Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_pilon, whole genome shotgun sequence
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: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1621515 original size:20 final size:20
Alignment explanation
Indices: 1621490--1621528 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1621480 TCGAGTTGCG
*
1621490 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGAGTTGCGAATTTC
1621510 ATTTTCGAGTTGCGAATTT
1 ATTTTCGAGTTGCGAATTT
1621529 GAATATCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTC
Found at i:1621534 original size:54 final size:54
Alignment explanation
Indices: 1621452--1621569 Score: 175
Period size: 54 Copynumber: 2.2 Consensus size: 54
1621442 TGATTTCAAT
* *
1621452 TTTCATTTTCGCATTGTGAATTTAAATATCGAGTTGCGATTTTCGTGTTGCGAA
1 TTTCATTTTCGCATTGCGAATTTAAATATCAAGTTGCGATTTTCGTGTTGCGAA
* *
1621506 TTTCATTTTCG-AGTTGCGAATTTGAATATCAAGTTGCGATTTTTGTGTTGCGAA
1 TTTCATTTTCGCA-TTGCGAATTTAAATATCAAGTTGCGATTTTCGTGTTGCGAA
*
1621560 TTTGATTTTC
1 TTTCATTTTC
1621570 TTAAAGGTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.02
54 57 0.98
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.47
Consensus pattern (54 bp):
TTTCATTTTCGCATTGCGAATTTAAATATCAAGTTGCGATTTTCGTGTTGCGAA
Found at i:1621540 original size:20 final size:20
Alignment explanation
Indices: 1621498--1621544 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1621488 CGATTTTCGT
* * *
1621498 GTTGCGAATTTCATTTTCGA
1 GTTGCGAATTTCAATATCAA
*
1621518 GTTGCGAATTTGAATATCAA
1 GTTGCGAATTTCAATATCAA
1621538 GTTGCGA
1 GTTGCGA
1621545 TTTTTGTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTCAATATCAA
Found at i:1623453 original size:20 final size:21
Alignment explanation
Indices: 1623426--1623521 Score: 133
Period size: 21 Copynumber: 4.6 Consensus size: 21
1623416 TGGAATGTGG
*
1623426 ATCTTGAACGATGGGAGGTG-
1 ATCTTGAACGATGGGAGGGGC
*
1623446 ATCATGAACGATGGGAGGGG-
1 ATCTTGAACGATGGGAGGGGC
1623466 ACTCTTGAACGATGGGAGGGGC
1 A-TCTTGAACGATGGGAGGGGC
*
1623488 CTCTTGAACGATGGGAGGGGC
1 ATCTTGAACGATGGGAGGGGC
*
1623509 CTCTTGAACGATG
1 ATCTTGAACGATG
1623522 AGAGATGAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
20 19 0.27
21 51 0.73
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (21 bp):
ATCTTGAACGATGGGAGGGGC
Found at i:1623484 original size:41 final size:42
Alignment explanation
Indices: 1623427--1623574 Score: 158
Period size: 42 Copynumber: 3.6 Consensus size: 42
1623417 GGAATGTGGA
1623427 TCTTGAACGATGGGAGGTG-ATCATGAACGATGGGAGGGGAC
1 TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGGGGAC
* ** * *
1623468 TCTTGAACGATGGGAGGGGCCTCTTGAACGATGGGAGGGGCC
1 TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGGGGAC
* * * *
1623510 TCTTGAACGATGAGAGATGAATCATGAACAAT-GGAGGTGGAT
1 TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGG-GGAC
* * *
1623552 TC-TGAACAATGGTAGGTGGATCA
1 TCTTGAACGATGGGAGGTGAATCA
1623575 GGCTTCTTCT
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
41 39 0.45
42 48 0.55
ACGTcount: A:0.28, C:0.14, G:0.37, T:0.22
Consensus pattern (42 bp):
TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGGGGAC
Found at i:1623559 original size:20 final size:21
Alignment explanation
Indices: 1623534--1623572 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1623524 AGATGAATCA
1623534 TGAACAATGG-AGGTGGATTC
1 TGAACAATGGTAGGTGGATTC
1623554 TGAACAATGGTAGGTGGAT
1 TGAACAATGGTAGGTGGAT
1623573 CAGGCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.26
Consensus pattern (21 bp):
TGAACAATGGTAGGTGGATTC
Found at i:1623881 original size:21 final size:21
Alignment explanation
Indices: 1623857--1624055 Score: 138
Period size: 21 Copynumber: 9.5 Consensus size: 21
1623847 TGAAACAATC
*
1623857 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* * *
1623878 TCACGTAAAGCAGCTACGTAA
1 TCACGTAAAGCACCTACCTCA
* **
1623899 CCACGTAAAGCACCGT-TGTCA
1 TCACGTAAAGCACC-TACCTCA
** *
1623920 TCACGTAAAATAGCTACCTCA
1 TCACGTAAAGCACCTACCTCA
1623941 TCACGTAAAG-ACCATACCTCA
1 TCACGTAAAGCACC-TACCTCA
** * **
1623962 TCACGCCATGCACC-ATTTTCA
1 TCACGTAAAGCACCTA-CCTCA
* *
1623983 TCACGTAAAACACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
*
1624004 TCATGTAAAGCA-CTGACCTCA
1 TCACGTAAAGCACCT-ACCTCA
* *
1624025 TCACGTAAAACACCTAACTCA
1 TCACGTAAAGCACCTACCTCA
1624046 TC-CTGTAAAG
1 TCAC-GTAAAG
1624056 GTGGAGAATA
Statistics
Matches: 135, Mismatches: 34, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
20 6 0.04
21 122 0.90
22 7 0.05
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:1623975 original size:63 final size:63
Alignment explanation
Indices: 1623857--1624029 Score: 163
Period size: 63 Copynumber: 2.7 Consensus size: 63
1623847 TGAAACAATC
* * * * * * ** * *
1623857 TCACGTAGAGCACCTACCTCATCACGTAAAGCAGCT-ACGTAACCACGTAAAGCACCGTTGTCA
1 TCACGTAAAACACCGACCTCATCACGTAAAGCA-CTGACCTCATCACGCCATGCACCATTGTCA
* * * *
1623920 TCACGTAAAATAGCTACCTCATCACGTAAAG-ACCAT-ACCTCATCACGCCATGCACCATTTTCA
1 TCACGTAAAACACCGACCTCATCACGTAAAGCA-C-TGACCTCATCACGCCATGCACCATTGTCA
*
1623983 TCACGTAAAACACCGACCTCATCATGTAAAGCACTGACCTCATCACG
1 TCACGTAAAACACCGACCTCATCACGTAAAGCACTGACCTCATCACG
1624030 TAAAACACCT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
62 3 0.03
63 86 0.96
64 1 0.01
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (63 bp):
TCACGTAAAACACCGACCTCATCACGTAAAGCACTGACCTCATCACGCCATGCACCATTGTCA
Found at i:1624249 original size:42 final size:42
Alignment explanation
Indices: 1624147--1624291 Score: 188
Period size: 42 Copynumber: 3.5 Consensus size: 42
1624137 GTGATGGAAT
*
1624147 AGGTGATGGATCTCGGTGTCGAGGTGTAGAGTCGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
*
1624186 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
* * * * **
1624228 AGGTGATGGATCTTGGAGTCGAAGTGGAGAATCTACTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
*
1624270 AGGTGATGGATCACGGTGTCGA
1 AGGTGATGGATCTCGGTGTCGA
1624292 AGTGGATAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 35 0.38
41 1 0.01
42 55 0.60
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
Found at i:1624303 original size:42 final size:41
Alignment explanation
Indices: 1624147--1624312 Score: 167
Period size: 42 Copynumber: 4.0 Consensus size: 41
1624137 GTGATGGAAT
* * * *
1624147 AGGTGATGGATCTCGGTGTCGAGGTGTAGAGTCGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATC-TCTCGATG
* * * *
1624186 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATC-TCTCGATG
* *
1624228 AGGTGATGGATCTTGGAGTCGAAGTGGAGAATCTACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCT-CTCGATG
* *
1624270 AGGTGATGGATCACGGTGTCGAAGTGGATAATCTCATCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCTC-TCGATG
1624312 A
1 A
1624313 AAAAGTGAGG
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 35 0.32
41 2 0.02
42 73 0.66
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (41 bp):
AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCTCTCGATG
Found at i:1625774 original size:13 final size:13
Alignment explanation
Indices: 1625750--1625802 Score: 76
Period size: 13 Copynumber: 4.2 Consensus size: 13
1625740 TTTAGTAATT
1625750 TTAAGATTTTGAAA
1 TTAAG-TTTTGAAA
1625764 TTAAGTTTTGAAA
1 TTAAGTTTTGAAA
1625777 TT---TTTTGAAA
1 TTAAGTTTTGAAA
1625787 TTAAGTTTTGAAA
1 TTAAGTTTTGAAA
1625800 TTA
1 TTA
1625803 CTCCCCCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.28
13 21 0.58
14 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTTTTGAAA
Found at i:1625786 original size:23 final size:23
Alignment explanation
Indices: 1625756--1625801 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1625746 AATTTTAAGA
1625756 TTTTGAAATTAAGTTTTGAAATT
1 TTTTGAAATTAAGTTTTGAAATT
1625779 TTTTGAAATTAAGTTTTGAAATT
1 TTTTGAAATTAAGTTTTGAAATT
1625802 ACTCCCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (23 bp):
TTTTGAAATTAAGTTTTGAAATT
Found at i:1627705 original size:21 final size:21
Alignment explanation
Indices: 1627670--1627728 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1627660 CAGAACCCAT
* *
1627670 GGGGGTATCGATTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
*
1627690 GGAGGGAATCGGTTCCAATCAAA
1 GG-GGGAATCGGTTCC-CTCAAA
1627713 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
1627729 CTTCAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.06
21 11 0.34
22 15 0.47
23 4 0.12
ACGTcount: A:0.24, C:0.22, G:0.34, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1631698 original size:117 final size:117
Alignment explanation
Indices: 1631478--1631699 Score: 288
Period size: 117 Copynumber: 1.9 Consensus size: 117
1631468 TTTTCAAATC
*
1631478 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
* *
1631543 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
1631595 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAAAAT
* * **
1631658 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
1631700 ATTATTTTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 2 0.02
117 84 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:1634441 original size:15 final size:15
Alignment explanation
Indices: 1634423--1634455 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1634413 CTTGAAACTT
1634423 AAATTCGCAACACGA
1 AAATTCGCAACACGA
*
1634438 AAA-TCGCAACTCGA
1 AAATTCGCAACACGA
1634452 AAAT
1 AAAT
1634456 GAAATTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.15
Consensus pattern (15 bp):
AAATTCGCAACACGA
Found at i:1634514 original size:60 final size:60
Alignment explanation
Indices: 1634441--1634555 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
1634431 AACACGAAAA
1634441 TCGCAACTCGAAAATGAAATT-TGCAAGTCAAATTTTGAATTCGCAA-GTCGAATTTTGAAT
1 TCGCAACTCGAAAATGAAATTCT-CAAGTCAAATTTTGAATTCGCAACG-CGAATTTTGAAT
**
1634501 TCGCAACTCGAAAATGAAATTCTCAAGTTGAATTTTGAATTCGCAACGCGAATTT
1 TCGCAACTCGAAAATGAAATTCTCAAGTCAAATTTTGAATTCGCAACGCGAATTT
1634556 CTTTTTCGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (60 bp):
TCGCAACTCGAAAATGAAATTCTCAAGTCAAATTTTGAATTCGCAACGCGAATTTTGAAT
Found at i:1634553 original size:20 final size:20
Alignment explanation
Indices: 1634458--1634555 Score: 101
Period size: 20 Copynumber: 4.9 Consensus size: 20
1634448 TCGAAAATGA
* *
1634458 AATTTGCAAGTCAAATTTTG
1 AATTCGCAAGTCGAATTTTG
1634478 AATTCGCAAGTCGAATTTTG
1 AATTCGCAAGTCGAATTTTG
* **
1634498 AATTCGCAACTCGAA-AATG
1 AATTCGCAAGTCGAATTTTG
* *
1634517 AAATTCTCAAGTTGAATTTTG
1 -AATTCGCAAGTCGAATTTTG
1634538 AATTCGCAACG-CGAATTT
1 AATTCGCAA-GTCGAATTT
1634556 CTTTTTCGAG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.92
21 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (20 bp):
AATTCGCAAGTCGAATTTTG
Found at i:1634571 original size:20 final size:20
Alignment explanation
Indices: 1634548--1634642 Score: 94
Period size: 20 Copynumber: 5.0 Consensus size: 20
1634538 AATTCGCAAC
*
1634548 GCGAATTTCTTTTTCGAGTT
1 GCGAATTTCATTTTCGAGTT
* *
1634568 GCGATTTTCATTTTTGAGTT
1 GCGAATTTCATTTTCGAGTT
* *
1634588 GCGAATTTCAATTTCAAGTT
1 GCGAATTTCATTTTCGAGTT
*
1634608 GCG------ATTTTCGTGTT
1 GCGAATTTCATTTTCGAGTT
1634622 GCGAATTTCATTTTCGAGTT
1 GCGAATTTCATTTTCGAGTT
1634642 G
1 G
1634643 AGATTTCGTG
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
14 11 0.19
20 47 0.81
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.47
Consensus pattern (20 bp):
GCGAATTTCATTTTCGAGTT
Found at i:1634655 original size:33 final size:34
Alignment explanation
Indices: 1634585--1634672 Score: 126
Period size: 34 Copynumber: 2.6 Consensus size: 34
1634575 TCATTTTTGA
*
1634585 GTTGCGAATTTCAATTTCAAGTTGCGATTTTCGT
1 GTTGCGAATTTCAATTTCAAGTTGAGATTTTCGT
* *
1634619 GTTGCGAATTTCATTTTCGAGTTGAGA-TTTCGT
1 GTTGCGAATTTCAATTTCAAGTTGAGATTTTCGT
1634652 GTTGCGAATTT-AAGTTTCAAG
1 GTTGCGAATTTCAA-TTTCAAG
1634673 AATAAACTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 1 0.02
33 23 0.48
34 24 0.50
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (34 bp):
GTTGCGAATTTCAATTTCAAGTTGAGATTTTCGT
Found at i:1635087 original size:22 final size:21
Alignment explanation
Indices: 1635039--1635084 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
1635029 ATATGGGGAC
*
1635039 GGATGTCGCCAGAGATGGAGA
1 GGATGTCGCCAGAGAAGGAGA
1635060 TGGATGTCGCCAGAGAGAGTGAGA
1 -GGATGTCGCCAGAGA-AG-GAGA
1635084 G
1 G
1635085 ATGGAGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 15 0.71
23 2 0.10
24 4 0.19
ACGTcount: A:0.28, C:0.13, G:0.43, T:0.15
Consensus pattern (21 bp):
GGATGTCGCCAGAGAAGGAGA
Found at i:1635089 original size:26 final size:22
Alignment explanation
Indices: 1635021--1635075 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1635011 ATGGAGGAGG
* * * *
1635021 GTCGTCAGATATGGGGACGGAT
1 GTCGCCAGAGATGGAGATGGAT
1635043 GTCGCCAGAGATGGAGATGGAT
1 GTCGCCAGAGATGGAGATGGAT
1635065 GTCGCCAGAGA
1 GTCGCCAGAGA
1635076 GAGTGAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.40, T:0.18
Consensus pattern (22 bp):
GTCGCCAGAGATGGAGATGGAT
Found at i:1635215 original size:20 final size:20
Alignment explanation
Indices: 1635160--1635270 Score: 93
Period size: 20 Copynumber: 5.5 Consensus size: 20
1635150 ATTTACATTT
* *
1635160 GTGTTGCAAAAATAAAA-GC
1 GTGTTGCGAAAATAAAATTC
*
1635179 TGTTTTG-GAAAATTAAAATTC
1 -GTGTTGCGAAAA-TAAAATTC
*
1635200 GTGTTGCGAAAATAAATTTC
1 GTGTTGCGAAAATAAAATTC
* * *
1635220 GCGTTGC-AAATTTAAAAATC
1 GTGTTGCGAAA-ATAAAATTC
* *
1635240 GTGTTGCGAAAAAAAAACTC
1 GTGTTGCGAAAATAAAATTC
1635260 GTGTTGCGAAA
1 GTGTTGCGAAA
1635271 TCGTCAAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.10
20 57 0.78
21 9 0.12
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.30
Consensus pattern (20 bp):
GTGTTGCGAAAATAAAATTC
Found at i:1635266 original size:40 final size:40
Alignment explanation
Indices: 1635160--1635271 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
1635150 ATTTACATTT
* * * *
1635160 GTGTTGC-AAAAATAAAAGCT-GTTTTGGAAAATTAAAATTC
1 GTGTTGCGAAAAA-AAAA-CTCGTGTTGCAAATTTAAAAATC
* ** *
1635200 GTGTTGCGAAAATAAATTTCGCGTTGCAAATTTAAAAATC
1 GTGTTGCGAAAAAAAAACTCGTGTTGCAAATTTAAAAATC
1635240 GTGTTGCGAAAAAAAAACTCGTGTTGCGAAAT
1 GTGTTGCGAAAAAAAAACTCGTGTTGC-AAAT
1635272 CGTCAAATTC
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.02
40 48 0.84
41 8 0.14
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (40 bp):
GTGTTGCGAAAAAAAAACTCGTGTTGCAAATTTAAAAATC
Found at i:1635291 original size:42 final size:40
Alignment explanation
Indices: 1635188--1635291 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
1635178 CTGTTTTGGA
* **
1635188 AAAT-TAAAATTCGTGTTGCGAAAATAAATTTCGCGTTGC
1 AAATGTAAAATTCGTGTTGCGAAAAAAAAACTCGCGTTGC
* * *
1635227 AAATTTAAAAATCGTGTTGCGAAAAAAAAACTCGTGTTGC
1 AAATGTAAAATTCGTGTTGCGAAAAAAAAACTCGCGTTGC
* *
1635267 GAAATCGTCAAATTCGAGTTGCGAA
1 -AAAT-GTAAAATTCGTGTTGCGAA
1635292 TTTGACTTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
39 4 0.08
40 30 0.57
41 4 0.08
42 15 0.28
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (40 bp):
AAATGTAAAATTCGTGTTGCGAAAAAAAAACTCGCGTTGC
Found at i:1638302 original size:29 final size:32
Alignment explanation
Indices: 1638268--1638334 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 32
1638258 AATAGTATTA
1638268 TATTTTATATT-AAT-ATA-TTATATAAATAT
1 TATTTTATATTAAATAATATTTATATAAATAT
* *
1638297 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATATTTATATAAATAT
1638330 TATTT
1 TATTT
1638335 ATTTATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 10 0.31
31 3 0.09
32 3 0.09
33 16 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTTTATATTAAATAATATTTATATAAATAT
Found at i:1638343 original size:17 final size:17
Alignment explanation
Indices: 1638283--1638347 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
1638273 TATATTAATA
1638283 TATTATATAAATATTATT
1 TATT-TATAAATATTATT
*
1638301 T-TTTATTAAAATAATATT
1 TATTTA-T-AAATATTATT
*
1638319 TA--TATAATTATTATT
1 TATTTATAAATATTATT
*
1638334 TATTTATAATTATT
1 TATTTATAAATATT
1638348 TTTTTTTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
15 10 0.26
16 3 0.08
17 15 0.38
18 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTATAAATATTATT
Found at i:1640084 original size:21 final size:21
Alignment explanation
Indices: 1640054--1640101 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1640044 GCAGGGGTAC
* *
1640054 ATGCCCAGCCCTCCACTTAAT
1 ATGCCAAGCCCACCACTTAAT
* *
1640075 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCACTTAAT
1640096 ATGCCA
1 ATGCCA
1640102 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTAAT
Found at i:1640131 original size:21 final size:21
Alignment explanation
Indices: 1640105--1640219 Score: 128
Period size: 21 Copynumber: 5.5 Consensus size: 21
1640095 TATGCCATCT
*
1640105 CCGCAGGGTTACATTCCGAGA
1 CCGCAGGGTTACATTCCGAGC
*
1640126 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
1640147 CCGCCA-GGTTACATTCCGAGC
1 CCG-CAGGGTTACATTCCGAGC
* *
1640168 CCGCAGGGTTACATTCCTAAC
1 CCGCAGGGTTACATTCCGAGC
* *
1640189 CCGCCA-AGTTACATGT-CTAGC
1 CCG-CAGGGTTACAT-TCCGAGC
1640210 CCGCAGGGTT
1 CCGCAGGGTT
1640220 TTATACCATA
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.05
21 72 0.89
22 5 0.06
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1640172 original size:42 final size:42
Alignment explanation
Indices: 1640111--1640219 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
1640101 ATCTCCGCAG
* *
1640111 GGTTACATTCCGAGACCGCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAACCCGCCA
1640153 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAACCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAACCCGCCA
* *
1640195 AGTTACATGT-CTAGCCCGCAGGGTT
1 GGTTACAT-TCCGAGCCCGCAGGGTT
1640220 TTATACCATA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 61 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.23
Consensus pattern (42 bp):
GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAACCCGCCA
Found at i:1640665 original size:32 final size:33
Alignment explanation
Indices: 1640620--1640721 Score: 111
Period size: 32 Copynumber: 3.2 Consensus size: 33
1640610 GATAATATTT
* * *
1640620 TTAAAATACAAATATATTATTCAAAATTTAAAA
1 TTAAAAAAAAAATATATTATTCGAAATTTAAAA
1640653 -TAAAAAAAAAATA-ATATATTCGAAATTTAAAA
1 TTAAAAAAAAAATATAT-TATTCGAAATTTAAAA
* * * *
1640685 TTAAAATATAAAT-TAGTATTCGAAATTTAACA
1 TTAAAAAAAAAATATATTATTCGAAATTTAAAA
1640717 TTAAA
1 TTAAA
1640722 TTTCAACTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
31 2 0.03
32 46 0.78
33 11 0.19
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (33 bp):
TTAAAAAAAAAATATATTATTCGAAATTTAAAA
Found at i:1645138 original size:2 final size:2
Alignment explanation
Indices: 1645133--1645163 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1645123 TATATGGATT
1645133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1645164 TGCACGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1645508 original size:21 final size:21
Alignment explanation
Indices: 1645484--1645530 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1645474 TGACATAGCG
1645484 GTCCACTATGTTAATGTGATA
1 GTCCACTATGTTAATGTGATA
1645505 GTCCACTATGTTAATGTGATA
1 GTCCACTATGTTAATGTGATA
1645526 GTCCA
1 GTCCA
1645531 TAGTAACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (21 bp):
GTCCACTATGTTAATGTGATA
Found at i:1645716 original size:33 final size:32
Alignment explanation
Indices: 1645656--1645722 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
1645646 AAATTATTTT
* *
1645656 AAATTATAAATATAAAACTATTCAAAAATTCAA
1 AAATTATAAATATAAAAATACTCAAAAATT-AA
*
1645689 AAATTTTAAATATAAAAAATACT-AAAAATTAA
1 AAATTATAAATAT-AAAAATACTCAAAAATTAA
1645721 AA
1 AA
1645723 TCAAATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 4 0.13
33 19 0.63
34 7 0.23
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (32 bp):
AAATTATAAATATAAAAATACTCAAAAATTAA
Found at i:1645793 original size:2 final size:2
Alignment explanation
Indices: 1645788--1645814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1645778 ATTCTAAAAA
1645788 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1645815 AGGTTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1645865 original size:15 final size:15
Alignment explanation
Indices: 1645845--1645875 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1645835 ATAAAATATT
*
1645845 AAAATATTTTTTATA
1 AAAATATTTTTCATA
1645860 AAAATATTTTTCATA
1 AAAATATTTTTCATA
1645875 A
1 A
1645876 CATATATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATATTTTTCATA
Found at i:1646135 original size:24 final size:24
Alignment explanation
Indices: 1646091--1646138 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1646081 AAAAAGATAG
*
1646091 TAAATTTGACTAATTTAAAATTTT
1 TAAATTTAACTAATTTAAAATTTT
1646115 TAAATCTTAACTAATTT-AAATTTT
1 TAAAT-TTAACTAATTTAAAATTTT
1646139 GAAAGACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAATTTAACTAATTTAAAATTTT
Found at i:1646395 original size:17 final size:16
Alignment explanation
Indices: 1646358--1646403 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1646348 TATTTTTAGC
1646358 ATTTTTATATTTAATT
1 ATTTTTATATTTAATT
*
1646374 TTTTTTAATATTTCAA-T
1 ATTTTT-ATATTT-AATT
1646391 A-TTTTATATTTAA
1 ATTTTTATATTTAA
1646404 AATTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.08
15 6 0.23
16 9 0.35
17 7 0.27
18 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTTATATTTAATT
Found at i:1647982 original size:176 final size:175
Alignment explanation
Indices: 1647684--1648039 Score: 570
Period size: 176 Copynumber: 2.0 Consensus size: 175
1647674 AATATTAAAT
* * ** *
1647684 ATATTATATATAACCTATGGGTTTAGCCCAAACCATTTAAAATTCAATTAATAATTTAAGATTTA
1 ATATTATATATAACATATGGGTTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATTCA
1647749 ATAAATTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTTATTTTATAAT
66 ATAAATTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTTATTTTATAAT
* *
1647814 TATATATTATTTAAATTAATTGTAAACTGTTTTTCTGAATTAAAAA
131 TATATATTATTTAAATTAATTATAAACTATTTTT-TGAATTAAAAA
* *
1647860 ATATTATATATAACATATGGGTTCAGCCCTAACTATTTAAAACCCAATTAATAATTTAAGA-TCA
1 ATATTATATATAACATATGGGTTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATTCA
* * *
1647924 ATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTTTTATTTTATAA
66 ATAAATTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAA-ATTTTATTTTATAA
*
1647989 TTATATATTATTTAAATTAATTATAAACTATTTTTTTAATTAAAAA
130 TTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAAAA
1648035 ATATT
1 ATATT
1648040 TAATTTTTTA
Statistics
Matches: 166, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
175 65 0.39
176 101 0.61
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (175 bp):
ATATTATATATAACATATGGGTTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAAGATTCA
ATAAATTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTTATTTTATAAT
TATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAAAA
Found at i:1648398 original size:16 final size:17
Alignment explanation
Indices: 1648377--1648410 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1648367 ATTTTTATTA
*
1648377 TTTTA-TTAATTAATTT
1 TTTTATTTAATAAATTT
1648393 TTTTATTTAATAAATTT
1 TTTTATTTAATAAATTT
1648410 T
1 T
1648411 GTATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTTAATAAATTT
Found at i:1648431 original size:42 final size:39
Alignment explanation
Indices: 1648367--1648460 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 39
1648357 TGTCTTCCCT
* *
1648367 ATTTTTATTATTTTATTAATTAATTTTTTTATTTAATAA
1 ATTTTTATTATTTTATTAATTAATTTTTGTATTCAATAA
*
1648406 ATTTTGTATTATTTTTGATTAATTAATTTTTGTATTCAATAC
1 ATTTT-TATTA-TTTT-ATTAATTAATTTTTGTATTCAATAA
*
1648448 TTTTTTGATTATT
1 ATTTTT-ATTATT
1648461 CAATTGTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 5 0.11
40 5 0.11
41 7 0.15
42 30 0.64
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (39 bp):
ATTTTTATTATTTTATTAATTAATTTTTGTATTCAATAA
Found at i:1649172 original size:2 final size:2
Alignment explanation
Indices: 1649167--1649196 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1649157 AGGAAAAAAA
1649167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1649197 CAAAGTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1649426 original size:27 final size:29
Alignment explanation
Indices: 1649377--1649434 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
1649367 GTTTTTTTTT
1649377 TAAAAAAATAAATATAATGAATAAAAAAA
1 TAAAAAAATAAATATAATGAATAAAAAAA
*
1649406 TAAAAATAATAAA-A-AAT-AATATAAAAA
1 TAAAAA-AATAAATATAATGAATAAAAAAA
1649433 TA
1 TA
1649435 TAGTTATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 11 0.41
28 3 0.11
29 7 0.26
30 6 0.22
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (29 bp):
TAAAAAAATAAATATAATGAATAAAAAAA
Found at i:1649429 original size:21 final size:21
Alignment explanation
Indices: 1649377--1649434 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1649367 GTTTTTTTTT
*
1649377 TAAAAAAATAAATATAATGAA
1 TAAAAAAATAAAAATAATGAA
1649398 TAAAAAAATAAAAATAAT-AA
1 TAAAAAAATAAAAATAATGAA
1649418 -AAAATAATATAAAAATA
1 TAAAA-AA-ATAAAAATA
1649435 TAGTTATAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 26 0.76
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAAAAATAAAAATAATGAA
Found at i:1649431 original size:11 final size:11
Alignment explanation
Indices: 1649405--1649434 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1649395 GAATAAAAAA
1649405 ATAAAAATAAT
1 ATAAAAATAAT
1649416 A-AAAAATAAT
1 ATAAAAATAAT
1649426 ATAAAAATA
1 ATAAAAATA
1649435 TAGTTATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:1650171 original size:34 final size:34
Alignment explanation
Indices: 1650129--1650195 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1650119 GAATCCTAGC
1650129 AAAATTCTATCATATCTTTAGGAGTTTGAATCCA
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCA
* *
1650163 AAAATTCTATCCTATTTTTAGGAGTTTGAATCC
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCC
1650196 TAGTAGGACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCA
Found at i:1651029 original size:105 final size:105
Alignment explanation
Indices: 1650726--1651557 Score: 1255
Period size: 105 Copynumber: 8.0 Consensus size: 105
1650716 CATTGTTCCA
* * * ** * * *
1650726 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
1650791 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1650832 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
1650892 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1650932 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1650997 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1651037 AGTCTAATATCCTTCGTTGTGAAGTTGACATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
1651102 GGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1651142 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1651207 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1651247 AGTCGAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1651312 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1651352 AGTCCAATATCTTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGAC-AGA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG-
1651416 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1651457 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTAGAAGTTGTTTGTTGACAA-
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
1651521 CAAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 C-AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1651558 CCTCGAGTGC
Statistics
Matches: 670, Mismatches: 47, Indels: 18
0.91 0.06 0.02
Matches are distributed among these distances:
100 82 0.12
101 1 0.00
102 4 0.01
103 4 0.01
104 5 0.01
105 498 0.74
106 75 0.11
107 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1652296 original size:68 final size:67
Alignment explanation
Indices: 1652159--1652352 Score: 232
Period size: 68 Copynumber: 2.9 Consensus size: 67
1652149 AAAGAGATAG
* * * *
1652159 AATTCGTTTTAAGGGAAAT-GATCTCAAAGATATTTGTTGTTTCATGAGAAACGGTCTCAAGGGA
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGA
1652223 AACAA
63 AACAA
** * *
1652228 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAA
1652293 CAA
65 CAA
* * *
1652296 AATTTGTTTTAGGGGAAATAAATTCAAAG-GTTT-TGTTTCAAGGGAAACTGTCTCAAG
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
1652353 ATAGACGAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
65 22 0.20
66 3 0.03
67 22 0.20
68 32 0.29
69 8 0.07
70 20 0.18
71 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (67 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAAC
AA
Found at i:1652368 original size:65 final size:67
Alignment explanation
Indices: 1652159--1652588 Score: 236
Period size: 65 Copynumber: 6.3 Consensus size: 67
1652149 AAAGAGATAG
* * * * * *
1652159 AATTCGTTTTAAGGGAAAT-GATCTCAAAGATATTTGTTGTTTCATGAGAAACGGTCTCAAGGGA
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGA-GTTTG-TGTTTCAAGAGAAACTGTCTCAAGAGA
*
1652223 AACAA
63 GACAA
** * * *
1652228 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1652293 CAA
65 CAA
* * *
1652296 AATTTGTTTTAGGGGAAATAAATTCAAAG-GTTT-TGTTTCAAGGGAAACTGTCTCAAGATAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1652359 GAA
66 -AA
* * * * * * *
1652362 AA-TTGTTTCAAGAGAAACT--GTCTCAAGAGAGACAAAACTT-AGTTCCAAAAGAAACTGTCTC
1 AATTTGTTTTAAGGGAAA-TAAAT-TCAA-AGAG------TTTGTGTTTCAAGAGAAACTGTCTC
* **
1652423 AAGGGAGACGG
57 AAGAGAGACAA
* * * * * * * *
1652434 AATTTGTTTCAAAGAAAACATATTCAAATA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGAA
1 AATTTGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1652497 AA
66 AA
* * * *
1652499 AATTTATTTCAAGGGAAACT--GTCTCAAGATAGACGAAATT-TGTTTCAAGAGAAACTGTCTCA
1 AATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-AGA-G--TTTGTGTTTCAAGAGAAACTGTCTCA
1652561 AGAGAGACAA
58 AGAGAGACAA
*
1652571 AATTTGTTTCAAGGGAAA
1 AATTTGTTTTAAGGGAAA
1652589 CTGTCTCAAG
Statistics
Matches: 281, Mismatches: 55, Indels: 47
0.73 0.14 0.12
Matches are distributed among these distances:
64 2 0.01
65 85 0.30
66 11 0.04
67 24 0.09
68 34 0.12
69 8 0.03
70 19 0.07
71 2 0.01
72 53 0.19
73 42 0.15
74 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (67 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
AA
Found at i:1652379 original size:36 final size:35
Alignment explanation
Indices: 1652328--1652608 Score: 263
Period size: 36 Copynumber: 8.0 Consensus size: 35
1652318 TTCAAAGGTT
* *
1652328 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1652364 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1652399 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
1652437 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* *
1652466 TTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1652501 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1652538 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1652573 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1652609 CTCTTCTAGT
Statistics
Matches: 203, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 133 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1652438 original size:138 final size:137
Alignment explanation
Indices: 1652276--1652589 Score: 423
Period size: 138 Copynumber: 2.3 Consensus size: 137
1652266 TTTCAAGAGT
* * * *
1652276 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * *
1652341 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGA-AAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
1652405 TCCAAAAGA
129 TCCAAAAGA
** * * * *
1652414 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
1652479 AACTGTCTCAAGAGAGAAAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGAAAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
1652544 CAAGAGA
131 CAAAAGA
*
1652551 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1652590 TGTCTCAAGA
Statistics
Matches: 151, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
137 49 0.32
138 102 0.68
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGAAAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:1652544 original size:101 final size:103
Alignment explanation
Indices: 1652364--1652552 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 103
1652354 TAGACGAAAA
* *
1652364 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
*
1652429 GACGGAATTTGTTTCAA-AGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * ** *
1652466 TTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
1652530 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAAGAGAAA
1652553 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 36 0.47
102 41 0.53
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (103 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:1652630 original size:35 final size:36
Alignment explanation
Indices: 1652470--1652642 Score: 163
Period size: 36 Copynumber: 4.8 Consensus size: 36
1652460 AATATTTTGT
* * * **
1652470 TTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
1652506 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
1652542 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
1652578 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
1652612 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
1652643 TCTTGTTTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 91 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:1653563 original size:22 final size:22
Alignment explanation
Indices: 1653537--1653585 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1653527 TTGTGTTTGG
* *
1653537 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
1653559 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
1653581 TCAAA
1 TCAAA
1653586 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:1653592 original size:22 final size:22
Alignment explanation
Indices: 1653549--1653592 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1653539 AAAGGTTTGG
* * *
1653549 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
1653571 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
1653593 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:1654241 original size:16 final size:17
Alignment explanation
Indices: 1654222--1654267 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1654212 TCTTTTTGAT
*
1654222 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
1654238 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
1654255 TTTTTCT-TTGTTT
1 TTTTGCTCTTGTTT
1654268 TTTTTTTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:1658419 original size:34 final size:34
Alignment explanation
Indices: 1658365--1658433 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1658355 GAATCCTAGC
*
1658365 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTGAATCCT
* *
1658399 AAAATTATATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTGAATCCT
1658433 A
1 A
1658434 GTAGGACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTATATCATATCTTTAGGAGTTTGAATCCT
Found at i:1659697 original size:3 final size:3
Alignment explanation
Indices: 1659689--1659734 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1659679 TTTTTTCCTT
1659689 TTA TTA TTA TT- TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1659735 AATAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1659701 original size:17 final size:17
Alignment explanation
Indices: 1659689--1659733 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
1659679 TTTTTTCCTT
1659689 TTATTATTATTTTATTA
1 TTATTATTATTTTATTA
*
1659706 TTATTATTATATTATTA
1 TTATTATTATTTTATTA
1659723 TTATTATTATT
1 TTATTATTATT
1659734 AAATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATTATTTTATTA
Found at i:1659708 original size:14 final size:14
Alignment explanation
Indices: 1659689--1659734 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
1659679 TTTTTTCCTT
1659689 TTATTATTATTTTA
1 TTATTATTATTTTA
*
1659703 TTATTATTATTATA
1 TTATTATTATTTTA
1659717 TTATTATTATTATTA
1 TTATTATTATT-TTA
1659732 TTA
1 TTA
1659735 AATAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:1659750 original size:20 final size:20
Alignment explanation
Indices: 1659700--1659746 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1659690 TATTATTATT
* *
1659700 TTATTATTATTATTATATTA
1 TTATTATTATTATTAAATAA
1659720 TTATTATTATTATTAAATAA
1 TTATTATTATTATTAAATAA
1659740 TT-TTATT
1 TTATTATT
1659747 TATTTACAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATTATTATTAAATAA
Found at i:1661336 original size:151 final size:151
Alignment explanation
Indices: 1661021--1661390 Score: 357
Period size: 151 Copynumber: 2.5 Consensus size: 151
1661011 GATTAAATAA
* * * *
1661021 TAATATTTATTTATTTTTTAA-ATATCAAGAAATGGTTGTCTTAAAATAACTAGATGTCATATTC
1 TAATATTTATTTATTTTTTAATAT-TAAAGAAAGGGCTGTCTTAAAATAACTAGAGGTCATATTC
* * * *
1661085 TGATATTTTAAAAATAAATAAATATCATGCTTATAATATATATATATACTTCATTTGTATTTAAA
65 TGATATTTTAAAAATAAATAAATATCATACTTATAATAAAAATATATACTTCAGTTGTATTTAAA
* **
1661150 TTATTTATTATCATATTATTAT
130 TCATAAATTATCATATTATTAT
* *
1661172 TAATATTTATTTATTTTTTAATATTAAAGAAAGGGCTGTCTTAAATTAACTAGAGGTCCTATTCT
1 TAATATTTATTTATTTTTTAATATTAAAGAAAGGGCTGTCTTAAAATAACTAGAGGTCATATTCT
* *
1661237 GATATTTT-TAAATAAATAAATA-CATTATTTATAAAAATAAAAATATATA-TAT-AGTTGT-TT
66 GATATTTTAAAAATAAATAAATATCA-TACTTAT---AATAAAAATATATACT-TCAGTTGTATT
* *
1661297 T-AATCA-AAATTATCTTATTCTTAT
126 TAAATCATAAATTATCATATTATTAT
* * * * * * *
1661321 T--TATTCATTT-TTTTATATTATATTGAAGAAAAGGGCTATCTTAAAGTAACTAGATGTCATTT
1 TAATATTTATTTATTTT-T-TAATATTAAAG-AAAGGGCTGTCTTAAAATAACTAGAGGTCATAT
*
1661383 TCTAATAT
63 TCTGATAT
1661391 ATCCTATTTA
Statistics
Matches: 184, Mismatches: 26, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
146 4 0.02
147 9 0.05
148 9 0.05
149 52 0.28
150 22 0.12
151 67 0.36
152 8 0.04
153 13 0.07
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (151 bp):
TAATATTTATTTATTTTTTAATATTAAAGAAAGGGCTGTCTTAAAATAACTAGAGGTCATATTCT
GATATTTTAAAAATAAATAAATATCATACTTATAATAAAAATATATACTTCAGTTGTATTTAAAT
CATAAATTATCATATTATTAT
Found at i:1663750 original size:12 final size:11
Alignment explanation
Indices: 1663733--1663779 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
1663723 ATCTTTGCAT
1663733 TTTCATTTTACA
1 TTTCA-TTTACA
1663745 TTTCATTT-CA
1 TTTCATTTACA
1663755 TTTCA-TTACA
1 TTTCATTTACA
1663765 TTTTCATTTACA
1 -TTTCATTTACA
1663777 TTT
1 TTT
1663780 GCATCTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.06
10 9 0.28
11 11 0.34
12 10 0.31
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTCATTTACA
Found at i:1663759 original size:22 final size:22
Alignment explanation
Indices: 1663740--1663779 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1663730 CATTTTCATT
1663740 TTACA-TTTCATTT-CATTTCA
1 TTACATTTTCATTTACATTTCA
1663760 TTACATTTTCATTTACATTT
1 TTACATTTTCATTTACATTT
1663780 GCATCTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.57
Consensus pattern (22 bp):
TTACATTTTCATTTACATTTCA
Found at i:1666156 original size:73 final size:72
Alignment explanation
Indices: 1666037--1666181 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 72
1666027 ATACAGTAAA
*
1666037 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAAATATTTAGCTAG
1 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGAT-AATATTCAGCTAG
1666102 CCTGTTAT
65 CCTGTTAT
1666110 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCC-GACTTTATGGATAATATTCAGCTAG
1 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCCAG-CTTTATGGATAATATTCAGCTAG
1666174 CCTGTTAT
65 CCTGTTAT
1666182 ACTATTATAT
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
72 21 0.30
73 49 0.70
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (72 bp):
GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGC
CTGTTAT
Found at i:1668366 original size:79 final size:81
Alignment explanation
Indices: 1668214--1668368 Score: 224
Period size: 79 Copynumber: 1.9 Consensus size: 81
1668204 TCATATCAAC
* *
1668214 AAATGTTGGGGCATGCTGAAAGCCCATTTCAACCAAAAATAGAATATTGAGATATTTTGAAAGCT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAACCAAAAATAGAATATTGACACATTTTGAAAGCT
1668279 CACATCAACAAGAAGT
66 CACATCAACAAGAAGT
* ** * * *
1668295 AAATGTTGGGGCATGCTGAAAG-CTATTTCAATTAAAAATAGGA-ATTGACACATTTTGAACGTT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAACCAAAAATAGAATATTGACACATTTTGAAAGCT
1668358 CACATCAACAA
66 CACATCAACAA
1668369 ATGTTGGGGC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
79 27 0.41
80 17 0.26
81 22 0.33
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (81 bp):
AAATGTTGGGGCATGCTGAAAGCCCATTTCAACCAAAAATAGAATATTGACACATTTTGAAAGCT
CACATCAACAAGAAGT
Found at i:1668736 original size:54 final size:54
Alignment explanation
Indices: 1668651--1668756 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
1668641 GATGATTGAG
*
1668651 AAATCTGGGCAGAAGCCACATGAAAGAATGAATGTGTTACCAAATGTTTTACGA
1 AAATCTGGGCAGAAGCCACAGGAAAGAATGAATGTGTTACCAAATGTTTTACGA
**
1668705 AAATCTGGGCAGAAGCCACAGGAAATG-ATGAATGTGTTGTCAAATGTTTTAC
1 AAATCTGGGCAGAAGCCACAGGAAA-GAATGAATGTGTTACCAAATGTTTTAC
1668757 AAACCAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
54 47 0.98
55 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (54 bp):
AAATCTGGGCAGAAGCCACAGGAAAGAATGAATGTGTTACCAAATGTTTTACGA
Found at i:1669764 original size:123 final size:123
Alignment explanation
Indices: 1669554--1669998 Score: 622
Period size: 123 Copynumber: 3.6 Consensus size: 123
1669544 ATTTCTAGGT
*
1669554 AGAGTTCATAATGAGAAGAACTCATCTATCTGAAGAGGAAA-AAGAAGTTTATAATGAGAAGAAC
1 AGAGTTCATAATGAGAAGAA--C-TC-ATCTGAAGA-GAAAGAAGAAGTTCATAATGAGAAGAAC
* *
1669618 TTGTTCAACCTTTTTCTCGATTCTATCATAGAAGGAGATAGATCAACATCAATATTTCCAGAA
61 TTGTTCAACCTTTTGCTCGATTCTATCATAGAAGGAGATAGATCAACATCAACATTTCCAGAA
*
1669681 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAATTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * **
1669746 CAACCTTTTGCTCAATTCTATCACAGAAGGAGATAGATCATCATCAACATTTCCAGGT
66 CAACCTTTTGCTCGATTCTATCATAGAAGGAGATAGATCAACATCAACATTTCCAGAA
* * * *
1669804 AGAGTTTATAATGTGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * * * *
1669869 CAACCTTTGGCTTGACTCTATCATAGAAAGAAATAGATCAACACCAACATTTTCGGAA
66 CAACCTTTTGCTCGATTCTATCATAGAAGGAGATAGATCAACATCAACATTTCCAGAA
* *
1669927 AGAGTTCATAATGAGAAGAACTCATCTGGAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1669992 CGACCTT
66 CAACCTT
1669999 AACTTGATTC
Statistics
Matches: 285, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
122 4 0.01
123 258 0.91
124 2 0.01
125 1 0.00
127 20 0.07
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTCGATTCTATCATAGAAGGAGATAGATCAACATCAACATTTCCAGAA
Found at i:1670270 original size:137 final size:137
Alignment explanation
Indices: 1669913--1670274 Score: 446
Period size: 139 Copynumber: 2.6 Consensus size: 137
1669903 AGATCAACAC
* *
1669913 CAACATTTTCGGAAAGAGTTCATAATGAGAAGAACTCATCTGGAGAGGAAGAAGAAGTTCATAAT
1 CAACATTTTCAGAAGGAGTTCATAATGAGAAGAACTCATCT-GAGAGGAAGAAGAAGTTCATAAT
* * * *
1669978 GAGAAGAACTTGTTCGACCTTAACTTGATTCATCATCTATGGAGTTGAATGAAAGAAGAACCTCA
65 GAGAAGAACTTGTTCAACCTTAACTTAATTCATCATCTATGAAGTTGAATCAAAGAAGAA-CTCA
*
1670043 CTTGAGGGT
129 CTTGAGGAT
* * *
1670052 CAATATTTTCA-TAGGAAGTTCATAATGAGAAGAACTCATATGAAGAGGAAGAAGAAGTTCATAA
1 CAACATTTTCAGAAGG-AGTTCATAATGAGAAGAACTCATCTG-AGAGGAAGAAGAAGTTCATAA
* *
1670116 TGAGAAGAACTTGTTCAACCTT-GCATTAATTCATCA-CATATGAAGTTGAATCAACGACA-AA-
64 TGAGAAGAACTTGTTCAACCTTAAC-TTAATTCATCATC-TATGAAGTTGAATCAAAGA-AGAAC
*** *
1670177 TTTTTTTAGGAT
126 TCACTTGAGGAT
* * *
1670189 CAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGATGAGAAAGAAAAAGTTCATAAT
1 CAACATTTTCAGAAGGAGTTCATAATGAGAAGAACTCATCTGA-GAGGAAGAAGAAGTTCATAAT
1670254 GAGAAGAACTTGTTCAACCTT
65 GAGAAGAACTTGTTCAACCTT
1670275 TTGCTAGATT
Statistics
Matches: 194, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
136 1 0.01
137 81 0.42
138 8 0.04
139 103 0.53
140 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (137 bp):
CAACATTTTCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTAACTTAATTCATCATCTATGAAGTTGAATCAAAGAAGAACTCACT
TGAGGAT
Found at i:1671838 original size:2 final size:2
Alignment explanation
Indices: 1671827--1671864 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1671817 ATATCATGCT
1671827 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1671865 TTACTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1673167 original size:9 final size:9
Alignment explanation
Indices: 1673144--1673173 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1673134 AAAAGAAAAG
1673144 AAAATAAAT
1 AAAATAAAT
1673153 -AAATAAAT
1 AAAATAAAT
1673161 AAAATAAAT
1 AAAATAAAT
1673170 AAAA
1 AAAA
1673174 CAAAGTATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1674467 original size:22 final size:22
Alignment explanation
Indices: 1674441--1674482 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1674431 GATATACATG
1674441 TTATACCATATAATAAAAATGT
1 TTATACCATATAATAAAAATGT
** *
1674463 TTATATTATATAATATAAAT
1 TTATACCATATAATAAAAAT
1674483 AACATATTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TTATACCATATAATAAAAATGT
Found at i:1675853 original size:34 final size:34
Alignment explanation
Indices: 1675814--1675881 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1675804 GAAAAAAGAA
1675814 AAACAAACAGTACATGACAAACATTCTAAAAAGT
1 AAACAAACAGTACATGACAAACATTCTAAAAAGT
1675848 AAACAAACAGTACATGACAAACATTCTAAAAAGT
1 AAACAAACAGTACATGACAAACATTCTAAAAAGT
1675882 GAATACATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.18
Consensus pattern (34 bp):
AAACAAACAGTACATGACAAACATTCTAAAAAGT
Found at i:1679895 original size:22 final size:22
Alignment explanation
Indices: 1679825--1679895 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1679815 AAGGAATGAC
* *
1679825 TGAAAATTAAATTTGAAAGAGAA
1 TGAAAATTGAATTCGAAAGA-AA
* * * *
1679848 T-AAAATGGAGTACTGAATGAAA
1 TGAAAATTGAATTC-GAAAGAAA
1679870 -GAAAATTGAATTCGAAAGAAA
1 TGAAAATTGAATTCGAAAGAAA
1679891 TGAAA
1 TGAAA
1679896 TAAGAAAGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 7
0.67 0.19 0.13
Matches are distributed among these distances:
21 7 0.20
22 22 0.63
23 6 0.17
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.23
Consensus pattern (22 bp):
TGAAAATTGAATTCGAAAGAAA
Found at i:1686851 original size:9 final size:8
Alignment explanation
Indices: 1686811--1686912 Score: 60
Period size: 9 Copynumber: 11.5 Consensus size: 8
1686801 AAGATTAAAC
1686811 AAAAAAAT
1 AAAAAAAT
*
1686819 AAAGAAAT
1 AAAAAAAT
1686827 AAAATAAAAT
1 -AAA-AAAAT
*
1686837 AAAAACAT
1 AAAAAAAT
*
1686845 AAAAAACCT
1 AAAAAA-AT
*
1686854 AAAGAAAT
1 AAAAAAAT
*
1686862 AACCAAGAAAA
1 AA--AA-AAAT
1686873 AAATAAAAT
1 AAA-AAAAT
*
1686882 AAAATAAT
1 AAAAAAAT
1686890 AAAATAAAT
1 AAAA-AAAT
1686899 AAAACAAAGT
1 AAAA-AAA-T
1686909 AAAA
1 AAAA
1686913 GAGGAAAAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
8 27 0.38
9 29 0.40
10 11 0.15
11 5 0.07
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1688979 original size:19 final size:19
Alignment explanation
Indices: 1688955--1689010 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
1688945 AAAATATTAA
1688955 TAAAATACATTTGAGTTAT
1 TAAAATACATTTGAGTTAT
1688974 TAAAAT--A-TT-A---A-
1 TAAAATACATTTGAGTTAT
1688985 TAAAATACATTTGAGTTAT
1 TAAAATACATTTGAGTTAT
1689004 TAAAATA
1 TAAAATA
1689011 TTAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 6 0.21
12 1 0.03
13 1 0.03
14 2 0.07
15 2 0.07
16 2 0.07
17 1 0.03
18 1 0.03
19 13 0.45
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (19 bp):
TAAAATACATTTGAGTTAT
Found at i:1688980 original size:30 final size:30
Alignment explanation
Indices: 1688944--1689036 Score: 168
Period size: 30 Copynumber: 3.1 Consensus size: 30
1688934 GAGTTATTAA
1688944 TAAAATATTAATAAAATACATTTGAGTTAT
1 TAAAATATTAATAAAATACATTTGAGTTAT
1688974 TAAAATATTAATAAAATACATTTGAGTTAT
1 TAAAATATTAATAAAATACATTTGAGTTAT
* *
1689004 TAAAATATTAATAAAATAAATTTAAGTTAT
1 TAAAATATTAATAAAATACATTTGAGTTAT
1689034 TAA
1 TAA
1689037 TAAAATAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (30 bp):
TAAAATATTAATAAAATACATTTGAGTTAT
Found at i:1689028 original size:22 final size:22
Alignment explanation
Indices: 1689003--1689048 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1688993 ATTTGAGTTA
1689003 TTAAAATATTAATAAAATAAAT
1 TTAAAATATTAATAAAATAAAT
**
1689025 TTAAGTTATTAATAAAATAAAT
1 TTAAAATATTAATAAAATAAAT
1689047 TT
1 TT
1689049 GAGTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAAAATATTAATAAAATAAAT
Found at i:1689053 original size:22 final size:22
Alignment explanation
Indices: 1689009--1689059 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1688999 GTTATTAAAA
1689009 TATTAATAAAATAAATTTAAGT
1 TATTAATAAAATAAATTTAAGT
*
1689031 TATTAATAAAATAAATTTGAGT
1 TATTAATAAAATAAATTTAAGT
1689053 TATTAAT
1 TATTAAT
1689060 TGATGTCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
TATTAATAAAATAAATTTAAGT
Found at i:1689892 original size:18 final size:19
Alignment explanation
Indices: 1689866--1689901 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1689856 TCTAAAAAGA
1689866 AAACACAAAA-TTTGAAAT
1 AAACACAAAACTTTGAAAT
*
1689884 AAACCCAAAACTTTGAAA
1 AAACACAAAACTTTGAAA
1689902 ATCTTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (19 bp):
AAACACAAAACTTTGAAAT
Found at i:1692727 original size:28 final size:30
Alignment explanation
Indices: 1692668--1692730 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1692658 AGAGCTACTC
*
1692668 TTTATGTATCTATTTTGATTAAAAAATAAT
1 TTTAAGTATCTATTTTGATTAAAAAATAAT
* *
1692698 TTTAAGTATTTATTTTGA-T-AAAAATTAT
1 TTTAAGTATCTATTTTGATTAAAAAATAAT
1692726 TTTAA
1 TTTAA
1692731 ATACCTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 13 0.43
29 1 0.03
30 16 0.53
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (30 bp):
TTTAAGTATCTATTTTGATTAAAAAATAAT
Found at i:1692911 original size:19 final size:19
Alignment explanation
Indices: 1692887--1692923 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1692877 AACGTCAAGT
1692887 ATCTATCTTAATTTAAAAC
1 ATCTATCTTAATTTAAAAC
1692906 ATCTATCTTAATTTAAAA
1 ATCTATCTTAATTTAAAA
1692924 GAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (19 bp):
ATCTATCTTAATTTAAAAC
Found at i:1694644 original size:67 final size:70
Alignment explanation
Indices: 1694507--1694645 Score: 169
Period size: 67 Copynumber: 2.0 Consensus size: 70
1694497 AGTTACACAG
* * * **
1694507 TGCTCGACTCGTGCTCATTAAAAAATTTGGTGCTCGACTTGACTTGTTTCTTGTTAAGCTCGTTA
1 TGCTCGACTCGTGCTCATTAAAAAATTTGGT-CTCGACTTGACTAGTTGCTCGTTAAGCTCACTA
1694572 AAATTT
65 AAATTT
*
1694578 TGCTCGACTCGTGCTCGTTAAGAAAATTT-GT-T-G-CTTGACTAGTTGCTCGTTAAGCTCACTA
1 TGCTCGACTCGTGCTCATTAA-AAAATTTGGTCTCGACTTGACTAGTTGCTCGTTAAGCTCACTA
*
1694639 TAATTT
65 AAATTT
1694645 T
1 T
1694646 TATTTTGTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
67 29 0.48
68 1 0.02
69 1 0.02
71 22 0.37
72 7 0.12
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (70 bp):
TGCTCGACTCGTGCTCATTAAAAAATTTGGTCTCGACTTGACTAGTTGCTCGTTAAGCTCACTAA
AATTT
Found at i:1695858 original size:19 final size:19
Alignment explanation
Indices: 1695834--1695899 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
1695824 TGTCTTTCTT
1695834 AAATAAATATTTTTTAGAA
1 AAATAAATATTTTTTAGAA
*
1695853 AAATAAATATGTTTTAGAA
1 AAATAAATATTTTTTAGAA
* *
1695872 AAATAATATTTTTATTTTGAA
1 AAATAA-ATATTT-TTTAGAA
1695893 AAATAAA
1 AAATAAA
1695900 AAATATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 24 0.59
20 5 0.12
21 12 0.29
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (19 bp):
AAATAAATATTTTTTAGAA
Found at i:1695911 original size:22 final size:22
Alignment explanation
Indices: 1695833--1695925 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 22
1695823 ATGTCTTTCT
1695833 TAAATAAATATTTTTTAGAAAAA
1 TAAA-AAATATTTTTTAGAAAAA
*
1695856 T---AAATATGTTTTAGAAAAA
1 TAAAAAATATTTTTTAGAAAAA
* * *
1695875 T--AATATTTTTATTTTGAAAAA
1 TAAAAAATATTT-TTTAGAAAAA
* *
1695896 TAAAAAATATTTTTTTGAAAAG
1 TAAAAAATATTTTTTAGAAAAA
1695918 TATAAAAA
1 TA-AAAAA
1695926 CGAAAGATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
19 18 0.32
20 5 0.09
21 10 0.18
22 11 0.19
23 13 0.23
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (22 bp):
TAAAAAATATTTTTTAGAAAAA
Found at i:1696864 original size:17 final size:17
Alignment explanation
Indices: 1696842--1696879 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1696832 TGTAACATTA
*
1696842 AAAACTTGAATTGATTG
1 AAAACTTGAATGGATTG
1696859 AAAACTTGAATGGATTG
1 AAAACTTGAATGGATTG
1696876 AAAA
1 AAAA
1696880 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (17 bp):
AAAACTTGAATGGATTG
Found at i:1702065 original size:3 final size:3
Alignment explanation
Indices: 1702052--1702127 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
1702042 TTACCCATTT
* * * * *
1702052 TTA TT- TTA TTA TTA TAA TTA TTA -TA ATA TAA TTA TAA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1702098 TTA -TA ATA TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
1702128 AAAAAATAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
2 6 0.10
3 50 0.85
4 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1702159 original size:11 final size:11
Alignment explanation
Indices: 1702130--1702164 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1702120 TATTATTAAA
* *
1702130 AAAATAAAAAA
1 AAAATAATAAT
1702141 AAAATAATAAT
1 AAAATAATAAT
1702152 AAAATAATAAT
1 AAAATAATAAT
1702163 AA
1 AA
1702165 TAGTTACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:1702165 original size:14 final size:14
Alignment explanation
Indices: 1702127--1702166 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1702117 TATTATTATT
*
1702127 AAAAA-AATAAAAA
1 AAAAATAATAATAA
1702140 AAAAATAATAATAA
1 AAAAATAATAATAA
*
1702154 AATAATAATAATA
1 AAAAATAATAATA
1702167 GTTACAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAATAATAATAA
Found at i:1703569 original size:15 final size:16
Alignment explanation
Indices: 1703530--1703576 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1703520 ATAATAAATA
1703530 ATAATTTATTTTTTAC
1 ATAATTTATTTTTTAC
*
1703546 ATAAATTA-TTTTTATC
1 ATAATTTATTTTTTA-C
1703562 AT-ATTTATTTATTTA
1 ATAATTTATTT-TTTA
1703577 TTTATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATTTTTTAC
Found at i:1703782 original size:23 final size:26
Alignment explanation
Indices: 1703750--1703799 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1703740 CCTTTTCTGA
*
1703750 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
1703773 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
1703799 T
1 T
1703800 TTTCTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:1707668 original size:15 final size:15
Alignment explanation
Indices: 1707648--1707694 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
1707638 TCAATACCTT
1707648 TTTTGCATACATACA
1 TTTTGCATACATACA
1707663 TTTTGCATACATACA
1 TTTTGCATACATACA
*
1707678 TTTTGCATACATTCA
1 TTTTGCATACATACA
1707693 TT
1 TT
1707695 ATTCATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:1710016 original size:26 final size:26
Alignment explanation
Indices: 1709979--1710039 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
1709969 CAAGTGAAAG
*
1709979 CAAAAGGAAAAACCATGGTAATACCC
1 CAAAAGGTAAAACCATGGTAATACCC
1710005 CAAAAGGTAAAACCATGGTAATACCC
1 CAAAAGGTAAAACCATGGTAATACCC
1710031 CAAAAGGTA
1 CAAAAGGTA
1710040 TTTGATGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.49, C:0.21, G:0.16, T:0.13
Consensus pattern (26 bp):
CAAAAGGTAAAACCATGGTAATACCC
Found at i:1711516 original size:11 final size:11
Alignment explanation
Indices: 1711500--1711524 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1711490 ATGGCAATCA
1711500 TTTTTTACATT
1 TTTTTTACATT
1711511 TTTTTTACATT
1 TTTTTTACATT
1711522 TTT
1 TTT
1711525 ACATTTATTT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTACATT
Found at i:1715068 original size:9 final size:8
Alignment explanation
Indices: 1715054--1715121 Score: 66
Period size: 8 Copynumber: 8.0 Consensus size: 8
1715044 TGCTTGAAGA
1715054 AAAAAAAG
1 AAAAAAAG
1715062 AACAAAAAAG
1 -A-AAAAAAG
1715072 AACAAAAAAG
1 -A-AAAAAAG
*
1715082 AAGAAAA-
1 AAAAAAAG
*
1715089 AAAAGAAG
1 AAAAAAAG
1715097 AAAAAAAAG
1 -AAAAAAAG
1715106 AAAAAAAG
1 AAAAAAAG
1715114 AAAAAAAG
1 AAAAAAAG
1715122 GGGTCAAGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
7 5 0.10
8 21 0.40
9 9 0.17
10 17 0.33
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1715070 original size:10 final size:9
Alignment explanation
Indices: 1715050--1715120 Score: 78
Period size: 9 Copynumber: 8.1 Consensus size: 9
1715040 ATTATGCTTG
1715050 AAGAAAAAA
1 AAGAAAAAA
1715059 AAGAACAAAA
1 AAGAA-AAAA
1715069 AAGAACAAAA
1 AAGAA-AAAA
*
1715079 AAG--AAGA
1 AAGAAAAAA
*
1715086 AA-AAAAAG
1 AAGAAAAAA
1715094 AAGAAAAAA
1 AAGAAAAAA
1715103 AAG-AAAAA
1 AAGAAAAAA
1715111 AAGAAAAAA
1 AAGAAAAAA
1715120 A
1 A
1715121 GGGGTCAAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
7 5 0.09
8 12 0.23
9 19 0.36
10 17 0.32
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:1715070 original size:12 final size:12
Alignment explanation
Indices: 1715053--1715112 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 12
1715043 ATGCTTGAAG
1715053 AAAAAAAAGAAC
1 AAAAAAAAGAAC
1715065 --AAAAAAGAAC
1 AAAAAAAAGAAC
*
1715075 --AAAAAAGAAG
1 AAAAAAAAGAAC
*
1715085 AAAAAAAAGAAG
1 AAAAAAAAGAAC
1715097 AAAAAAAAGAA-
1 AAAAAAAAGAAC
1715108 AAAAA
1 AAAAA
1715113 GAAAAAAAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
10 19 0.42
11 5 0.11
12 21 0.47
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAC
Found at i:1715085 original size:32 final size:30
Alignment explanation
Indices: 1715049--1715120 Score: 101
Period size: 32 Copynumber: 2.4 Consensus size: 30
1715039 TATTATGCTT
1715049 GAAGAAAAAAAAGAACAAAAAAGAACAAAAAA
1 GAAGAAAAAAAAGAACAAAAAA-AA-AAAAAA
* *
1715081 GAAGAAAAAAAAGAAGAAAAAAAAGAAAAA
1 GAAGAAAAAAAAGAACAAAAAAAAAAAAAA
1715111 -AAGAAAAAAA
1 GAAGAAAAAAA
1715121 GGGGTCAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 10 0.26
30 5 0.13
31 2 0.05
32 21 0.55
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (30 bp):
GAAGAAAAAAAAGAACAAAAAAAAAAAAAA
Found at i:1716647 original size:115 final size:115
Alignment explanation
Indices: 1716390--1716626 Score: 361
Period size: 115 Copynumber: 2.1 Consensus size: 115
1716380 TTGGAGCAAG
* *
1716390 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGAAAGTGTTCTTTGAGTTAT
1 TGAATCTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTAT
* * * * * *
1716455 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTAAAAGA
66 CTGATCTAGTTCGGTAGGAACCACAAAAACCAATCATTGGAATTAAAAGA
* *
1716505 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATCTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTAT
*
1716570 CTGATCTAGTTCGGTAGGAACCAC-AGAACCAATCATTGGAATTAAAAGA
66 CTGATCTAGTTCGGTAGGAACCACAAAAACCAATCATTGGAATTAAAAGA
1716619 TGAA-CTGC
1 TGAATCTGC
1716627 ATGATCGTCT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 3 0.03
114 26 0.23
115 83 0.74
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (115 bp):
TGAATCTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTAT
CTGATCTAGTTCGGTAGGAACCACAAAAACCAATCATTGGAATTAAAAGA
Found at i:1717547 original size:113 final size:113
Alignment explanation
Indices: 1717341--1717665 Score: 490
Period size: 113 Copynumber: 2.9 Consensus size: 113
1717331 CGACTTTTCC
* * * ** * **
1717341 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCAATGGATC
1 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
* * **** *
1717405 AGCATTACCAGTTCGAGTTTATAATGAGAAGAACTCATCTGAAGAAGGA
65 AGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1717454 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
*
1717519 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1717567 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1717632 GCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
66 GCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
1717666 TGTTCAACTT
Statistics
Matches: 195, Mismatches: 16, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
113 192 0.98
114 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
GCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:1717654 original size:186 final size:186
Alignment explanation
Indices: 1717454--1717815 Score: 537
Period size: 186 Copynumber: 1.9 Consensus size: 186
1717444 TGAAGAAGGA
* **
1717454 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
* * *
1717519 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 GCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
1717584 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
131 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
* ** **
1717640 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTTATCATTCAATGGATC
1 AGAAGAAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
**** *
1717704 AGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
65 AGCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
* * *
1717769 GAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGAT
130 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGAT
1717816 TAACAATGCC
Statistics
Matches: 156, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
185 3 0.02
186 153 0.98
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (186 bp):
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
GCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
Found at i:1717694 original size:73 final size:73
Alignment explanation
Indices: 1717567--1717738 Score: 193
Period size: 73 Copynumber: 2.4 Consensus size: 73
1717557 TGAAGAAGGA
* **
1717567 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
* *
1717631 AGCTTTTCC
65 AGCATTACC
* ** **
1717640 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTTATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
1717705 GCATTACC
66 GCATTACC
**** *
1717713 AGTTCGAGTTCATAATAAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
1717739 CATCTGAAGA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 3 0.04
73 80 0.96
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (73 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
GCATTACC
Found at i:1717849 original size:299 final size:298
Alignment explanation
Indices: 1717309--1717963 Score: 1073
Period size: 299 Copynumber: 2.2 Consensus size: 298
1717299 TAGCAAAGAT
1717309 TCAAATCCATCATTTGATGGATC-GACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
1 TCAAATCCATCATTTGATGGATCAG-CTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
* * *
1717373 ACTTTTTGTTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTTATAATGAGAAGAA
65 ACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAA
1717438 CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCC
130 CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCC
* ** *
1717503 ATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC-TGAAGAAGGA
195 ATCATTTGATGGATCAACAATGCCAGAGAAAGTTCATAATGAGAAGAACTCATCAT-AAGAA-GA
1717567 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
258 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1717608 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAA
*
1717673 CTTTTTGCTTGAATTTATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAAC
66 CTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAAC
* * * *
1717738 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCA
131 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
* * * * **
1717803 TCATTTGATGGATTAACAATGCCAG-GTAGAGTTCATAATTAGAAGAACTCGTCATCTGAAGAAG
196 TCATTTGATGGATCAACAATGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCATAAGAAGAAG
1717867 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
260 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1717906 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
1717964 CATCTGAAGA
Statistics
Matches: 333, Mismatches: 20, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
298 100 0.30
299 231 0.69
300 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (298 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAA
CTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAAC
TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
TCATTTGATGGATCAACAATGCCAGAGAAAGTTCATAATGAGAAGAACTCATCATAAGAAGAAGA
AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1717901 original size:112 final size:110
Alignment explanation
Indices: 1717640--1718012 Score: 439
Period size: 113 Copynumber: 3.4 Consensus size: 110
1717630 CAGCTTTTCC
* * * **
1717640 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTTATCATTCAATGGATC
1 AGAAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATC
* *
1717704 AGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGA
66 AGCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAAGA
* *
1717749 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGG
1 A-GAAG-A-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
* * * * *
1717814 ATTAACAATGCCAGGTAGAGTTCATAATTAGAAGAACTCGTCATCTGAAGA
63 ATCAGCATTACCAGGTAGAGTTCATAATAAGAAGAA--C-TCATCTGAAGA
* * * *
1717865 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
1 AGAAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATC
* * * *
1717929 AGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
66 AGCATTACCAG-GTAGAGTTCATAATAAGAAGAACTCATCTGAAGA
* *
1717974 AGAAG-AAGTTCACAATGAGAAGAGCTTGTTCAACCTTTT
1 AGAAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
1718013 ACATAATTTT
Statistics
Matches: 227, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
108 2 0.01
109 45 0.20
110 4 0.02
112 77 0.34
113 81 0.36
114 1 0.00
115 5 0.02
116 12 0.05
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (110 bp):
AGAAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATC
AGCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAAGA
Found at i:1718173 original size:124 final size:124
Alignment explanation
Indices: 1717933--1718225 Score: 343
Period size: 124 Copynumber: 2.4 Consensus size: 124
1717923 TGGATCAGCT
* *
1717933 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG---AAG-AAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATCAGA
* * * * * * *
1717994 AGAGCTTGTTCAACCTTTTACATAATTTTATCATAGAAGAAGATATATTAGCATCAACC
66 AGAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGAAGATAGATCAACATCAACC
*
1718053 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCATAATCAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATCAGA
* * * *
1718118 GGAGCTTATTCAACCTTTTGA-ATGACTCTATCACAGAAGGAA-ATAGGTCAACATCATCC
66 AGAGCTTATTCAACCTTTT-ACATAACTCTATCACAGAA-GAAGATAGATCAACATCAACC
*
1718177 ---CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
1718226 TTTATTCAAC
Statistics
Matches: 149, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
120 37 0.25
121 4 0.03
122 31 0.21
123 8 0.05
124 65 0.44
125 4 0.03
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (124 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATCAGA
AGAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGAAGATAGATCAACATCAACC
Found at i:1718387 original size:3 final size:3
Alignment explanation
Indices: 1718381--1718444 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
1718371 ATTAATAATA
* * * *
1718381 ATT ATT ATT ATA ATT ATT ATT ATT ATA ATA ATT ATT A-T AAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
1718426 ATT ATT ATT ATA ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
1718445 AAAAAATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1718438 original size:18 final size:15
Alignment explanation
Indices: 1718364--1718444 Score: 103
Period size: 15 Copynumber: 5.4 Consensus size: 15
1718354 TTACCCATTT
1718364 TTATT-TTATTAATAA
1 TTATTATTATT-ATAA
*
1718379 TAATTATTATTATAA
1 TTATTATTATTATAA
1718394 TTATTATTATTATAA
1 TTATTATTATTATAA
* *
1718409 TAATTATTATAAT-A
1 TTATTATTATTATAA
1718423 TATATTATTATTATAA
1 T-TATTATTATTATAA
1718439 TTATTA
1 TTATTA
1718445 AAAAAATAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
14 2 0.04
15 48 0.84
16 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATTATAA
Found at i:1718466 original size:14 final size:14
Alignment explanation
Indices: 1718443--1718472 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1718433 TTATAATTAT
1718443 TAAAAAAATAATAA
1 TAAAAAAATAATAA
*
1718457 TAAAATAATAATAA
1 TAAAAAAATAATAA
1718471 TA
1 TA
1718473 GTTACAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAAAAAATAATAA
Found at i:1720082 original size:23 final size:26
Alignment explanation
Indices: 1720050--1720099 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1720040 CATTTTCTGA
*
1720050 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
1720073 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
1720099 T
1 T
1720100 TTTCTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:1723210 original size:45 final size:44
Alignment explanation
Indices: 1723160--1723538 Score: 172
Period size: 45 Copynumber: 9.4 Consensus size: 44
1723150 TTATGTTGAA
*
1723160 AATGCACCCATATGCATTTCAACTTTAGCATCATTTCATGCCAAT
1 AATGCACCCATATGCATTTCAAC-TAAGCATCATTTCATGCCAAT
* * *
1723205 AATGCACCCATATGCA-TT--A-T-----TC-TTTTATGTCGAT
1 AATGCACCCATATGCATTTCAACTAAGCATCATTTCATGCCAAT
* * * **
1723239 AATGTACCCATATACATTTCAGCTAAGACATCATTTCATGTAAAT
1 AATGCACCCATATGCATTTCAACTAAG-CATCATTTCATGCCAAT
* * * *
1723284 AAAGCACCCATATACATTTCAGCTAAGGCATCTTTTCATGCCAAT
1 AATGCACCCATATGCATTTCAACTAA-GCATCATTTCATGCCAAT
* *
1723329 AATGCACCCATATGCA-TT--A-T-----TC-TTTTATGCCGAT
1 AATGCACCCATATGCATTTCAACTAAGCATCATTTCATGCCAAT
* ** * * *
1723363 AATGTACCCATATAAATTTCAGCTAAGGCATCCTTTTATGCCAAT
1 AATGCACCCATATGCATTTCAACTAA-GCATCATTTCATGCCAAT
*
1723408 AATGCACCCATATGCA-TT--A-T-----TC-TTTTATGCCAAT
1 AATGCACCCATATGCATTTCAACTAAGCATCATTTCATGCCAAT
* * *
1723442 AATGCACCCATATGCA-TT--A-T-----TC-TTTTATGTCGAT
1 AATGCACCCATATGCATTTCAACTAAGCATCATTTCATGCCAAT
* * *
1723476 AATGTACCCATATACATTTCAGCTAAGACATCATTTCATGCCAAT
1 AATGCACCCATATGCATTTCAACTAAG-CATCATTTCATGCCAAT
*
1723521 AATGTACCCATATGCATT
1 AATGCACCCATATGCATT
1723539 ATTCTTTTAT
Statistics
Matches: 263, Mismatches: 37, Indels: 68
0.71 0.10 0.18
Matches are distributed among these distances:
34 104 0.40
35 12 0.05
38 3 0.01
40 1 0.00
41 2 0.01
42 1 0.00
44 12 0.05
45 127 0.48
46 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (44 bp):
AATGCACCCATATGCATTTCAACTAAGCATCATTTCATGCCAAT
Found at i:1723285 original size:79 final size:79
Alignment explanation
Indices: 1723148--1723301 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 79
1723138 GATAGCATTA
* * * * *
1723148 TTTTATGTTGAAAATGCACCCATATGCATTTCAACTTTAGCATCATTTCATGCCAATAATGCACC
1 TTTTATGTCGAAAATGCACCCATATACATTTCAACTTAAGCATCATTTCATGCAAATAAAGCACC
*
1723213 CATATGCATTATTC
66 CATATACATTATTC
* * * *
1723227 TTTTATGTCGATAATGTACCCATATACATTTCAGC-TAAGACATCATTTCATGTAAATAAAGCAC
1 TTTTATGTCGAAAATGCACCCATATACATTTCAACTTAAG-CATCATTTCATGCAAATAAAGCAC
1723291 CCATATACATT
65 CCATATACATT
1723302 TCAGCTAAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 3 0.05
79 61 0.95
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (79 bp):
TTTTATGTCGAAAATGCACCCATATACATTTCAACTTAAGCATCATTTCATGCAAATAAAGCACC
CATATACATTATTC
Found at i:1723345 original size:124 final size:121
Alignment explanation
Indices: 1723160--1723538 Score: 549
Period size: 124 Copynumber: 3.1 Consensus size: 121
1723150 TTATGTTGAA
*
1723160 AATGCACCCATATGCATTTCAACTTTAGCATCATTTCATGCCAATAATGCACCCATATGCATTAT
1 AATGCACCCATATGCATTTC-AC--TAGCATCTTTTCATGCCAATAATGCACCCATATGCATTAT
**
1723225 TCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGACATCATTTCATGTAAAT
63 TCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGACATCATTTCATGCCAAT
* *
1723284 AAAGCACCCATATACATTTCAGCTAAGGCATCTTTTCATGCCAATAATGCACCCATATGCATTAT
1 AATGCACCCATATGCATTTCA-CT-A-GCATCTTTTCATGCCAATAATGCACCCATATGCATTAT
* * * * *
1723349 TCTTTTATGCCGATAATGTACCCATATAAATTTCAGCTAAGGCATCCTTTTATGCCAAT
63 TCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGACATCATTTCATGCCAAT
1723408 AATGCACCCATATGCA-TT-A-T----TCTTTT-ATGCCAATAATGCACCCATATGCATTATTCT
1 AATGCACCCATATGCATTTCACTAGCATCTTTTCATGCCAATAATGCACCCATATGCATTATTCT
1723465 TTTATGTCGATAATGTACCCATATACATTTCAGCTAAGACATCATTTCATGCCAAT
66 TTTATGTCGATAATGTACCCATATACATTTCAGCTAAGACATCATTTCATGCCAAT
*
1723521 AATGTACCCATATGCATT
1 AATGCACCCATATGCATT
1723539 ATTCTTTTAT
Statistics
Matches: 233, Mismatches: 18, Indels: 18
0.87 0.07 0.07
Matches are distributed among these distances:
113 97 0.42
114 7 0.03
120 1 0.00
122 2 0.01
123 4 0.02
124 122 0.52
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (121 bp):
AATGCACCCATATGCATTTCACTAGCATCTTTTCATGCCAATAATGCACCCATATGCATTATTCT
TTTATGTCGATAATGTACCCATATACATTTCAGCTAAGACATCATTTCATGCCAAT
Found at i:1723365 original size:34 final size:34
Alignment explanation
Indices: 1723314--1723493 Score: 180
Period size: 34 Copynumber: 4.9 Consensus size: 34
1723304 AGCTAAGGCA
1723314 TCTTTTCATGCCAATAATGCACCCATATGCATTAT
1 TCTTTT-ATGCCAATAATGCACCCATATGCATTAT
* * **
1723349 TCTTTTATGCCGATAATGTACCCATATAAATTTCAGCT
1 TCTTTTATGCCAATAATGCACCCATATGCA-TT-A--T
1723387 AAGGCATCCTTTTATGCCAATAATGCACCCATATGCATTAT
1 ------T-CTTTTATGCCAATAATGCACCCATATGCATTAT
1723428 TCTTTTATGCCAATAATGCACCCATATGCATTAT
1 TCTTTTATGCCAATAATGCACCCATATGCATTAT
* * * *
1723462 TCTTTTATGTCGATAATGTACCCATATACATT
1 TCTTTTATGCCAATAATGCACCCATATGCATT
1723494 TCAGCTAAGA
Statistics
Matches: 122, Mismatches: 12, Indels: 23
0.78 0.08 0.15
Matches are distributed among these distances:
34 81 0.66
35 9 0.07
36 1 0.01
38 1 0.01
41 1 0.01
43 1 0.01
44 3 0.02
45 25 0.20
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (34 bp):
TCTTTTATGCCAATAATGCACCCATATGCATTAT
Found at i:1723420 original size:79 final size:79
Alignment explanation
Indices: 1723281--1723454 Score: 296
Period size: 79 Copynumber: 2.2 Consensus size: 79
1723271 ATTTCATGTA
* *
1723281 AATAAAGCACCCATATACATTTCAGCTAAGGCATCTTTTCATGCCAATAATGCACCCATATGCAT
1 AATAATGCACCCATATAAATTTCAGCTAAGGCATCTTTTCATGCCAATAATGCACCCATATGCAT
1723346 TATTCTTTTATGCC
66 TATTCTTTTATGCC
* *
1723360 GATAATGTACCCATATAAATTTCAGCTAAGGCATCCTTTT-ATGCCAATAATGCACCCATATGCA
1 AATAATGCACCCATATAAATTTCAGCTAAGGCAT-CTTTTCATGCCAATAATGCACCCATATGCA
1723424 TTATTCTTTTATGCC
65 TTATTCTTTTATGCC
1723439 AATAATGCACCCATAT
1 AATAATGCACCCATAT
1723455 GCATTATTCT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
79 83 0.94
80 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.33
Consensus pattern (79 bp):
AATAATGCACCCATATAAATTTCAGCTAAGGCATCTTTTCATGCCAATAATGCACCCATATGCAT
TATTCTTTTATGCC
Found at i:1723519 original size:113 final size:113
Alignment explanation
Indices: 1723314--1723572 Score: 410
Period size: 113 Copynumber: 2.3 Consensus size: 113
1723304 AGCTAAGGCA
1723314 TCTTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATAAA
1 TCTTTT-ATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATAAA
* * *
1723379 TTTCAGCTAAGGCATCCTTTTATGCCAATAATGCACCCATATGCATTAT
65 TTTCAGCTAAGACATCATTTCATGCCAATAATGCACCCATATGCATTAT
* *
1723428 TCTTTTATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCGATAATGTACCCATATACAT
1 TCTTTTATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATAAAT
*
1723493 TTCAGCTAAGACATCATTTCATGCCAATAATGTACCCATATGCATTAT
66 TTCAGCTAAGACATCATTTCATGCCAATAATGCACCCATATGCATTAT
*** * *
1723541 TCTTTTATGTTGATAATGTACCCATATACATT
1 TCTTTTATGCCAATAATGCACCCATATGCATT
1723573 TTAGCTAAGG
Statistics
Matches: 134, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
113 128 0.96
114 6 0.04
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (113 bp):
TCTTTTATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATATAAAT
TTCAGCTAAGACATCATTTCATGCCAATAATGCACCCATATGCATTAT
Found at i:1723565 original size:79 final size:79
Alignment explanation
Indices: 1723434--1723606 Score: 292
Period size: 79 Copynumber: 2.2 Consensus size: 79
1723424 TTATTCTTTT
*
1723434 ATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCGATAATGTACCCATATACATTTCAGC
1 ATGCCAATAATGTACCCATATGCATTATTCTTTTATGTCGATAATGTACCCATATACATTTCAGC
1723499 TAAGACATCATTTC
66 TAAGACATCATTTC
* *
1723513 ATGCCAATAATGTACCCATATGCATTATTCTTTTATGTTGATAATGTACCCATATACATTTTAGC
1 ATGCCAATAATGTACCCATATGCATTATTCTTTTATGTCGATAATGTACCCATATACATTTCAGC
* *
1723578 TAAGGCATCCTTTC
66 TAAGACATCATTTC
*
1723592 ATACCAATAATGTAC
1 ATGCCAATAATGTAC
1723607 ACACAATGCT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 88 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (79 bp):
ATGCCAATAATGTACCCATATGCATTATTCTTTTATGTCGATAATGTACCCATATACATTTCAGC
TAAGACATCATTTC
Found at i:1724088 original size:22 final size:22
Alignment explanation
Indices: 1724044--1724117 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
1724034 TGACCCTTCA
* *
1724044 GTATCGATAC--CCCTACTATG
1 GTATCGATACTACCCCATTATG
1724064 GTATCGATACTACCCCATTATG
1 GTATCGATACTACCCCATTATG
1724086 GTATCGATACTACCCCATTATG
1 GTATCGATACTACCCCATTATG
1724108 GTATCGATAC
1 GTATCGATAC
1724118 CCCCTTCCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 10 0.20
22 40 0.80
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (22 bp):
GTATCGATACTACCCCATTATG
Found at i:1724131 original size:41 final size:39
Alignment explanation
Indices: 1724037--1724137 Score: 98
Period size: 44 Copynumber: 2.5 Consensus size: 39
1724027 AAATTTTTGA
*
1724037 CCCTTCAGTATCGATACCCCTACTATGGTATCGATACTAC
1 CCCTTCAGTATCGATACCCCCACTATGGTATCGATAC-AC
*
1724077 CCCATT-ATGGTATCGATACTACCCCATTATGGTATCGATAC-C
1 CCC-TTCA--GTATCGATAC--CCCCACTATGGTATCGATACAC
*
1724119 CCCTTCCAGTATCAATACC
1 CCCTT-CAGTATCGATACC
1724138 AAATTTGACG
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
39 1 0.02
40 4 0.08
41 13 0.25
42 14 0.27
43 1 0.02
44 18 0.35
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.30
Consensus pattern (39 bp):
CCCTTCAGTATCGATACCCCCACTATGGTATCGATACAC
Found at i:1724189 original size:17 final size:18
Alignment explanation
Indices: 1724153--1724191 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1724143 TGACGTAGCC
1724153 TGGTATCGATACCCTCACTA
1 TGGTATCGATA--CTCACTA
1724173 TGGTATCGATA-TCACTA
1 TGGTATCGATACTCACTA
1724190 TG
1 TG
1724192 CTATGGTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
20 11 0.58
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (18 bp):
TGGTATCGATACTCACTA
Found at i:1728852 original size:34 final size:34
Alignment explanation
Indices: 1728814--1729104 Score: 141
Period size: 34 Copynumber: 7.6 Consensus size: 34
1728804 TTTCATGCTA
* *
1728814 ATAATGCACCCATATGCATTATTCTTTTATGTCG
1 ATAATGCACCCATATACATTATTCTTTTATGCCG
* * *
1728848 ATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCA
1 ATAATGCACCCATATACA-TT-A--T------T-CTTTTATGCCG
*
1728893 ATAATGCACCCATATGCATTATTCTTTTATGCCG
1 ATAATGCACCCATATACATTATTCTTTTATGCCG
* **
1728927 ATAATGTACCCATATACATTTCATCTAAGGCATCATTTCATGCTA
1 ATAATGCACCCATATACA-TT-AT-T----C-T--TTT-ATGCCG
* *
1728972 ATAATGCACCCATATTCATTATTCTTTTATGTCG
1 ATAATGCACCCATATACATTATTCTTTTATGCCG
* * *
1729006 ATAATGTACCCATATACATTTCAACTAAGGCATCCTTTGATGCCA
1 ATAATGCACCCATATACA-TT--A-T------T-CTTTTATGCCG
*
1729051 ATAATGCACCCATATGCATTATTCTTTTATGCCG
1 ATAATGCACCCATATACATTATTCTTTTATGCCG
*
1729085 ATAATGTACCCATATACATT
1 ATAATGCACCCATATACATT
1729105 TCAGCTAAGG
Statistics
Matches: 195, Mismatches: 29, Indels: 66
0.67 0.10 0.23
Matches are distributed among these distances:
34 87 0.45
35 11 0.06
36 3 0.02
37 3 0.02
38 3 0.02
41 3 0.02
42 3 0.02
43 3 0.02
44 11 0.06
45 68 0.35
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (34 bp):
ATAATGCACCCATATACATTATTCTTTTATGCCG
Found at i:1728886 original size:79 final size:79
Alignment explanation
Indices: 1728755--1729216 Score: 703
Period size: 79 Copynumber: 5.9 Consensus size: 79
1728745 TATTGATAGC
* * * * * ** *
1728755 ATTCTTTTATGTTGAAAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCTAATAATG
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
1728820 CACCCATATGCATT
66 CACCCATATGCATT
1728834 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
1728899 CACCCATATGCATT
66 CACCCATATGCATT
* * * *
1728913 ATTCTTTTATGCCGATAATGTACCCATATACATTTCATCTAAGGCATCATTTCATGCTAATAATG
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
*
1728978 CACCCATATTCATT
66 CACCCATATGCATT
* *
1728992 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAACTAAGGCATCCTTTGATGCCAATAATG
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
1729057 CACCCATATGCATT
66 CACCCATATGCATT
* * *
1729071 ATTCTTTTATGCCGATAATGTACCCATATACATTTCAGCTAAGGCATCATTTCATGCCAATAATA
1 ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
*
1729136 CACTCATATGCATT
66 CACCCATATGCATT
* **
1729150 ATTCTTTTATG-CTGATAATGCACTTATATACATTTCAGCTAAGGCATCCTTTCATGCC-ATAAT
1 ATTCTTTTATGTC-GATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAAT
1729213 GCAC
65 GCAC
1729217 ACACAATGCT
Statistics
Matches: 352, Mismatches: 30, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
78 9 0.03
79 343 0.97
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (79 bp):
ATTCTTTTATGTCGATAATGTACCCATATACATTTCAGCTAAGGCATCCTTTCATGCCAATAATG
CACCCATATGCATT
Done.