAT
*
10209707 CAGTATCAGTGTAGGCCTTAGCCCATTTCAATA
1 CAGTATCAGTGTAGGCCTTAGCCCATTACAATA
10209740 ATAGTAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (34 bp):
CAGTATCAGTGTAGGCCTTAGCCCATTACAATAT
Found at i:10210043 original size:27 final size:27
Alignment explanation
Indices: 10210010--10210061 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
10210000 GTCATATATA
**
10210010 TCATAGGGGCATGTCAGTCATTTTACC
1 TCATAGGGGCATAACAGTCATTTTACC
*
10210037 TCATAGGGGTATAACAGTCATTTTA
1 TCATAGGGGCATAACAGTCATTTTA
10210062 TCAAATTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (27 bp):
TCATAGGGGCATAACAGTCATTTTACC
Found at i:10224109 original size:55 final size:55
Alignment explanation
Indices: 10224016--10224120 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
10224006 ACGGGTACTT
* *
10224016 GGCACGGGCGTGTCGCACCCCCGTGTTAATTTGACAGGTTCAG-CCACGGGTTCAA
1 GGCACGGGCGTGTCGCACCCCAGTGCTAATTTGACAGGTTC-GTCCACGGGTTCAA
* * * * *
10224071 GGCACGGGCGTGTTGCACGCTAGTGCTATTTTGGCAGGTTCGTCCACGGG
1 GGCACGGGCGTGTCGCACCCCAGTGCTAATTTGACAGGTTCGTCCACGGG
10224121 CATGTCGCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 1 0.02
55 41 0.98
ACGTcount: A:0.15, C:0.27, G:0.34, T:0.24
Consensus pattern (55 bp):
GGCACGGGCGTGTCGCACCCCAGTGCTAATTTGACAGGTTCGTCCACGGGTTCAA
Found at i:10236774 original size:43 final size:42
Alignment explanation
Indices: 10236696--10236847 Score: 162
Period size: 42 Copynumber: 3.6 Consensus size: 42
10236686 TCTTACAATT
* * ** *
10236696 CCATATCCCGGATATGGTCTTACATGTAATCTCATATCGATG
1 CCATAGCCCAGATATGGTCTTACACATAATATCATATCGATG
* * *
10236738 CCAATAGCCCAGTTATGGTCTTACACAAAATTTCATATCGATG
1 CC-ATAGCCCAGATATGGTCTTACACATAATATCATATCGATG
* * * *
10236781 CCA-AGTCCCAGACATGGGCTTACACATGATATCATACCGATG
1 CCATAG-CCCAGATATGGTCTTACACATAATATCATATCGATG
*
10236823 CCATATCCCAGATATGGTCTTACAC
1 CCATAGCCCAGATATGGTCTTACAC
10236848 GTATTCTCAT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.02
42 52 0.58
43 36 0.40
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
CCATAGCCCAGATATGGTCTTACACATAATATCATATCGATG
Found at i:10255839 original size:49 final size:49
Alignment explanation
Indices: 10255665--10255980 Score: 509
Period size: 49 Copynumber: 6.6 Consensus size: 49
10255655 CCCTTCGGGA
* * * * **
10255665 CTTATCACAT-T-TATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* * *
10255712 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
10255759 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
10255806 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
10255855 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
10255904 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
10255953 CTTATCACATATATATACACTTTCACAT
1 CTTATCACATATATATACACTTTCACAT
10255981 ATGGGTTTAA
Statistics
Matches: 255, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 89 0.35
49 165 0.65
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:10265129 original size:37 final size:39
Alignment explanation
Indices: 10265073--10265148 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
10265063 CCCTTATAAA
*
10265073 AAATATTTCCCAGACACTG-CCAATCTGCGTAATAGTCG
1 AAATATTTCCCAGACACTGCCCAATCTGAGTAATAGTCG
* * *
10265111 AAAT-TTTTCCAGACACTGCCCAGTCTGAGTACTAGTCG
1 AAATATTTCCCAGACACTGCCCAATCTGAGTAATAGTCG
10265149 CTTCAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 13 0.39
38 20 0.61
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (39 bp):
AAATATTTCCCAGACACTGCCCAATCTGAGTAATAGTCG
Found at i:10266436 original size:40 final size:40
Alignment explanation
Indices: 10266392--10266653 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
10266382 GCTCCTCGTT
* *
10266392 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
10266432 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
10266472 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
10266511 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
10266550 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
10266589 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
10266630 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
10266654 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:10267954 original size:11 final size:11
Alignment explanation
Indices: 10267938--10267962 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10267928 CCTCACTAGG
10267938 CCAACATGTTC
1 CCAACATGTTC
10267949 CCAACATGTTC
1 CCAACATGTTC
10267960 CCA
1 CCA
10267963 CCCATAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.40, G:0.08, T:0.24
Consensus pattern (11 bp):
CCAACATGTTC
Found at i:10273511 original size:47 final size:47
Alignment explanation
Indices: 10273451--10273580 Score: 183
Period size: 47 Copynumber: 2.8 Consensus size: 47
10273441 ATGCGAATGA
* *
10273451 TACCTTGATTTGGCTAT-GAGCCATGGTATAGGTATTCGAAGA-AGAGT
1 TACCTTGATTTGGCTATAG-GCCATGGTATAGGTACTCCAAGATA-AGT
* *
10273498 TACCTTGATTTGGCTATAGGCCATGGTATAGATACTCCAGGATAAGT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCCAAGATAAGT
*
10273545 TACCTTGATTTGGTTATAGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACT
10273581 ATCGATAGAG
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 73 0.97
48 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCCAAGATAAGT
Found at i:10275930 original size:42 final size:42
Alignment explanation
Indices: 10275848--10275976 Score: 124
Period size: 42 Copynumber: 3.0 Consensus size: 42
10275838 GTTTTACATG
*
10275848 TAATCTCATATCGATGCCAATAG-CCCAG-CTATGGTCTTACACGA
1 TAATATCATATCGATGCC-AT-GTCCCAGAC-ATGGTCTTACAC-A
* *
10275892 -AGT-TTAGTATCGATGCCATGTCCCAGACATGGTCTTACACA
1 TAATATCA-TATCGATGCCATGTCCCAGACATGGTCTTACACA
* *
10275933 TAATATCATA-CGTATGCCATATCCCAGATATGGTCTTACACA
1 TAATATCATATCG-ATGCCATGTCCCAGACATGGTCTTACACA
10275975 TA
1 TA
10275977 TTCTTATCTT
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
41 4 0.05
42 54 0.74
43 15 0.21
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (42 bp):
TAATATCATATCGATGCCATGTCCCAGACATGGTCTTACACA
Found at i:10292110 original size:91 final size:92
Alignment explanation
Indices: 10292002--10292201 Score: 287
Period size: 91 Copynumber: 2.2 Consensus size: 92
10291992 ATGAAATGTG
* * **
10292002 TAAGACCATGGTTGAAAGATGCCATGGCAACAG-GATATAAAATGTGTAAGACCATGATTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAAC-GTGACATAAAATGAATAAGACCATGATTGAAAG
*
10292066 ATACCATGGCAACATGAC-GAGAATGAA
65 ATACCATGGCAACATGACAGAAAATGAA
* * *
10292093 TAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATAAAATGAATAAGACCATGATTGAAAGA
*
10292158 TACCATGGCAACATGACAGAAAATGAG
66 TACCATGGCAACATGACAGAAAATGAA
*
10292185 TAAGACCATAGTTGAAA
1 TAAGACCATGGTTGAAA
10292202 CACACTATGG
Statistics
Matches: 97, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 1 0.01
91 73 0.75
92 23 0.24
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATAAAATGAATAAGACCATGATTGAAAGA
TACCATGGCAACATGACAGAAAATGAA
Found at i:10292213 original size:46 final size:46
Alignment explanation
Indices: 10291995--10292201 Score: 274
Period size: 46 Copynumber: 4.5 Consensus size: 46
10291985 CTCTGATATG
* * * * *
10291995 AAATGTGTAAGACCATGGTTGAAAGATGCCATGGCAACAGGATATA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
* *
10292041 AAATGTGTAAGACCATGATTGAAAGATACCATGGCAACATGAC-GA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
* * * *
10292086 GAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATG-
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GA
*
10292132 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
*
10292178 AAATGAGTAAGACCATAGTTGAAA
1 AAATGAGTAAGACCATGGTTGAAA
10292202 CACACTATGG
Statistics
Matches: 142, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
45 39 0.27
46 102 0.72
47 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
Found at i:10292232 original size:91 final size:90
Alignment explanation
Indices: 10292048--10292233 Score: 239
Period size: 91 Copynumber: 2.0 Consensus size: 90
10292038 ATAAAATGTG
* * * *
10292048 TAAGACCATGATTGAAAGATACCATGGCAACATGACGAGAATGAATAAGACCATGGTTGAAAGAT
1 TAAGACCATGATTGAAAGATACCATGGCAACATGACGAAAATGAATAAGACCATAGTTGAAACAC
* *
10292113 ACCATGGCAGCGTGACATGAAATGAA
66 ACCATGGCAGCATGACA-GAAATAAA
* *
10292139 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAACA
1 TAAGACCATGATTGAAAGATACCATGGCAACATGAC-GAAAATGAATAAGACCATAGTTGAAACA
* * *
10292204 CACTATGGCATCATGTCA-AAGATAAA
65 CACCATGGCAGCATGACAGAA-ATAAA
10292230 TAAG
1 TAAG
10292234 TCCGTGGATG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 2 0.02
91 43 0.52
92 37 0.45
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (90 bp):
TAAGACCATGATTGAAAGATACCATGGCAACATGACGAAAATGAATAAGACCATAGTTGAAACAC
ACCATGGCAGCATGACAGAAATAAA
Found at i:10294502 original size:23 final size:26
Alignment explanation
Indices: 10294458--10294505 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
10294448 CTCCAATATT
*
10294458 AACAATAACGACAGTAATAGAATAAC
1 AACAATAACGACAATAATAGAATAAC
10294484 AACAATAAC-A-AATAA-AGAATAA
1 AACAATAACGACAATAATAGAATAA
10294506 TAATGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 1 0.05
26 9 0.43
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (26 bp):
AACAATAACGACAATAATAGAATAAC
Found at i:10297374 original size:16 final size:17
Alignment explanation
Indices: 10297332--10297377 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
10297322 TTAATAATTA
10297332 ATATAATAATATATTATT
1 ATATAA-AATATATTATT
10297350 ATATAAAATATATTA-T
1 ATATAAAATATATTATT
10297366 ACT-TAAAATATA
1 A-TATAAAATATA
10297378 AGTAAATACC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.41
17 10 0.37
18 6 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAAATATATTATT
Found at i:10298020 original size:7 final size:7
Alignment explanation
Indices: 10298008--10298052 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
10297998 TTGAACAATA
10298008 AGTTGAG
1 AGTTGAG
10298015 AGTTGAG
1 AGTTGAG
10298022 AGTTGAG
1 AGTTGAG
*
10298029 ACTTGAG
1 AGTTGAG
10298036 AGTTGA-
1 AGTTGAG
10298042 ATGTTGAG
1 A-GTTGAG
10298050 AGT
1 AGT
10298053 GAACTGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 1 0.03
7 32 0.94
8 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.38, T:0.31
Consensus pattern (7 bp):
AGTTGAG
Found at i:10298727 original size:21 final size:21
Alignment explanation
Indices: 10298698--10298746 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
10298688 TATTGACAAC
*
10298698 ATAATTAAATAGAAATGATA-A
1 ATAAATAAATA-AAATGATACA
*
10298719 TTAAATAAATAAAATGATACA
1 ATAAATAAATAAAATGATACA
10298740 ATAAATA
1 ATAAATA
10298747 CTAAAGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (21 bp):
ATAAATAAATAAAATGATACA
Found at i:10301466 original size:49 final size:49
Alignment explanation
Indices: 10301412--10301511 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 49
10301402 ACTCTACTAC
* *
10301412 TTGTCAATTCGTTTTGTCTTATTTTTTATATGAATT-CTTTCATGTTTAA
1 TTGTCAATTCGTTTCGTCTTATTTTATATATGAATTAC-TTCATGTTTAA
* *
10301461 TTGTCATTTCGTTTCGTTTTATTTTATATATGAATTACTTCATGTTTAA
1 TTGTCAATTCGTTTCGTCTTATTTTATATATGAATTACTTCATGTTTAA
10301510 TT
1 TT
10301512 CTCTTCTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 45 0.98
50 1 0.02
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (49 bp):
TTGTCAATTCGTTTCGTCTTATTTTATATATGAATTACTTCATGTTTAA
Found at i:10314008 original size:4 final size:4
Alignment explanation
Indices: 10313999--10314026 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
10313989 CTCAACGGAA
10313999 ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10314027 GTAAACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:10317157 original size:6 final size:6
Alignment explanation
Indices: 10317143--10317181 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
10317133 TGTGTACCGC
* *
10317143 TACTGT TACTAT TACTGT TACTGT TACTGT TACTAT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TAC
10317182 CCTTACGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:10317187 original size:12 final size:12
Alignment explanation
Indices: 10317143--10317181 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
10317133 TGTGTACCGC
10317143 TACTGTTACTAT
1 TACTGTTACTAT
*
10317155 TACTGTTACTGT
1 TACTGTTACTAT
10317167 TACTGTTACTAT
1 TACTGTTACTAT
10317179 TAC
1 TAC
10317182 CCTTACGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (12 bp):
TACTGTTACTAT
Found at i:10333566 original size:5 final size:5
Alignment explanation
Indices: 10333556--10333597 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
10333546 TATTTATTTA
*
10333556 TTATT TTATT TTATG TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
10333598 TATTCAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:10349225 original size:18 final size:18
Alignment explanation
Indices: 10349190--10349225 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10349180 ATCCTTGAGT
*
10349190 AGTCATGGAATGGACACA
1 AGTCATGGAATAGACACA
*
10349208 AGTCATGGAATAGTCACA
1 AGTCATGGAATAGACACA
10349226 CTTGCATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (18 bp):
AGTCATGGAATAGACACA
Found at i:10356359 original size:15 final size:15
Alignment explanation
Indices: 10356339--10356369 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10356329 CCCCTCATTT
10356339 AAGTGATTACCTTTG
1 AAGTGATTACCTTTG
10356354 AAGTGATTACCTTTG
1 AAGTGATTACCTTTG
10356369 A
1 A
10356370 TTCAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (15 bp):
AAGTGATTACCTTTG
Found at i:10359849 original size:11 final size:11
Alignment explanation
Indices: 10359829--10359865 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
10359819 ACCAAGAGTC
*
10359829 AAAAGGAGCCA
1 AAAACGAGCCA
*
10359840 AAAACTAGCCA
1 AAAACGAGCCA
10359851 AAAACGAGCCA
1 AAAACGAGCCA
10359862 AAAA
1 AAAA
10359866 GGGACAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.59, C:0.22, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAACGAGCCA
Found at i:10360923 original size:13 final size:13
Alignment explanation
Indices: 10360905--10360929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10360895 GTTTAATTAC
10360905 TTAATTAGTTTAG
1 TTAATTAGTTTAG
10360918 TTAATTAGTTTA
1 TTAATTAGTTTA
10360930 ATAAACAACC
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:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTAATTAGTTTAG
Found at i:10373156 original size:13 final size:13
Alignment explanation
Indices: 10373138--10373172 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
10373128 AATCGTACAA
*
10373138 GGGCGTGTCACAT
1 GGGCGTGTCACAC
10373151 GGGCGTGTCACAC
1 GGGCGTGTCACAC
10373164 GGGCGTGTC
1 GGGCGTGTC
10373173 CCTACCGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.11, C:0.26, G:0.43, T:0.20
Consensus pattern (13 bp):
GGGCGTGTCACAC
Found at i:10380589 original size:26 final size:26
Alignment explanation
Indices: 10380559--10380608 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
10380549 ATGGTTTGGT
10380559 ATATATGTTCGGTTTGGTGTTTGTGC
1 ATATATGTTCGGTTTGGTGTTTGTGC
10380585 ATATATGTTCGGTTTGGTGTTTGT
1 ATATATGTTCGGTTTGGTGTTTGT
10380609 AGGTTGACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.06, G:0.30, T:0.52
Consensus pattern (26 bp):
ATATATGTTCGGTTTGGTGTTTGTGC
Found at i:10389158 original size:18 final size:18
Alignment explanation
Indices: 10389127--10389163 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10389117 AAGTTAAGTC
10389127 TGAGATTCATCGAGCTGTA
1 TGAGATTCATCGAGC-GTA
10389146 TGAGATT-ATCGAGCGTA
1 TGAGATTCATCGAGCGTA
10389163 T
1 T
10389164 CGGGTCGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 7 0.39
19 7 0.39
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (18 bp):
TGAGATTCATCGAGCGTA
Found at i:10392727 original size:24 final size:25
Alignment explanation
Indices: 10392678--10392727 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
10392668 ACCCTTCTCA
* *
10392678 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCCCTCTCATTGTTC
10392703 TCTCTTCA-TTCCCT-TCCATTGTTC
1 TCTCTTCACTTCCCTCT-CATTGTTC
10392727 T
1 T
10392728 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 1 0.05
24 13 0.59
25 8 0.36
ACGTcount: A:0.08, C:0.36, G:0.02, T:0.54
Consensus pattern (25 bp):
TCTCTTCACTTCCCTCTCATTGTTC
Found at i:10394531 original size:39 final size:39
Alignment explanation
Indices: 10394487--10394564 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
10394477 AGTTAGCAGA
10394487 AATATTCCTCATGAAGTATTTCCTGCCTAGCAAGAATGC
1 AATATTCCTCATGAAGTATTTCCTGCCTAGCAAGAATGC
10394526 AATATTCCTCATGAAGTATTTCCTGCCTAGCAAGAATGC
1 AATATTCCTCATGAAGTATTTCCTGCCTAGCAAGAATGC
10394565 TAAGTTGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (39 bp):
AATATTCCTCATGAAGTATTTCCTGCCTAGCAAGAATGC
Found at i:10395819 original size:89 final size:89
Alignment explanation
Indices: 10395612--10395911 Score: 283
Period size: 89 Copynumber: 3.4 Consensus size: 89
10395602 CTGATATTTC
* * * * * * * * **
10395612 GATCTGCTCTCCGTCGAACACAAAGATGTCAAATCTACTAT-TTCTGATTTGCTCTCT-AACCAT
1 GATCTGCTCTCTGAC-AATACAGAGATGCCAAATCTGCTATCTTC-GATCTGGTCTCTGAAAAAT
10395675 ACAGAGATGCCAAATCTGCTATC-CT
64 ACAGAGATGCCAAATCTGCTATCTCT
* * * *
10395700 CGATCTGCTC-CTGACAATACAGGGATGCCAAATCTGCT-TCTTGGAT-T-TTCTCCTCGTTAAA
1 -GATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTGGTCT-CT-G-AAAA
* *
10395761 ATAC-GAAGATGCCAAATCTACTTTCTCT
62 ATACAG-AGATGCCAAATCTGCTATCTCT
* * *
10395789 GATTTGCTCTCTGACCATACAGAAATGCCAAATCTGCTATCTTCGATCTGGTCTCTGAAAAATAC
1 GATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTGGTCTCTGAAAAATAC
* *
10395854 AGAGACGCCAAATCTGCTATCTTT
66 AGAGATGCCAAATCTGCTATCTCT
*
10395878 GATCTGCCCTCTGACAATACAGAGATGCCAAATC
1 GATCTGCTCTCTGACAATACAGAGATGCCAAATC
10395912 ATCTTAGATT
Statistics
Matches: 170, Mismatches: 29, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
84 3 0.02
85 3 0.02
86 4 0.02
87 21 0.12
88 33 0.19
89 91 0.54
90 9 0.05
91 3 0.02
92 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (89 bp):
GATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTGGTCTCTGAAAAATAC
AGAGATGCCAAATCTGCTATCTCT
Found at i:10395869 original size:45 final size:44
Alignment explanation
Indices: 10395609--10395911 Score: 274
Period size: 44 Copynumber: 6.8 Consensus size: 44
10395599 ATGCTGATAT
* * * * * *
10395609 TTCGATCTGCTCTCCGTCGAACACAAAGATGTCAAATCTACTAT-
1 TTCGATCTGCTCTCTGAC-AATACAGAGATGCCAAATCTGCTATC
* * *
10395653 TTCTGATTTGCTCTCTAACCATACAGAGATGCCAAATCTGCTATC
1 TTC-GATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATC
* *
10395698 CTCGATCTGCTC-CTGACAATACAGGGATGCCAAATCTGCT-TC
1 TTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATC
* * * * * * *
10395740 TTGGATTTTCTCCTCGTTAAAATAC-GAAGATGCCAAATCTACTTTC
1 TTCGATCTGCT-CTC-TGACAATACAG-AGATGCCAAATCTGCTATC
* * *
10395786 -TCTGATTTGCTCTCTGACCATACAGAAATGCCAAATCTGCTATC
1 TTC-GATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATC
* * *
10395830 TTCGATCTGGTCTCTGAAAAATACAGAGACGCCAAATCTGCTATC
1 TTCGATCTGCTCTCTG-ACAATACAGAGATGCCAAATCTGCTATC
* *
10395875 TTTGATCTGCCCTCTGACAATACAGAGATGCCAAATC
1 TTCGATCTGCTCTCTGACAATACAGAGATGCCAAATC
10395912 ATCTTAGATT
Statistics
Matches: 207, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
42 9 0.04
43 26 0.13
44 85 0.41
45 78 0.38
46 9 0.04
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (44 bp):
TTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATC
Found at i:10408168 original size:12 final size:13
Alignment explanation
Indices: 10408152--10408189 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
10408142 AAGTAATGTA
10408152 AGGTATAATATAT
1 AGGTATAATATAT
*
10408165 -GGTAAAATATAT
1 AGGTATAATATAT
10408177 AGTGTATAATATA
1 AG-GTATAATATA
10408190 ATTTGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
13 1 0.05
14 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (13 bp):
AGGTATAATATAT
Found at i:10408235 original size:21 final size:19
Alignment explanation
Indices: 10408203--10408256 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
10408193 TGTAAACAAA
10408203 ATATATAATAATATAAACC
1 ATATATAATAATATAAACC
**
10408222 ATATGATAAGTAATATAAAAA
1 ATAT-ATAA-TAATATAAACC
10408243 ATATATATATAATA
1 ATATATA-ATAATA
10408257 AGATGTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 14 0.47
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
ATATATAATAATATAAACC
Found at i:10408277 original size:12 final size:12
Alignment explanation
Indices: 10408247--10408369 Score: 64
Period size: 12 Copynumber: 10.4 Consensus size: 12
10408237 TAAAAAATAT
10408247 ATATATAATAAGA
1 ATATATAATAA-A
*
10408260 TGTATATAATAAA
1 -ATATATAATAAA
10408273 ATATATAAT-AA
1 ATATATAATAAA
*
10408284 A-A-AGAA-AAA
1 ATATATAATAAA
*
10408293 ATACTATAAGGAATA
1 ATA-TATAA-TAA-A
10408308 ATATATAATAAA
1 ATATATAATAAA
**
10408320 ATATGAT-ATGTA
1 ATAT-ATAATAAA
**
10408332 ATA-A-AATATG
1 ATATATAATAAA
*
10408342 ATATGTAATAAA
1 ATATATAATAAA
10408354 ATATA-AATAAA
1 ATATATAATAAA
10408365 ATATA
1 ATATA
10408370 ATGAAATAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
9 6 0.07
10 9 0.11
11 14 0.16
12 30 0.35
13 5 0.06
14 17 0.20
15 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:10408328 original size:17 final size:17
Alignment explanation
Indices: 10408308--10408357 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
10408298 ATAAGGAATA
*
10408308 ATATATAATAAAATATG
1 ATATGTAATAAAATATG
10408325 ATATGTAATAAAATATG
1 ATATGTAATAAAATATG
10408342 ATATGTAATAAAATAT
1 ATATGTAATAAAATAT
10408358 AAATAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
ATATGTAATAAAATATG
Found at i:10408484 original size:21 final size:20
Alignment explanation
Indices: 10408460--10408577 Score: 62
Period size: 21 Copynumber: 5.8 Consensus size: 20
10408450 ATTAATGAAT
*
10408460 AATAATACATAATTTATAGAA
1 AATAATA-ATAATATATAGAA
* *
10408481 AATAAAAAATAATATATATAA
1 AAT-AATAATAATATATAGAA
* *
10408502 AATATATAATAAAATATA-ATT
1 AATA-ATAATAATATATAGA-A
* *
10408523 TATAAGTAA-AATATATA-AT
1 AATAA-TAATAATATATAGAA
* * *
10408542 AATAAAAATAATATAATGGAT
1 AATAATAATAATAT-ATAGAA
*
10408563 AATAAAAATAATATA
1 AATAATAATAATATA
10408578 CATTATTTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
18 2 0.03
19 10 0.13
20 14 0.18
21 50 0.63
22 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (20 bp):
AATAATAATAATATATAGAA
Found at i:10408507 original size:11 final size:12
Alignment explanation
Indices: 10408482--10408519 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
10408472 TTTATAGAAA
10408482 ATAA-AAAATAAT
1 ATAATAAAAT-AT
10408494 ATATATAAAATAT
1 ATA-ATAAAATAT
10408507 ATAATAAAATAT
1 ATAATAAAATAT
10408519 A
1 A
10408520 ATTTATAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 13 0.54
13 6 0.25
14 5 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATAAAATAT
Found at i:10408512 original size:28 final size:30
Alignment explanation
Indices: 10408481--10408556 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 30
10408471 ATTTATAGAA
10408481 AATAAAAAATAATATAT-A-TAAAATATAT
1 AATAAAAAATAATATATAAGTAAAATATAT
* *
10408509 AATAAAATATAATTTATAAGTAAAATATAT
1 AATAAAAAATAATATATAAGTAAAATATAT
10408539 AATAATAAAAATAATATA
1 AAT-A-AAAAATAATATA
10408557 ATGGATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 15 0.38
29 1 0.03
30 13 0.32
31 1 0.03
32 10 0.25
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (30 bp):
AATAAAAAATAATATATAAGTAAAATATAT
Found at i:10408520 original size:19 final size:19
Alignment explanation
Indices: 10408496--10408557 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
10408486 AAAATAATAT
10408496 ATATAAAATATATAATAAA
1 ATATAAAATATATAATAAA
*
10408515 ATAT--AATTTATAAGTAAA
1 ATATAAAATATATAA-TAAA
* *
10408533 ATATATAATA-ATAAAAATA
1 ATATAAAATATATAATAA-A
10408552 ATATAA
1 ATATAA
10408558 TGGATAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 8 0.23
18 10 0.29
19 14 0.40
20 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATATAAAATATATAATAAA
Found at i:10408557 original size:30 final size:28
Alignment explanation
Indices: 10408484--10408558 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 28
10408474 TATAGAAAAT
10408484 AAAAAATAATATATATAAAATATATAATA
1 AAAAAATAATATA-ATAAAATATATAATA
*
10408513 AAATATAAT-TTATAAGTAAAATATATAATA
1 AAA-A-AATAATATAA-TAAAATATATAATA
10408543 ATAAAAATAATATAAT
1 A-AAAAATAATATAAT
10408559 GGATAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
29 8 0.21
30 26 0.67
31 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAAAATAATATAATAAAATATATAATA
Found at i:10408572 original size:18 final size:17
Alignment explanation
Indices: 10408479--10408572 Score: 59
Period size: 17 Copynumber: 5.4 Consensus size: 17
10408469 TAATTTATAG
*
10408479 AAAATA-AAAAATAATA
1 AAAATATAATAATAATA
* * *
10408495 TATATAAAATATATAAT-
1 AAAATATAATA-ATAATA
*
10408512 AAAATATAATTTATAAGTA
1 AAAATATAA-TAATAA-TA
10408531 AAATATATAATAATAA-A
1 AAA-ATATAATAATAATA
*
10408548 AATAATATAATGGATAATA
1 AA-AATATAAT-AATAATA
10408567 AAAATA
1 AAAATA
10408573 ATATACATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
16 4 0.07
17 23 0.38
18 16 0.27
19 11 0.18
20 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAATATAATAATAATA
Found at i:10408572 original size:37 final size:37
Alignment explanation
Indices: 10408496--10408569 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
10408486 AAAATAATAT
* * **
10408496 ATATAAAATATATAATAAAATATAATTTATAAGTAAA
1 ATATATAATATATAAAAAAATATAATGGATAAGTAAA
10408533 ATATATAATA-ATAAAAATAATATAATGGATAA-TAAA
1 ATATATAATATATAAAAA-AATATAATGGATAAGTAAA
10408569 A
1 A
10408570 ATAATATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 11 0.34
37 21 0.66
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (37 bp):
ATATATAATATATAAAAAAATATAATGGATAAGTAAA
Found at i:10418007 original size:40 final size:40
Alignment explanation
Indices: 10417940--10418016 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
10417930 TTGGTGCCAC
* *
10417940 ATATAGCCGAAGCTATTCTAATTCACACACTAAGTGCTAT
1 ATATAGCCGAAGCTATTCGAATACACACACTAAGTGCTAT
**
10417980 ATATAGCCGAAGCTATCTCGAA-ACACACGGTAAGTGC
1 ATATAGCCGAAGCTAT-TCGAATACACACACTAAGTGC
10418017 CAACCATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (40 bp):
ATATAGCCGAAGCTATTCGAATACACACACTAAGTGCTAT
Found at i:10422833 original size:44 final size:47
Alignment explanation
Indices: 10422778--10422899 Score: 146
Period size: 44 Copynumber: 2.7 Consensus size: 47
10422768 ATACGCGTGT
10422778 TGATGCATGTCCCAGACATGTCTTACACTAGAAC-AACTCT-T-A-GC
1 TGATGCATGTCCCAGACATGTCTTACACTAG-ACTAACTCTGTCAGGC
* * * *
10422822 TGATGCGTGTCCCAGACACGTCTTACACT-GGCTATCTCTGTCGAGGC
1 TGATGCATGTCCCAGACATGTCTTACACTAGACTAACTCTGTC-AGGC
*
10422869 CGATGCATGTCCCAGACATGTCTTACACTAG
1 TGATGCATGTCCCAGACATGTCTTACACTAG
10422900 CCCTCATCTG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
42 1 0.02
43 6 0.09
44 28 0.43
46 1 0.02
47 28 0.43
48 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
TGATGCATGTCCCAGACATGTCTTACACTAGACTAACTCTGTCAGGC
Found at i:10422883 original size:47 final size:46
Alignment explanation
Indices: 10422823--10422949 Score: 130
Period size: 47 Copynumber: 2.7 Consensus size: 46
10422813 ACTCTTAGCT
*
10422823 GATGCGTGTCCCAGACACGTCTTACACTGGCTATC-TCTGTCGAGGCC
1 GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCTG--GAGGCC
* * ** *
10422870 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCATCTGGATGCC
1 GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCTGGAGGCC
* * *
10422916 GATGCCATGTCCTAGATATGGTCTTACACTGGCT
1 GATG-CATGTCCCAGACA-CGTCTTACACTGGCT
10422950 CTAATAATGT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
46 9 0.14
47 41 0.62
48 16 0.24
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCTGGAGGCC
Found at i:10425768 original size:15 final size:16
Alignment explanation
Indices: 10425727--10425761 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10425717 GTATATTTAC
*
10425727 TTATTATATAAGTATA
1 TTATTAAATAAGTATA
10425743 TTATTAAATAA-TATA
1 TTATTAAATAAGTATA
10425758 TTAT
1 TTAT
10425762 ATAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTATTAAATAAGTATA
Found at i:10426010 original size:19 final size:20
Alignment explanation
Indices: 10425964--10426004 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
10425954 AAAAGCAGTG
10425964 AAAGAAAGAACGAAAGGAGA
1 AAAGAAAGAACGAAAGGAGA
10425984 AAAGAAAGAA-GAAAGG-GA
1 AAAGAAAGAACGAAAGGAGA
10426002 AAA
1 AAA
10426005 TTAAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAACGAAAGGAGA
Found at i:10427320 original size:18 final size:19
Alignment explanation
Indices: 10427278--10427329 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
10427268 AAAGATCGAC
10427278 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* *
10427297 TGTTACTGTAT-ATTTGAT
1 TGTTACTGAATAATTTAAT
*
10427315 TTTTACTGAATAATT
1 TGTTACTGAATAATT
10427330 GACTATTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.52
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:10427338 original size:18 final size:18
Alignment explanation
Indices: 10427275--10427339 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
10427265 TGGAAAGATC
10427275 GACTGTTACTGAATAATTT
1 GACTGTTACTGAATAA-TT
* * * *
10427294 AATTGTTACTGTATATTT
1 GACTGTTACTGAATAATT
* *
10427312 GATTTTTACTGAATAATT
1 GACTGTTACTGAATAATT
*
10427330 GACTATTACT
1 GACTGTTACT
10427340 AGATAACCGA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
18 24 0.67
19 12 0.33
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (18 bp):
GACTGTTACTGAATAATT
Found at i:10433164 original size:94 final size:92
Alignment explanation
Indices: 10432916--10433189 Score: 267
Period size: 94 Copynumber: 2.9 Consensus size: 92
10432906 TGGGATATAT
* * * *
10432916 TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATACGTGTGCTGATGCATGTCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTG-GCCGAAGCATGTCC
*
10432981 CAGACATGTCTTACACTAGCACAACTTTTA
64 CAAACATGTCTTACACTAGCAC-ACTTTTA
* *** * *
10433011 -GCCGAT-CCGTGTCCCAGACA-CACCTTACACTGGCTAT-AT-CTGTCGAGGCC-AATGCATGT
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT---GGCCGAA-GCATGT
10433070 CCCAAACATGTCTTACACTAGC-C-CTTGTCTAGA
62 CCCAAACATGTCTTACACTAGCACACTT-T-T--A
*
10433103 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCA
* *
10433168 AACATGTCTTACATTGGCACAC
66 AACATGTCTTACACTAGCACAC
10433190 AAATCACCCA
Statistics
Matches: 143, Mismatches: 20, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
88 3 0.02
89 3 0.02
90 3 0.02
91 31 0.22
92 15 0.10
93 19 0.13
94 47 0.33
95 16 0.11
96 3 0.02
97 3 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (92 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCA
AACATGTCTTACACTAGCACACTTTTA
Found at i:10440733 original size:13 final size:13
Alignment explanation
Indices: 10440715--10440741 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10440705 GAAGTAATCA
10440715 CACACGGGCGTGT
1 CACACGGGCGTGT
10440728 CACACGGGCGTGT
1 CACACGGGCGTGT
10440741 C
1 C
10440742 CCTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:10442333 original size:22 final size:19
Alignment explanation
Indices: 10442308--10442349 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
10442298 TGATAATCAT
10442308 TAATATATAATTATATGTATTA
1 TAATATAT-ATTA-AT-TATTA
10442330 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
10442349 T
1 T
10442350 CAACTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:10442414 original size:15 final size:16
Alignment explanation
Indices: 10442388--10442420 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
10442378 AAATTTGATC
10442388 ATATTTTATTTAATAA
1 ATATTTTATTTAATAA
10442404 ATATTTT-TTTAATAA
1 ATATTTTATTTAATAA
10442419 AT
1 AT
10442421 TAATAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTATTTAATAA
Found at i:10442960 original size:3 final size:3
Alignment explanation
Indices: 10442952--10442989 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
10442942 TGAGGATCCT
*
10442952 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
10442990 TCCCACAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:10448448 original size:29 final size:29
Alignment explanation
Indices: 10448415--10448513 Score: 180
Period size: 29 Copynumber: 3.4 Consensus size: 29
10448405 TTGTGTGTAC
*
10448415 AATGTGAAAAGGGATAGCTTCGGCTATCA
1 AATGTGAAAAGGGATAGCTTCGGCTATCG
*
10448444 AATGTGAAAAGGGATAGCTTCAGCTATCG
1 AATGTGAAAAGGGATAGCTTCGGCTATCG
10448473 AATGTGAAAAGGGATAGCTTCGGCTATCG
1 AATGTGAAAAGGGATAGCTTCGGCTATCG
10448502 AATGTGAAAAGG
1 AATGTGAAAAGG
10448514 AAAGGTATAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.23
Consensus pattern (29 bp):
AATGTGAAAAGGGATAGCTTCGGCTATCG
Found at i:10448543 original size:33 final size:33
Alignment explanation
Indices: 10448506--10448634 Score: 143
Period size: 33 Copynumber: 3.9 Consensus size: 33
10448496 CTATCGAATG
10448506 TGAAAAGGAAAGGTATACTTTGTGTATACCATT
1 TGAAAAGGAAAGGTATACTTTGTGTATACCATT
*** * * * *
10448539 TGAAAAGTTTATGTACACTTTGTGTGTA-CACT
1 TGAAAAGGAAAGGTATACTTTGTGTATACCATT
* **
10448571 TGGAAAGGTTAGGTATACTTTGTGTATACCATT
1 TGAAAAGGAAAGGTATACTTTGTGTATACCATT
* *
10448604 TGAAAAGGAAATGTATACTTTGTGTGTACCA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCA
10448635 CTCGGAAAGA
Statistics
Matches: 77, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (33 bp):
TGAAAAGGAAAGGTATACTTTGTGTATACCATT
Found at i:10448585 original size:65 final size:66
Alignment explanation
Indices: 10448516--10448643 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 66
10448506 TGAAAAGGAA
*** *
10448516 AGGTATACTTTGTGTATACCATTTGAAAAGTTTATGTACACTTTGTGTGTA-CACTTGGAAAGGT
1 AGGTATACTTTGTGTATACCATTTGAAAAGGAAATGTACACTTTGTGTGTACCACTCGGAAAGGT
10448580 T
66 T
*
10448581 AGGTATACTTTGTGTATACCATTTGAAAAGGAAATGTATACTTTGTGTGTACCACTCGGAAAG
1 AGGTATACTTTGTGTATACCATTTGAAAAGGAAATGTACACTTTGTGTGTACCACTCGGAAAG
10448644 AAATGTACAC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
65 47 0.82
66 10 0.18
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.37
Consensus pattern (66 bp):
AGGTATACTTTGTGTATACCATTTGAAAAGGAAATGTACACTTTGTGTGTACCACTCGGAAAGGT
T
Found at i:10451567 original size:43 final size:43
Alignment explanation
Indices: 10451469--10451568 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 43
10451459 TCAGATAATC
*
10451469 ACACATATAGTACAATGCCAACGTCCCAGACGTGGTCTTACATGT
1 ACACATATA-T-CGATGCCAACGTCCCAGACGTGGTCTTACATGT
*
10451514 A-ATCACATATCGATGCC-ACTGTCCCAGACAG-GGTCTTAC-TCGT
1 ACA-CATATATCGATGCCAAC-GTCCCAGAC-GTGGTCTTACAT-GT
10451557 ACACATATATCG
1 ACACATATATCG
10451569 GTGTCACATA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
42 3 0.06
43 34 0.72
44 4 0.09
45 6 0.13
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
ACACATATATCGATGCCAACGTCCCAGACGTGGTCTTACATGT
Found at i:10458728 original size:32 final size:32
Alignment explanation
Indices: 10458668--10458728 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
10458658 ATCAAAGATG
*
10458668 GTTTACAAATGCTAATCTAGGTACCAAATATT
1 GTTTACAAATGCTAATCTAGGAACCAAATATT
*
10458700 GTTTACAAATGCTAATCTAGGAAGCAAAT
1 GTTTACAAATGCTAATCTAGGAACCAAAT
10458729 CTAACTTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
GTTTACAAATGCTAATCTAGGAACCAAATATT
Found at i:10462374 original size:26 final size:26
Alignment explanation
Indices: 10462344--10462397 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
10462334 GGCTGATCAG
10462344 ATGCGGGCTCCGGGTTCTGATTCTGC
1 ATGCGGGCTCCGGGTTCTGATTCTGC
10462370 ATGCGGGCTCCGGGTTCTGATTCTGC
1 ATGCGGGCTCCGGGTTCTGATTCTGC
10462396 AT
1 AT
10462398 AGTCGCCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.09, C:0.26, G:0.33, T:0.31
Consensus pattern (26 bp):
ATGCGGGCTCCGGGTTCTGATTCTGC
Found at i:10469007 original size:34 final size:33
Alignment explanation
Indices: 10468961--10469024 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
10468951 TATGCATTAC
10468961 TGATACTGTACTGA-ATTGGGC-TAAGGCCCACAT
1 TGATACTGTACTGATA-TGGGCTTAA-GCCCACAT
*
10468994 TGATATTGCTACTGATATGGGCTTAAGCCCA
1 TGATACTG-TACTGATATGGGCTTAAGCCCA
10469025 GACTGTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 7 0.26
34 16 0.59
35 4 0.15
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (33 bp):
TGATACTGTACTGATATGGGCTTAAGCCCACAT
Found at i:10473231 original size:21 final size:21
Alignment explanation
Indices: 10473207--10473248 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
10473197 TCACTCCTCC
10473207 ACTATTGTAACGCTCAAATTT
1 ACTATTGTAACGCTCAAATTT
*
10473228 ACTATTGTAACGCTTAAATTT
1 ACTATTGTAACGCTCAAATTT
10473249 TCTTAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
ACTATTGTAACGCTCAAATTT
Found at i:10473378 original size:9 final size:9
Alignment explanation
Indices: 10473364--10473405 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
10473354 AATAAAGGGG
10473364 AAGAAAGAA
1 AAGAAAGAA
10473373 AAGAAAGAA
1 AAGAAAGAA
*
10473382 AAGAAA-AG
1 AAGAAAGAA
*
10473390 AAGAAAAACA
1 AAGAAAGA-A
10473400 AAGAAA
1 AAGAAA
10473406 CATGAAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.24
9 16 0.55
10 6 0.21
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAGAA
Found at i:10473382 original size:13 final size:13
Alignment explanation
Indices: 10473364--10473405 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
10473354 AATAAAGGGG
10473364 AAGAAAGAAAAGA
1 AAGAAAGAAAAGA
10473377 AAGAAAAGAAAAG-
1 AAG-AAAGAAAAGA
*
10473390 AAGAAAAACAAAGA
1 AAGAAAGA-AAAGA
10473404 AA
1 AA
10473406 CATGAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.16
13 10 0.40
14 11 0.44
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAAGA
Found at i:10473386 original size:14 final size:14
Alignment explanation
Indices: 10473367--10473405 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
10473357 AAAGGGGAAG
10473367 AAAGAAAAGAAAGA
1 AAAGAAAAGAAAGA
10473381 AAAGAAAAG-AAGA
1 AAAGAAAAGAAAGA
10473394 AAA-ACAAAGAAA
1 AAAGA-AAAGAAA
10473406 CATGAAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 11 0.48
14 11 0.48
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAGA
Found at i:10476044 original size:18 final size:18
Alignment explanation
Indices: 10476023--10476059 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10476013 AAAAGAAAAC
10476023 ACAAAATTGAATCTCTTT
1 ACAAAATTGAATCTCTTT
10476041 ACAAAATTGAATCTCTTT
1 ACAAAATTGAATCTCTTT
10476059 A
1 A
10476060 TTGATCTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (18 bp):
ACAAAATTGAATCTCTTT
Found at i:10478166 original size:120 final size:121
Alignment explanation
Indices: 10477944--10478167 Score: 317
Period size: 122 Copynumber: 1.9 Consensus size: 121
10477934 GCTCATTATT
* * * * * *
10477944 CTATCATTTAATTTATATTCTTAGGTTAGTTATCATGCATTTCGTGTTAAATCGAGTTCTTAGGA
1 CTATCATTTAATTTACATTCTTAGGTTAGTTACCATACATTCCGTGTTAAATCAAG-TATTAGGA
* *
10478009 AAACCTCATACCCATGACATTACTATGCTTATTCTCATGCTATTACTATATTAATGC
65 AAACCCCACACCCATGACATTACTATGCTTATTCTCATGCTATTACTATATTAATGC
* *
10478066 CTATTATTTAATTTGCATTCTTAGGTTAGTTACCATACATTCCGTGTTAAATCAAG-ATTAGGAA
1 CTATCATTTAATTTACATTCTTAGGTTAGTTACCATACATTCCGTGTTAAATCAAGTATTAGGAA
*
10478130 AACCCCACACCCATGACATTACTAT-TTTCATTCTCATG
66 AACCCCACACCCATGACATTACTATGCTT-ATTCTCATG
10478168 GTTAGGTTGG
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
119 2 0.02
120 39 0.43
122 49 0.54
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (121 bp):
CTATCATTTAATTTACATTCTTAGGTTAGTTACCATACATTCCGTGTTAAATCAAGTATTAGGAA
AACCCCACACCCATGACATTACTATGCTTATTCTCATGCTATTACTATATTAATGC
Found at i:10480549 original size:77 final size:77
Alignment explanation
Indices: 10480422--10480565 Score: 225
Period size: 77 Copynumber: 1.9 Consensus size: 77
10480412 CATGCGGCGG
* ** *
10480422 CTTCATATGCTGACATCTCTAAGCGCATCACCCGATTCGAGCAGTAGTGTTTTCAATGATTTGAC
1 CTTCATATGCTCACATCTCTAAGCGCATCACCCGATTCGAGCAACAGTGTTTTCAACGATTTGAC
10480487 AAAATGCAACGA
66 AAAATGCAACGA
* * *
10480499 CTTCATATGCTCACATCTCTAAGTGCCTCACCTGATTCGAGCAACAGTGTTTTCAACGATTTGAC
1 CTTCATATGCTCACATCTCTAAGCGCATCACCCGATTCGAGCAACAGTGTTTTCAACGATTTGAC
10480564 AA
66 AA
10480566 CATTGATGCT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 60 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (77 bp):
CTTCATATGCTCACATCTCTAAGCGCATCACCCGATTCGAGCAACAGTGTTTTCAACGATTTGAC
AAAATGCAACGA
Found at i:10498601 original size:122 final size:122
Alignment explanation
Indices: 10498379--10498605 Score: 429
Period size: 122 Copynumber: 1.9 Consensus size: 122
10498369 TGCTCATTAT
10498379 TCTATCATTTAATTTGTATTCTTAGGTTAGTTATCATACATTTCTTGTTAAATTAAGTTCTTAGG
1 TCTATCATTTAATTTGTATTCTTAGGTTAGTTATCATACATTTCTTGTTAAATTAAGTTCTTAGG
10498444 AAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACTATGCTAATG
66 AAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACTATGCTAATG
10498501 TCTATCATTTAATTTGTATTCTTAGGTTAGTTATCATACATTTCTTGTTAAATTAAGTTCTTAGG
1 TCTATCATTTAATTTGTATTCTTAGGTTAGTTATCATACATTTCTTGTTAAATTAAGTTCTTAGG
*
10498566 AAAACCCCATACCCATGACATTACTAT-TTTCATTCTCATG
66 AAAACCCCATACCCATGACATTACTATGCTT-ATTCTCATG
10498606 GTTATTTTGG
Statistics
Matches: 103, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
121 2 0.02
122 101 0.98
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (122 bp):
TCTATCATTTAATTTGTATTCTTAGGTTAGTTATCATACATTTCTTGTTAAATTAAGTTCTTAGG
AAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACTATGCTAATG
Found at i:10507657 original size:20 final size:20
Alignment explanation
Indices: 10507632--10507671 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10507622 CGAGAGATTC
10507632 ATGATTGAAAGGTTTTAAAT
1 ATGATTGAAAGGTTTTAAAT
10507652 ATGATTGAAAGGTTTTAAAT
1 ATGATTGAAAGGTTTTAAAT
10507672 TTAAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
ATGATTGAAAGGTTTTAAAT
Found at i:10507680 original size:20 final size:20
Alignment explanation
Indices: 10507637--10507681 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
10507627 GATTCATGAT
* *
10507637 TGAAAGGTTTTAAATATGAT
1 TGAAAGGTTTTAAATATAAA
*
10507657 TGAAAGGTTTTAAATTTAAA
1 TGAAAGGTTTTAAATATAAA
10507677 TGAAA
1 TGAAA
10507682 TTTTGTGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (20 bp):
TGAAAGGTTTTAAATATAAA
Found at i:10511292 original size:31 final size:29
Alignment explanation
Indices: 10511223--10511296 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
10511213 ACAAAATAAT
**
10511223 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
*
10511252 AACATAAGTGACTAAAATGTAACCTGGGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
10511283 AACAAAAGTGACTA
1 AACATAAGTGACTA
10511297 TTTTTATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:10513830 original size:6 final size:6
Alignment explanation
Indices: 10513815--10513864 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
10513805 AACAAACAAA
*
10513815 ACACAC ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACAC-T
1 ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT
10513862 ACA
1 ACA
10513865 AATAAAGCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 4 0.09
6 39 0.91
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (6 bp):
ACACAT
Found at i:10515569 original size:19 final size:19
Alignment explanation
Indices: 10515527--10515569 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
10515517 AATCTTTCTT
* *
10515527 AAAA-AAAAGGGAAAATAA
1 AAAATAAAAGGAAAAAGAA
10515545 AGAAATAAAAGGAAAAAGAA
1 A-AAATAAAAGGAAAAAGAA
10515565 AAAAT
1 AAAAT
10515570 TGTAATTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 7 0.33
20 13 0.62
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (19 bp):
AAAATAAAAGGAAAAAGAA
Found at i:10519150 original size:14 final size:14
Alignment explanation
Indices: 10519131--10519157 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10519121 CTTTTATTTC
10519131 CATTCATCGTTTAA
1 CATTCATCGTTTAA
10519145 CATTCATCGTTTA
1 CATTCATCGTTTA
10519158 GTAGAGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (14 bp):
CATTCATCGTTTAA
Found at i:10521249 original size:28 final size:27
Alignment explanation
Indices: 10521182--10521299 Score: 116
Period size: 25 Copynumber: 4.3 Consensus size: 27
10521172 ATTGCAAATA
*
10521182 ACGATAAGTACCAAAGTGAAAAATAAT
1 ACGATAAGCACCAAAGTGAAAAATAAT
10521209 --GATAAGCACCAAAGTGAAAAATAATT
1 ACGATAAGCACCAAAGTGAAAAATAA-T
**
10521235 ACGATAAGCACCAAAGTGCAAATTTTACA-
1 ACGATAAGCACCAAAGTG-AAA-AATA-AT
* * **
10521264 ACAATAAGCACCGAAGTGCCAAATAAT
1 ACGATAAGCACCAAAGTGAAAAATAAT
10521291 ACGATAAGC
1 ACGATAAGC
10521300 GCGCTAATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
25 23 0.31
26 2 0.03
27 10 0.14
28 17 0.23
29 19 0.26
30 2 0.03
31 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (27 bp):
ACGATAAGCACCAAAGTGAAAAATAAT
Found at i:10523549 original size:45 final size:47
Alignment explanation
Indices: 10523492--10523585 Score: 147
Period size: 46 Copynumber: 2.0 Consensus size: 47
10523482 TAAATTTCCA
*
10523492 TAAAATTTATTTTTT-ATTTTTAAAATGGTGTATTTAATAAAATTGT
1 TAAAATTTATTTTTTGATTTTTAAAATGATGTATTTAATAAAATTGT
* *
10523538 TAAAA-TTATTTTTTGTTTTTTTAAATGATGTATTTAATAAAATTGT
1 TAAAATTTATTTTTTGATTTTTAAAATGATGTATTTAATAAAATTGT
10523584 TA
1 TA
10523586 GGATATCGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 9 0.20
46 35 0.80
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (47 bp):
TAAAATTTATTTTTTGATTTTTAAAATGATGTATTTAATAAAATTGT
Found at i:10528578 original size:906 final size:906
Alignment explanation
Indices: 10526827--10528644 Score: 3575
Period size: 906 Copynumber: 2.0 Consensus size: 906
10526817 TTCTGACTTT
10526827 TATGCATTGATATTTTTTTTTCTACCAAGCACTCAAAGTTTATTTTATTTTATTTTTCCACTCAC
1 TATGCATTGATATTTTTTTTTCTACCAAGCACTCAAAGTTTATTTTATTTTATTTTTCCACTCAC
10526892 TTCTTTCATCCTTCTCAATTAAGCACCCCCCCTAAATGAATGATTAAAACTATCAACATTTAAAA
66 TTCTTTCATCCTTCTCAATTAAGCACCCCCCCTAAATGAATGATTAAAACTATCAACATTTAAAA
10526957 TAACTGGTCTGCATGCACACTCAAAAGGCCGATTTAAATCCTCAATCTATCTATTATGAAAAAAA
131 TAACTGGTCTGCATGCACACTCAAAAGGCCGATTTAAATCCTCAATCTATCTATTATGAAAAAAA
10527022 TTATGATTTTTAAATAATATACCCACATAATGACCATTTAGATTTCGTACTTTATACTAAATTTT
196 TTATGATTTTTAAATAATATACCCACATAATGACCATTTAGATTTCGTACTTTATACTAAATTTT
10527087 CTTAAATTTAATGTTAATAATTCATATCAATATTAATATTATTATGATAAAAAATAAATCAAAAT
261 CTTAAATTTAATGTTAATAATTCATATCAATATTAATATTATTATGATAAAAAATAAATCAAAAT
10527152 AAAATATTTAATTAAAAGTTTTTGAAACCCAGCAAAGGCGGTATAACAATTCTAGTTTATAATAA
326 AAAATATTTAATTAAAAGTTTTTGAAACCCAGCAAAGGCGGTATAACAATTCTAGTTTATAATAA
*
10527217 CAATTTTCCCTTTCCTTTAAAGAGTACTCATGTATTCATTACAAAGTTGTTCTTTTGACAAAATT
391 CAATTTTCCCTTTCCTTTAAAGAGTACTCATATATTCATTACAAAGTTGTTCTTTTGACAAAATT
10527282 ATGAACATGCACACTTCAAAAATGCAGCTTTTCTTTTAGAATTTAAATACAGTAATTACCTCATT
456 ATGAACATGCACACTTCAAAAATGCAGCTTTTCTTTTAGAATTTAAATACAGTAATTACCTCATT
*
10527347 GAAGTGAAGGGAAAGGAACATACAGCGAACTTTTCTTCTTATTCACAATTGAGGAGCTGAGTATT
521 GAAGTGAAGGGAAAGGAACATACAGCGAACTTTTCTTCTTATTCACAATTGAGAAGCTGAGTATT
10527412 TTGATTTCAGGGTGTAGAATTTACTGAAATCCCTTGTGGCATAGGGGAGCTTGATTGATCTTGAT
586 TTGATTTCAGGGTGTAGAATTTACTGAAATCCCTTGTGGCATAGGGGAGCTTGATTGATCTTGAT
10527477 GCAATGGGATAACAAGCCGCTGTAAGGGTTTTAAAGCTACCGTAAGGTCCGCAAAGGATGGACGC
651 GCAATGGGATAACAAGCCGCTGTAAGGGTTTTAAAGCTACCGTAAGGTCCGCAAAGGATGGACGC
*
10527542 AAACTCGGATCACTGGAAACAGAAGCATAAATAGGTTACACTGGAACCAAAATAGCAAAATAAGG
716 AAACTCGGATCACTGCAAACAGAAGCATAAATAGGTTACACTGGAACCAAAATAGCAAAATAAGG
10527607 GGTTAAAAAGTTCAAGTTTCTGTTTACTAACGTCTGCCAGCATTGCCAAATTATTCTTGCAACCA
781 GGTTAAAAAGTTCAAGTTTCTGTTTACTAACGTCTGCCAGCATTGCCAAATTATTCTTGCAACCA
10527672 AAGGATCAAGCTCCTTGGGAATGTCGAGGCGTCGATTCTGGAAACCTACTGCACCTACAAC
846 AAGGATCAAGCTCCTTGGGAATGTCGAGGCGTCGATTCTGGAAACCTACTGCACCTACAAC
10527733 TATGCATTGATATTTTTTTTTCTACCAAGCACTCAAAGTTTATTTTATTTTATTTTTCCACTCAC
1 TATGCATTGATATTTTTTTTTCTACCAAGCACTCAAAGTTTATTTTATTTTATTTTTCCACTCAC
10527798 TTCTTTCATCCTTCTCAATTAAGCACCCCCCCTAAATGAATGATTAAAACTATCAACATTTAAAA
66 TTCTTTCATCCTTCTCAATTAAGCACCCCCCCTAAATGAATGATTAAAACTATCAACATTTAAAA
10527863 TAACTGGTCTGCATGCACACTCAAAAGGCCGATTTAAATCCTCAATCTATCTATTATGAAAAAAA
131 TAACTGGTCTGCATGCACACTCAAAAGGCCGATTTAAATCCTCAATCTATCTATTATGAAAAAAA
10527928 TTATGATTTTTAAATAATATACCCACATAATGACCATTTAGATTTCGTACTTTATACTAAATTTT
196 TTATGATTTTTAAATAATATACCCACATAATGACCATTTAGATTTCGTACTTTATACTAAATTTT
10527993 CTTAAATTTAATGTTAATAATTCATATCAATATTAATATTATTATGATAAAAAATAAATCAAAAT
261 CTTAAATTTAATGTTAATAATTCATATCAATATTAATATTATTATGATAAAAAATAAATCAAAAT
10528058 AAAATATTTAATTAAAAGTTTTTGAAACCCAGCAAAGGCGGTATAACAATTCTAGTTTATAATAA
326 AAAATATTTAATTAAAAGTTTTTGAAACCCAGCAAAGGCGGTATAACAATTCTAGTTTATAATAA
10528123 CAATTTTCCCTTTCCTTTAAAGAGTACTCATATATTCATTACAAAGTTGTTCTTTTGACAAAATT
391 CAATTTTCCCTTTCCTTTAAAGAGTACTCATATATTCATTACAAAGTTGTTCTTTTGACAAAATT
10528188 ATGAACATGCACACTTCAAAAATGCAGCTTTTCTTTTAGAATTTAAATACAGTAATTACCTCATT
456 ATGAACATGCACACTTCAAAAATGCAGCTTTTCTTTTAGAATTTAAATACAGTAATTACCTCATT
10528253 GAAGTGAAGGGAAAGGAACATACAGCGAACTTTTCTTCTTATTCACAATTGAGAAGCTGAGTATT
521 GAAGTGAAGGGAAAGGAACATACAGCGAACTTTTCTTCTTATTCACAATTGAGAAGCTGAGTATT
10528318 TTGATTTCAGGGTGTAGAATTTACTGAAATCCCTTGTGGCATAGGGGAGCTTGATTGATCTTGAT
586 TTGATTTCAGGGTGTAGAATTTACTGAAATCCCTTGTGGCATAGGGGAGCTTGATTGATCTTGAT
*
10528383 GCAATGGGATAACAAGCCGCTGTAAGGGTTTTAAAGCTACCGTAAGGTCCGCAAAGGATGGGCGC
651 GCAATGGGATAACAAGCCGCTGTAAGGGTTTTAAAGCTACCGTAAGGTCCGCAAAGGATGGACGC
10528448 AAACTCGGATCACTGCAAACAGAAGCATAAATAGGTTACACTGGAACCAAAATAGCAAAATAAGG
716 AAACTCGGATCACTGCAAACAGAAGCATAAATAGGTTACACTGGAACCAAAATAGCAAAATAAGG
*
10528513 GGTTAAAACGTTCAAGTTTCTGTTTACTAACGTCTGCCAGCATTGCCAAATTATTCTTGCAACCA
781 GGTTAAAAAGTTCAAGTTTCTGTTTACTAACGTCTGCCAGCATTGCCAAATTATTCTTGCAACCA
*
10528578 AAGGATCGAGCTCCTTGGGAATGTCGAGGCGTCGATTCTGGAAACCTACTGCACCTACAAC
846 AAGGATCAAGCTCCTTGGGAATGTCGAGGCGTCGATTCTGGAAACCTACTGCACCTACAAC
10528639 T-TGCAT
1 TATGCAT
10528645 CGGATTCATT
Statistics
Matches: 906, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
905 5 0.01
906 901 0.99
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (906 bp):
TATGCATTGATATTTTTTTTTCTACCAAGCACTCAAAGTTTATTTTATTTTATTTTTCCACTCAC
TTCTTTCATCCTTCTCAATTAAGCACCCCCCCTAAATGAATGATTAAAACTATCAACATTTAAAA
TAACTGGTCTGCATGCACACTCAAAAGGCCGATTTAAATCCTCAATCTATCTATTATGAAAAAAA
TTATGATTTTTAAATAATATACCCACATAATGACCATTTAGATTTCGTACTTTATACTAAATTTT
CTTAAATTTAATGTTAATAATTCATATCAATATTAATATTATTATGATAAAAAATAAATCAAAAT
AAAATATTTAATTAAAAGTTTTTGAAACCCAGCAAAGGCGGTATAACAATTCTAGTTTATAATAA
CAATTTTCCCTTTCCTTTAAAGAGTACTCATATATTCATTACAAAGTTGTTCTTTTGACAAAATT
ATGAACATGCACACTTCAAAAATGCAGCTTTTCTTTTAGAATTTAAATACAGTAATTACCTCATT
GAAGTGAAGGGAAAGGAACATACAGCGAACTTTTCTTCTTATTCACAATTGAGAAGCTGAGTATT
TTGATTTCAGGGTGTAGAATTTACTGAAATCCCTTGTGGCATAGGGGAGCTTGATTGATCTTGAT
GCAATGGGATAACAAGCCGCTGTAAGGGTTTTAAAGCTACCGTAAGGTCCGCAAAGGATGGACGC
AAACTCGGATCACTGCAAACAGAAGCATAAATAGGTTACACTGGAACCAAAATAGCAAAATAAGG
GGTTAAAAAGTTCAAGTTTCTGTTTACTAACGTCTGCCAGCATTGCCAAATTATTCTTGCAACCA
AAGGATCAAGCTCCTTGGGAATGTCGAGGCGTCGATTCTGGAAACCTACTGCACCTACAAC
Found at i:10533729 original size:20 final size:21
Alignment explanation
Indices: 10533689--10533730 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10533679 GCTCATTCAG
*
10533689 TCCAATTCGACCTACCAAAAT
1 TCCAATTCAACCTACCAAAAT
*
10533710 TCCAATTCAACCT-TCAAAAT
1 TCCAATTCAACCTACCAAAAT
10533730 T
1 T
10533731 ATTAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (21 bp):
TCCAATTCAACCTACCAAAAT
Found at i:10534851 original size:27 final size:30
Alignment explanation
Indices: 10534793--10534852 Score: 90
Period size: 27 Copynumber: 2.1 Consensus size: 30
10534783 GTAAATTTAA
10534793 TTTTTATATTTTGATTTGATATTTTTAAATT
1 TTTTTATATTTT-ATTTGATATTTTTAAATT
10534824 TTTTTATA-TTT-TTTGA-ATTTTTAAATT
1 TTTTTATATTTTATTTGATATTTTTAAATT
10534851 TT
1 TT
10534853 AGTCTTGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 13 0.45
28 5 0.17
30 3 0.10
31 8 0.28
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (30 bp):
TTTTTATATTTTATTTGATATTTTTAAATT
Found at i:10536123 original size:22 final size:22
Alignment explanation
Indices: 10536053--10536123 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
10536043 TCCTTAACTA
*
10536053 AGTATATATGATTAAATAATAAAT
1 AGTATA-ATAATT-AATAATAAAT
* *
10536077 ATTAT-ATAATTTAATTAA-AATT
1 AGTATAATAA-TTAA-TAATAAAT
10536099 AGTATAATAATTAATAATAAAT
1 AGTATAATAATTAATAATAAAT
10536121 AGT
1 AGT
10536124 TCCATGTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
21 3 0.08
22 22 0.58
23 9 0.24
24 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (22 bp):
AGTATAATAATTAATAATAAAT
Found at i:10538692 original size:13 final size:14
Alignment explanation
Indices: 10538676--10538710 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
10538666 GAAATAGGGG
10538676 AAAGAAAG-AATAA
1 AAAGAAAGAAATAA
10538689 AAAGAAAGAAATAA
1 AAAGAAAGAAATAA
10538703 AAAGAAAG
1 AAAGAAAG
10538711 GGAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAGAAAGAAATAA
Found at i:10540400 original size:18 final size:18
Alignment explanation
Indices: 10540377--10540412 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10540367 GTTCAACTAT
10540377 GGTCTTACACATCTTCAC
1 GGTCTTACACATCTTCAC
10540395 GGTCTTACACATCTTCAC
1 GGTCTTACACATCTTCAC
10540413 ATAATGATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (18 bp):
GGTCTTACACATCTTCAC
Found at i:10540465 original size:42 final size:42
Alignment explanation
Indices: 10540395--10540488 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
10540385 ACATCTTCAC
*
10540395 GGTCTTACACATCTTCACATAATGATGCCATAGCCCAGCTAT
1 GGTCTTACACATATTCACATAATGATGCCATAGCCCAGCTAT
* * *
10540437 GGTCTTACACATATTCATAT-ATCTATGCCATAGCCTAGCTAT
1 GGTCTTACACATATTCACATAAT-GATGCCATAGCCCAGCTAT
*
10540479 GGTTTTACAC
1 GGTCTTACAC
10540489 GAATCACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.04
42 44 0.96
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (42 bp):
GGTCTTACACATATTCACATAATGATGCCATAGCCCAGCTAT
Found at i:10540642 original size:31 final size:31
Alignment explanation
Indices: 10540607--10540755 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
10540597 CTTGTCACTT
*
10540607 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
10540638 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
10540669 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
10540700 GTAGCCGAAACTACCACTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
10540731 GTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
10540756 TGTCATTTGT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:10543172 original size:24 final size:24
Alignment explanation
Indices: 10543145--10543194 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
10543135 TGAACTATGG
*
10543145 GTTCATGGAATGGTTATTGATATA
1 GTTCATGGAATGATTATTGATATA
10543169 GTTCATGGAATGATTATTGATATA
1 GTTCATGGAATGATTATTGATATA
10543193 GT
1 GT
10543195 GAGAAGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (24 bp):
GTTCATGGAATGATTATTGATATA
Found at i:10544795 original size:42 final size:42
Alignment explanation
Indices: 10544733--10544813 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
10544723 TTAAGTATGG
* *
10544733 GCACTTAGTGTGAGAAATTGAGATA-ACTTCGGTTATATATTT
1 GCACTTAGTATGAGAAATTGAGATATA-TTCGGCTATATATTT
* *
10544775 GCACTTAGTATGCGAGATTGAGATATATTCGGCTATATA
1 GCACTTAGTATGAGAAATTGAGATATATTCGGCTATATA
10544814 CACATATTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (42 bp):
GCACTTAGTATGAGAAATTGAGATATATTCGGCTATATATTT
Done.