Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 44 of 150
Found at i:12394557 original size:24 final size:24
Alignment explanation
Indices: 12394528--12394574 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12394518 ATATAAATAT
12394528 GAAAATATTCATTAAAAAATATAG
1 GAAAATATTCATTAAAAAATATAG
* *
12394552 GAAAATATTCGTTTAAAAATATA
1 GAAAATATTCATTAAAAAATATA
12394575 TATATGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (24 bp):
GAAAATATTCATTAAAAAATATAG
Found at i:12395223 original size:19 final size:19
Alignment explanation
Indices: 12395199--12395292 Score: 161
Period size: 19 Copynumber: 4.8 Consensus size: 19
12395189 AATCATATAT
12395199 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
12395218 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
12395239 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12395258 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
12395277 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
12395293 CTCAAAAATT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 52 0.73
21 19 0.27
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12395247 original size:40 final size:38
Alignment explanation
Indices: 12395192--12395292 Score: 161
Period size: 40 Copynumber: 2.7 Consensus size: 38
12395182 ATTACAAAAT
12395192 CATAT-AT-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
*
12395228 CATATATCATATCTAAGATTGCATATCATATCTAGGATTG
1 C--ATATCATATCTAAGATTGCATATCATATCTAAGATTG
12395268 CATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTGCATATC
12395293 CTCAAAAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
36 1 0.02
38 28 0.47
39 2 0.03
40 29 0.48
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGATTG
Found at i:12406777 original size:14 final size:16
Alignment explanation
Indices: 12406748--12406780 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
12406738 GTGCAGGATG
12406748 AAGGAGAGAAGAGAGA
1 AAGGAGAGAAGAGAGA
12406764 AAGGAGA-AAG-GAGA
1 AAGGAGAGAAGAGAGA
12406778 AAG
1 AAG
12406781 AAAATGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (16 bp):
AAGGAGAGAAGAGAGA
Found at i:12408895 original size:15 final size:15
Alignment explanation
Indices: 12408875--12408911 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
12408865 GCATGCAACA
12408875 CCCACACTTGTACAT
1 CCCACACTTGTACAT
12408890 CCCACACTTGTACAT
1 CCCACACTTGTACAT
12408905 CCCACAC
1 CCCACAC
12408912 CGTGAGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.46, G:0.05, T:0.22
Consensus pattern (15 bp):
CCCACACTTGTACAT
Found at i:12422724 original size:9 final size:9
Alignment explanation
Indices: 12422710--12422740 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12422700 GTTAAACGAA
12422710 TCGAGTTAT
1 TCGAGTTAT
*
12422719 TCGAGTTAA
1 TCGAGTTAT
12422728 TCGAGTTAT
1 TCGAGTTAT
12422737 TCGA
1 TCGA
12422741 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12422810 original size:9 final size:9
Alignment explanation
Indices: 12422793--12422829 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12422783 TGAGTTTTCG
12422793 AATTCGAAT
1 AATTCGAAT
*
12422802 AACTCGAAT
1 AATTCGAAT
12422811 AATTCGAAT
1 AATTCGAAT
12422820 AATTCGAAT
1 AATTCGAAT
12422829 A
1 A
12422830 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12423867 original size:5 final size:5
Alignment explanation
Indices: 12423857--12423882 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12423847 CTCGAAAATT
12423857 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
12423883 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:12429364 original size:27 final size:27
Alignment explanation
Indices: 12429331--12429385 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
12429321 GATTTTAGTG
*
12429331 TTCAATTTGATAATTAA-GTTTTTTTT
1 TTCAAATTGATAATTAAGGTTTTTTTT
**
12429357 TTCAAATTGATGTTTAAGGTTTTTTTT
1 TTCAAATTGATAATTAAGGTTTTTTTT
12429384 TT
1 TT
12429386 GTCTCATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.62
Consensus pattern (27 bp):
TTCAAATTGATAATTAAGGTTTTTTTT
Found at i:12430925 original size:32 final size:32
Alignment explanation
Indices: 12430831--12430930 Score: 113
Period size: 28 Copynumber: 3.3 Consensus size: 32
12430821 CCAATATAAT
12430831 ATTTGGTACTTGAACTTGACAC-TTTTTCCTA
1 ATTTGGTACTTGAACTTGACACTTTTTTCCTA
* * *
12430862 ATTTGGTACCTAAACTT-----TTTTTTACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTT-CCTA
*
12430890 ATTTGGTACTTGAGCTTGACACTTTTTTCCTA
1 ATTTGGTACTTGAACTTGACACTTTTTTCCTA
12430922 ATTTGGTAC
1 ATTTGGTAC
12430931 CCTAATTTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
27 5 0.09
28 17 0.31
31 15 0.27
32 12 0.22
33 6 0.11
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (32 bp):
ATTTGGTACTTGAACTTGACACTTTTTTCCTA
Found at i:12430936 original size:13 final size:13
Alignment explanation
Indices: 12430918--12430944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12430908 ACACTTTTTT
12430918 CCTAATTTGGTAC
1 CCTAATTTGGTAC
12430931 CCTAATTTGGTAC
1 CCTAATTTGGTAC
12430944 C
1 C
12430945 TAAACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CCTAATTTGGTAC
Found at i:12430967 original size:29 final size:29
Alignment explanation
Indices: 12430923--12431008 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 29
12430913 TTTTTCCTAA
12430923 TTTGGTACCCTAATTTGGTACCTAAACTTTT
1 TTTGG-ACCC-AATTTGGTACCTAAACTTTT
* * *
12430954 TTTGGACCCAATTTGGTACTTAAGC-ATT
1 TTTGGACCCAATTTGGTACCTAAACTTTT
* **
12430982 TTTAGATTCAATTTGGTACCTAAACTT
1 TTTGGACCCAATTTGGTACCTAAACTT
12431009 ATTAAATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
28 22 0.49
29 14 0.31
30 4 0.09
31 5 0.11
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (29 bp):
TTTGGACCCAATTTGGTACCTAAACTTTT
Found at i:12431189 original size:31 final size:31
Alignment explanation
Indices: 12431151--12431284 Score: 98
Period size: 31 Copynumber: 4.4 Consensus size: 31
12431141 TTAAAAAAGA
12431151 TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
* ***
12431182 TTAGGTACCAAATTGGGACCCCAAA---AAGT
1 TTAGGTACCAAATTAGGA-AAAAAAGTCAAGT
* * * *
12431211 TTAAGTACTAACTTA--AAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAA-AGTCAAGT
* ***
12431241 TTAGGTATCAAATTAGGAAAATGTGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
*
12431272 TCAGGTACCAAAT
1 TTAGGTACCAAAT
12431285 GTTATATTAA
Statistics
Matches: 76, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
26 2 0.03
27 1 0.01
29 15 0.20
30 15 0.20
31 36 0.47
32 7 0.09
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (31 bp):
TTAGGTACCAAATTAGGAAAAAAAGTCAAGT
Found at i:12431568 original size:26 final size:26
Alignment explanation
Indices: 12431528--12431579 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12431518 AACATTTAAC
*
12431528 TAGTATTATAAAATTTCAAATAAATAT
1 TAGTATTACAAAATTTCAAA-AAATAT
*
12431555 TAGTA-TACAAAATTTCATAAAATAT
1 TAGTATTACAAAATTTCAAAAAATAT
12431580 AACGTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (26 bp):
TAGTATTACAAAATTTCAAAAAATAT
Found at i:12448972 original size:23 final size:23
Alignment explanation
Indices: 12448937--12448981 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12448927 TAGAGTATAA
* *
12448937 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
12448960 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
12448982 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:12449034 original size:2 final size:2
Alignment explanation
Indices: 12449029--12449059 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12449019 GATATATATA
12449029 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12449060 ACTTAAGATT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12449454 original size:2 final size:2
Alignment explanation
Indices: 12449403--12449441 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12449393 TGTCTTAAGT
12449403 TA TA TA 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
12449442 GTTCGGATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12449658 original size:42 final size:42
Alignment explanation
Indices: 12449611--12449794 Score: 282
Period size: 42 Copynumber: 4.4 Consensus size: 42
12449601 CAGTGCCTAT
*
12449611 CAGGCTTAATGCTGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
12449653 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
*
12449695 CAGGCTTAATGCTGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
12449737 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
12449778 CAGGC-TAAGTGCCGGTG
1 CAGGCTTAA-TGCCGGTG
12449795 TACTGAATCA
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.02
41 30 0.23
42 98 0.75
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:12461494 original size:17 final size:17
Alignment explanation
Indices: 12461472--12461504 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12461462 CACTTTCTAT
*
12461472 ATGATATAATTGATATG
1 ATGATATAATTAATATG
12461489 ATGATATAATTAATAT
1 ATGATATAATTAATAT
12461505 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
ATGATATAATTAATATG
Found at i:12463051 original size:126 final size:124
Alignment explanation
Indices: 12462826--12463174 Score: 529
Period size: 126 Copynumber: 2.8 Consensus size: 124
12462816 TTTCGAGTTT
** * * * *
12462826 ACGTTTCTGATAAAAGAGTATAAAATAGCTTCTAACAGGATGCTATTTGAGAAGAATTAGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
*
12462891 TCGAGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTG
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGAAAGAAATAA-T-TTTTTTTG
12462952 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
* * * *
12463017 TCGCGGCCTCGT-CAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTG
66 TCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTTTTTTTG
* * *
12463076 ACATTTCTGAGCAAATAATATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
*
12463141 TCGCGCCCTCGTGGACGCGCTTTTGGTACAGTAG
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
12463175 CATGTTTGGG
Statistics
Matches: 204, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
124 99 0.49
125 3 0.01
126 102 0.50
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (124 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTTTTTTTG
Found at i:12463135 original size:124 final size:126
Alignment explanation
Indices: 12462844--12463174 Score: 517
Period size: 124 Copynumber: 2.6 Consensus size: 126
12462834 GATAAAAGAG
* * *
12462844 TATAAAAT-AGCTTCTAACAGGATGCTATTTGAGAAGAATTAGTGAAATCGAGCCCTCGTGGACG
1 TATAAAATCA-CTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACG
* *
12462908 CGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAG
65 CGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTGACATTTCTGAGCAAATAA
* * *
12462970 TATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGGCCTCGT-CAGCG
1 TATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGA-CG
* *
12463034 CGCTTTTGCTACAGTAGGTCATGTAAGAAATAA-T-TTTTTTTGACATTTCTGAGCAAATAA
65 CGCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTGACATTTCTGAGCAAATAA
12463094 TATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGC
1 TATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGC
*
12463159 GCTTTTGGTACAGTAG
66 GCTTTTGCTACAGTAG
12463175 CATGTTTGGG
Statistics
Matches: 188, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
124 99 0.53
125 3 0.02
126 86 0.46
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (126 bp):
TATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGC
GCTTTTGCTACAGTAGGTCACGAAAGAAATAATTATTTTTTTGACATTTCTGAGCAAATAA
Found at i:12466348 original size:23 final size:23
Alignment explanation
Indices: 12466319--12466714 Score: 322
Period size: 23 Copynumber: 15.9 Consensus size: 23
12466309 AAATTATGTA
12466319 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12466342 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 -AA--A--TTA-GGTTAGGGTTTTTAATT
12466371 AAATTAGGTTAGGGTTTTTAAGTT
1 AAATTAGGTTAGGGTTTTTAA-TT
*
12466395 -AA--GGGTTTAGGGTTTTTAATT
1 AAATTAGG-TTAGGGTTTTTAATT
*
12466416 AAATTAGGTTAGGTTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12466439 AATTTAGGTTAAGGTTAGGGTTTTTAATT
1 AA---A--TT-AGGTTAGGGTTTTTAATT
12466468 AAATTAGGTTAGGGTTAGGATTTTTAATT
1 AAATTAGGTTA--G---GG-TTTTTAATT
12466497 AAATTAGGTTAGGGTTTTTAATTAATT
1 AAATTAGGTTAGGG--TTT--TTAATT
12466524 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
12466547 AATTTAGGTTAAGGTTAGGGTTTTTAAGTT
1 AA---A--TT-AGGTTAGGGTTTTTAA-TT
**
12466577 -AA-GGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
12466598 AAATTAGGTTAGGGTTTCTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
12466621 AAATTAGGTTAGGGTTTTTAACTA
1 AAATTAGGTTAGGGTTTTTAA-TT
12466645 AATTACGTTAAGGTTAGGGTTTTTAAGTT
1 AA--A--TT-AGGTTAGGGTTTTTAA-TT
*
12466674 -AA--GGGTTTAGGGTTTTTAATT
1 AAATTAGG-TTAGGGTTTTTAATT
12466695 AAATTAGGTTAGGGTTTTTA
1 AAATTAGGTTAGGGTTTTTA
12466715 TTACATCAAA
Statistics
Matches: 312, Mismatches: 16, Indels: 89
0.75 0.04 0.21
Matches are distributed among these distances:
21 10 0.03
22 47 0.15
23 95 0.30
24 18 0.06
25 7 0.02
26 8 0.03
27 21 0.07
28 14 0.04
29 90 0.29
30 2 0.01
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:12466363 original size:29 final size:29
Alignment explanation
Indices: 12466325--12466386 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
12466315 TGTAAAATTA
12466325 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
12466354 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
12466383 GGTT
1 GGTT
12466387 TTTAAGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:12466410 original size:45 final size:45
Alignment explanation
Indices: 12466319--12466714 Score: 227
Period size: 52 Copynumber: 7.9 Consensus size: 45
12466309 AAATTATGTA
12466319 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT--A--A---TAGGGTTAGGGTTTTTAATT
12466371 AAATTAGGTTAGGGTTTTTAAGTT-A-AGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAA-TTAATAGGG-TTAGGGTTTTTAATT
*
12466416 AAATTAGGTTAGGTTTTTTAATTAATTTAGGTTAAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATTAA--TA-G----GGTTAGGGTTTTTAATT
12466468 AAATTAGGTTAGGGTTAGGATTTTTAATTAAATTA-GGTTAGGGTTTTTAATTAATT
1 AAATTAGGTTA--G---GG-TTTTTAATT-AA-TAGGGTTAGGG--TTT--TTAATT
12466524 AAATTAGGTTAGGGTTTTTAATTAATTTAGGTTAAGGTTAGGGTTTTTAAGTT
1 AAATTAGGTTAGGGTTTTTAATTAA--TA-G----GGTTAGGGTTTTTAA-TT
** *
12466577 -AA-GGGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTCTAATT
1 AAATTAGGTTAGGGTTTTTAATT-AA-TAGGGTTAGGGTTTTTAATT
*
12466621 AAATTAGGTTAGGGTTTTTAACTAAATTACGTTAAGGTTAGGGTTTTTAAGTT
1 AAATTAGGTTAGGGTTTTTAA-TTAA-TA-G----GGTTAGGGTTTTTAA-TT
*
12466674 -AA--GGGTTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTA
1 AAATTAGG-TTAGGGTTTTTAATT-AA-TAGGGTTAGGGTTTTTA
12466715 TTACATCAAA
Statistics
Matches: 290, Mismatches: 11, Indels: 93
0.74 0.03 0.24
Matches are distributed among these distances:
44 8 0.03
45 66 0.23
46 20 0.07
47 1 0.00
48 2 0.01
49 3 0.01
50 15 0.05
51 40 0.14
52 79 0.27
53 8 0.03
54 8 0.03
56 25 0.09
57 1 0.00
58 12 0.04
59 2 0.01
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (45 bp):
AAATTAGGTTAGGGTTTTTAATTAATAGGGTTAGGGTTTTTAATT
Found at i:12466427 original size:97 final size:98
Alignment explanation
Indices: 12466319--12466714 Score: 486
Period size: 97 Copynumber: 4.0 Consensus size: 98
12466309 AAATTATGTA
*
12466319 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAATTAGGTTAG
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAATTAGGTTAG
*
12466383 GGTTTTTAAGTT-AA-GGGTTTAGGGTTTTTAATT
66 GGTTTTTAA-TTAAATAGG-TTAGGGTTTTTAATT
* *
12466416 AAATTAGGTTAGGTTTTTTAATTAATTTAGGTTAAGGTTAGGGTTTTTAA-TTAAATTAGGTTAG
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAATTAGGTTA-
12466480 GGTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTTAATTAATT
65 -G---GG-TTTTTAATTAAA-TAGGTTAGGG--TTT--TTAATT
* **
12466524 AAATTAGGTTAGGGTTTTTAATTAATTTAGGTTAAGGTTAGGGTTTTTAAGTT-AA-GGGGTTAG
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAATTAGGTTAG
*
12466587 GGTTTTTAATTAAATTAGGTTAGGGTTTCTAATT
66 GGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATT
* * *
12466621 AAATTAGGTTAGGGTTTTTAACTAAATTACGTTAAGGTTAGGGTTTTTAAGTT-AA--GGGTTTA
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAATTAGG-TTA
12466683 GGGTTTTTAATTAAATTAGGTTAGGGTTTTTA
65 GGGTTTTTAATTAAA-TAGGTTAGGGTTTTTA
12466715 TTACATCAAA
Statistics
Matches: 272, Mismatches: 12, Indels: 30
0.87 0.04 0.10
Matches are distributed among these distances:
96 3 0.01
97 151 0.56
99 4 0.01
101 23 0.08
102 6 0.02
103 9 0.03
104 6 0.02
105 3 0.01
106 3 0.01
107 5 0.02
108 57 0.21
109 2 0.01
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (98 bp):
AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAATTAGGTTAG
GGTTTTTAATTAAATAGGTTAGGGTTTTTAATT
Found at i:12466473 original size:34 final size:32
Alignment explanation
Indices: 12466421--12466578 Score: 101
Period size: 29 Copynumber: 5.6 Consensus size: 32
12466411 TAATTAAATT
*
12466421 AGGTTAGGTTTTTTAATTAA-T--TTAGGTTA
1 AGGTTAGGATTTTTAATTAATTAATTAGGTTA
*
12466450 AGGTTAGGGTTTTTAATT-A--AATTAGGTTA
1 AGGTTAGGATTTTTAATTAATTAATTAGGTTA
*
12466479 GGGTTAGGATTTTTAATT-A--AATTAGGTT-
1 AGGTTAGGATTTTTAATTAATTAATTAGGTTA
12466507 A-G---GG-TTTTTAATTAATTAA--A--TT-
1 AGGTTAGGATTTTTAATTAATTAATTAGGTTA
*
12466529 AGGTTAGGGTTTTTAATTAA-T--TTAGGTTA
1 AGGTTAGGATTTTTAATTAATTAATTAGGTTA
*
12466558 AGGTTAGGGTTTTTAAGTTAA
1 AGGTTAGGATTTTTAA-TTAA
12466579 GGGGTTAGGG
Statistics
Matches: 109, Mismatches: 4, Indels: 31
0.76 0.03 0.22
Matches are distributed among these distances:
22 3 0.03
23 10 0.09
24 4 0.04
26 6 0.06
27 12 0.11
28 3 0.03
29 67 0.61
30 4 0.04
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (32 bp):
AGGTTAGGATTTTTAATTAATTAATTAGGTTA
Found at i:12466577 original size:20 final size:21
Alignment explanation
Indices: 12466549--12466599 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
12466539 TTTTAATTAA
*
12466549 TTTAGGTTAA-GGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
12466569 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
12466591 TTTAA-TTAA
1 TTTAAGTTAA
12466600 ATTAGGTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.32
21 4 0.14
22 15 0.54
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.45
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:12466606 original size:51 final size:51
Alignment explanation
Indices: 12466530--12466710 Score: 228
Period size: 51 Copynumber: 3.6 Consensus size: 51
12466520 AATTAAATTA
*
12466530 GGTTAGGGTTTTTAATTAATTTAGGTTAAGGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGG
* ** ** *
12466581 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT--TCTAATTAAATT-A--
1 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGG
* *
12466627 GGTTAGGGTTTTTAACTAAATTACGTTAAGGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGG
* *
12466678 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTT
12466711 TTTATTACAT
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
46 30 0.28
48 8 0.08
49 8 0.08
51 60 0.57
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.45
Consensus pattern (51 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGG
Found at i:12466980 original size:21 final size:21
Alignment explanation
Indices: 12466939--12466983 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12466929 GACGGTTGTT
* *
12466939 GTTCTTCCGGTGGGGATTCTG
1 GTTCTTCCGGTCGGCATTCTG
12466960 GTTCTTCCGGTTCGGCA-TCTG
1 GTTCTTCCGG-TCGGCATTCTG
12466981 GTT
1 GTT
12466984 GTCGGACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.04, C:0.22, G:0.33, T:0.40
Consensus pattern (21 bp):
GTTCTTCCGGTCGGCATTCTG
Found at i:12467904 original size:7 final size:7
Alignment explanation
Indices: 12467894--12467918 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12467884 TTATATACAT
12467894 AATACTA
1 AATACTA
12467901 AATACTA
1 AATACTA
12467908 AATACTA
1 AATACTA
12467915 AATA
1 AATA
12467919 TCAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:12469099 original size:29 final size:29
Alignment explanation
Indices: 12469067--12469151 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
12469057 AAAAAGGAAA
12469067 TTGAGAGGAAATTGAAATTAAATATGGAT
1 TTGAGAGGAAATTGAAATTAAATATGGAT
** *
12469096 TTGAGA-G-AATT----TTTGA-A-GGAAA
1 TTGAGAGGAAATTGAAATTAAATATGG-AT
12469118 TTGAGAGGAAATTGAAATTAAATATGGAT
1 TTGAGAGGAAATTGAAATTAAATATGGAT
12469147 TTGAG
1 TTGAG
12469152 CGAATTTTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 4 0.10
24 4 0.10
27 4 0.10
28 4 0.10
29 13 0.32
30 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (29 bp):
TTGAGAGGAAATTGAAATTAAATATGGAT
Found at i:12469115 original size:51 final size:51
Alignment explanation
Indices: 12469060--12469182 Score: 221
Period size: 51 Copynumber: 2.4 Consensus size: 51
12469050 TATTTTAAAA
*
12469060 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
*
12469111 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGCGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
12469162 AAGGAAATTGAGAGG-AATTGA
1 AAGGAAATTGAGAGGAAATTGA
12469183 GAGGAAATAT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 6 0.09
51 64 0.91
ACGTcount: A:0.43, C:0.01, G:0.28, T:0.28
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
Found at i:12469197 original size:12 final size:11
Alignment explanation
Indices: 12469163--12469197 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
12469153 GAATTTTGGA
12469163 AGGAAATTGAG
1 AGGAAATTGAG
12469174 AGG-AATTGAG
1 AGGAAATTGAG
12469184 AGGAAATATGAG
1 AGGAAAT-TGAG
12469196 AG
1 AG
12469198 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:12469735 original size:2 final size:2
Alignment explanation
Indices: 12469728--12469761 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12469718 AATGCTCTTA
12469728 AT AT 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 AT AT
12469762 TAAATTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12477283 original size:21 final size:20
Alignment explanation
Indices: 12477238--12477285 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
12477228 TCCTACTGTA
12477238 CAAATTTGTAATAAAACTAC
1 CAAATTTGTAATAAAACTAC
* *
12477258 AAAATTTGCTATTAAAA-TAC
1 CAAATTTG-TAATAAAACTAC
12477278 TCAAATTT
1 -CAAATTT
12477286 TGCATGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (20 bp):
CAAATTTGTAATAAAACTAC
Found at i:12483529 original size:44 final size:44
Alignment explanation
Indices: 12483349--12484458 Score: 247
Period size: 44 Copynumber: 25.2 Consensus size: 44
12483339 AAGATTGTAG
* * *
12483349 ATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * ** **
12483393 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAATCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * *** * *
12483437 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGGTTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* *
12483481 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
12483525 ATCTTATCTTTCC-AAG-A-TAGTGGGGAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT--GGAGCAGATTGAAGACGGCAA
** * * * * * * ** * *
12483569 GCCTTGTCTCCCTGAGCAGCAGTAGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
12483613 ATCTTATCTCCCTAAACAATAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
12483657 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * * ** * *
12483701 GCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
12483745 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAATACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * * **
12483789 ATCTTATCTTTCC-AAG-A-TAGCGGGAAGTAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAG-TGG-AGCAGATTGAAGACGGCAA
** * * * * * * ** * *
12483833 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* ** *
12483877 ATCTTATCTCCCTAAACAGTAGTGGAGCAGATCAAAGACAGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
12483921 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGTCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * * ** ***
12483965 GCCTTGTCTCACTGAGCAGCAGCGGAGAAGGTTGAAGATTGTGG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
** *
12484009 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGAAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
12484053 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
* * * * * * * * * ** * *
12484097 GTCTTGTCTCCTTGAGAAAGAAGAGGAGAAGATAGAAGATTGTAG
1 ATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
12484142 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* *
12484186 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCTAC--CAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACGGCAA
** * ** * * * * ** * *
12484230 GCCTTGTCTCCCCGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
12484274 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACAGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * **
12484318 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAGGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * * * ** * *
12484362 GCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
12484406 ATATTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
*
12484450 ATCATATCT
1 ATCTTATCT
12484459 TTCCAAGATA
Statistics
Matches: 708, Mismatches: 305, Indels: 106
0.63 0.27 0.09
Matches are distributed among these distances:
42 32 0.05
43 44 0.06
44 546 0.77
45 65 0.09
46 19 0.03
47 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
Found at i:12484521 original size:132 final size:132
Alignment explanation
Indices: 12483302--12484487 Score: 1940
Period size: 132 Copynumber: 9.0 Consensus size: 132
12483292 GGTGAAACAA
*
12483302 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGTA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
* *
12483367 GTAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAATCC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
12483432 AC
131 AC
*
12483434 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGGTTGTAGATCTTATCTCCCTAAGCA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
* *
12483499 GTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGCAGATTTAAGCC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
12483564 AC
131 AC
** * *
12483566 CAAGCCTTGTCTCCCTGAGCAGCAGTAGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
*
12483631 ATAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
12483696 AC
131 AC
*
12483698 CAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
* * * *
12483763 GTAGTGGAGCAGATCGAATACGACAAATCTTATCTTTCCAAGATAGCGGGAAGTAGATTTAAGCC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
12483828 AC
131 AC
* *
12483830 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAACA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
* * *
12483895 GTAGTGGAGCAGATCAAAGACAGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
12483960 AC
131 AC
* *
12483962 CAAGCCTTGTCTCACTGAGCAGCAGCGGAGAAGGTTGAAGATTGTGGATCTTATCTCCCTAAGCA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
* *
12484027 GTAGTGGAGCAGATCAAAGACGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
12484092 AC
131 AC
* * * * * * *
12484094 CAAGTCTTGTCTCCTTGAGAAAGAAGAGGAGAAGATAGAAGATTGTAGATCTTATCTCCCTAAGC
1 CAAGCCTTGTCTCCCTGAG-CAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
* *
12484159 AGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
65 AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
*
12484224 TAC
130 CAC
* *
12484227 CAAGCCTTGTCTCCCCGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
* * *
12484292 ATAGTGGAGCAGATCGAAGACAGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAGGCC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
12484357 AC
131 AC
* * *
12484359 CAAGCCTTGTCTCCCTGAGTAGCAGCGGAGTAGGTTGAAGATTGTAGATATTATCTCCCTAAGCA
1 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
* * * *
12484424 GTAGTGAAGCAGATCGAAGACGGCAAATCATATCTTTCCAAGATAGTGGGAAGCAAATTAAAGC
66 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
12484488 TGACAATCCT
Statistics
Matches: 973, Mismatches: 80, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
132 855 0.88
133 118 0.12
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
AC
Found at i:12484627 original size:44 final size:44
Alignment explanation
Indices: 12484576--12484738 Score: 156
Period size: 44 Copynumber: 3.7 Consensus size: 44
12484566 GATCGCATCT
*
12484576 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACT-AAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-AAGCA
* *
12484620 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCTGACTAAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGA-AGCA
* * * *
12484665 AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGCCAA-TA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG--AAGCA
* *
12484710 A-TCCTATCTCCCTAAAGTTGCAGTGGAGC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGC
12484739 GGATTAGAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
43 3 0.03
44 54 0.55
45 38 0.38
46 3 0.03
47 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAGCA
Found at i:12484686 original size:45 final size:43
Alignment explanation
Indices: 12484578--12484697 Score: 127
Period size: 45 Copynumber: 2.7 Consensus size: 43
12484568 TCGCATCTAG
*
12484578 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAGTAAGCAAG
1 TCTTATCT-CCTGAAGTTGCAGTGGAACAGACTAAGTAAGCAAA
* * *
12484622 TCTTATCCTCCTGAAGTTGCAGT-GAGGCTGACTAAAG-ATGGCAAA
1 TCTTAT-CTCCTGAAGTTGCAGTGGA-ACAGACT-AAGTA-AGCAAA
*
12484667 TCTTATCTCCATGAAGTTGCAGTGGAGCAGA
1 TCTTATCTCC-TGAAGTTGCAGTGGAACAGA
12484698 TTAAAGCCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
43 2 0.03
44 30 0.46
45 31 0.48
46 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCTGAAGTTGCAGTGGAACAGACTAAGTAAGCAAA
Found at i:12484762 original size:44 final size:44
Alignment explanation
Indices: 12484665--12484776 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 44
12484655 AAAGATGGCA
*
12484665 AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCATAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * *
12484709 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAGAA-CC-AT
1 AATCTTATCTCCATAAAGTTGCAGTGGAGCAGATTA-AAGCCAAT
* **
12484752 GGATCTTATCTCTTTAAAGTTGCAG
1 -AATCTTATCTCCATAAAGTTGCAG
12484777 CAGAGCAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 2 0.03
44 54 0.93
45 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCATAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:12485086 original size:19 final size:19
Alignment explanation
Indices: 12485062--12485115 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
12485052 AATCTTCGAG
*
12485062 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
12485081 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
12485100 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
12485116 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12485134 original size:23 final size:22
Alignment explanation
Indices: 12485075--12485138 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 22
12485065 ATGCAATCCT
*
12485075 AGATATGATATGCAATCTT---
1 AGATATGATATGTAATCTTAGA
12485094 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
12485116 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
12485139 GACTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.46
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:12485603 original size:15 final size:14
Alignment explanation
Indices: 12485577--12485607 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
12485567 ATTTTGTTGT
12485577 TATTATTATTATTA
1 TATTATTATTATTA
12485591 TATTATATATTATTA
1 TATTAT-TATTATTA
12485606 TA
1 TA
12485608 CCTACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:12485978 original size:51 final size:52
Alignment explanation
Indices: 12485868--12485980 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 52
12485858 TTCCACGTTT
* **
12485868 TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATATTTTA
1 TATATATATATTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTA
* * * *
12485919 TATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTATTTTA
1 TATATATATATTTATATATTTCATT-TTTTCATAAATGCATGAATATATTTTA
12485970 TATATATATAT
1 TATATATATAT
12485981 AAGTTTTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
51 29 0.56
52 23 0.44
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (52 bp):
TATATATATATTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTA
Found at i:12497976 original size:19 final size:19
Alignment explanation
Indices: 12497952--12497992 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12497942 ACCATTAGAA
*
12497952 GGTGTGCTAACTTGATACT
1 GGTGTGCTAACTCGATACT
12497971 GGTGTGCTAACTCGATACT
1 GGTGTGCTAACTCGATACT
12497990 GGT
1 GGT
12497993 CATTGTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (19 bp):
GGTGTGCTAACTCGATACT
Found at i:12498918 original size:23 final size:22
Alignment explanation
Indices: 12498892--12498943 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
12498882 AATTTTCTAA
12498892 ATTTTTCTATTTGAT-TTCCCATT
1 ATTTTT-TATTT-ATGTTCCCATT
* *
12498915 ATTTATTTATTTATGTTCTCTTT
1 ATTT-TTTATTTATGTTCCCATT
12498938 ATTTTT
1 ATTTTT
12498944 ATTAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 4 0.16
23 19 0.76
24 2 0.08
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTTTTTATTTATGTTCCCATT
Found at i:12499209 original size:21 final size:21
Alignment explanation
Indices: 12499185--12499227 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12499175 TACATCTGGA
12499185 GGCGGTCAAGTTGTTAGCGCC
1 GGCGGTCAAGTTGTTAGCGCC
12499206 GGCGGTCAAGTTGTTAGCGCC
1 GGCGGTCAAGTTGTTAGCGCC
12499227 G
1 G
12499228 TTTTCGGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.40, T:0.23
Consensus pattern (21 bp):
GGCGGTCAAGTTGTTAGCGCC
Found at i:12504060 original size:69 final size:69
Alignment explanation
Indices: 12503944--12504274 Score: 285
Period size: 69 Copynumber: 4.8 Consensus size: 69
12503934 GTTTAAGATA
* * * * * *
12503944 TAAGACAATAGCTTGGCTATGACAACCAATAGCA-TCTACCAGAATAGTAAACACGAGGATTATA
1 TAAGACCATAGCTAGACTATGACAACCAAT-GGAGTCTGCCAGGATAGTAAACACGAGGATTATA
*
12504008 AAGTG
65 AGGTG
* * * * *
12504013 TAAGACCATAGCTAGGCTATGACAACCAATGGAGTTTGCCAGGATAGTAAACA-TAGAAAATATA
1 TAAGACCATAGCTAGACTATGACAACCAATGGAGTCTGCCAGGATAGTAAACACGAG-GATTATA
12504077 AGGTG
65 AGGTG
* * * * * * **
12504082 TAAGACCATAGCTCA-ATTATGGCAACCAATGGAGCCCGTCAGGACAGTAAACATTAGGATTATA
1 TAAGACCATAGCT-AGACTATGACAACCAATGGAGTCTGCCAGGATAGTAAACACGAGGATTATA
12504146 AGGTG
65 AGGTG
* * * ** *
12504151 TAAGACCATAGCTCGACTATGGA-AACTAATGGATTCTGTTAGGATAGTAAACATGAGGATTATA
1 TAAGACCATAGCTAGACTAT-GACAACCAATGGAGTCTGCCAGGATAGTAAACACGAGGATTATA
**
12504215 AGGCA
65 AGGTG
* * * * *
12504220 TAAGACCATAGCTTA-AATATGACAACCAATAGAGTCTGCAAGGACAATAAACACG
1 TAAGACCATAGC-TAGACTATGACAACCAATGGAGTCTGCCAGGATAGTAAACACG
12504275 GGGAAGTCCG
Statistics
Matches: 212, Mismatches: 42, Indels: 16
0.79 0.16 0.06
Matches are distributed among these distances:
68 6 0.03
69 200 0.94
70 6 0.03
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (69 bp):
TAAGACCATAGCTAGACTATGACAACCAATGGAGTCTGCCAGGATAGTAAACACGAGGATTATAA
GGTG
Found at i:12504264 original size:138 final size:137
Alignment explanation
Indices: 12503943--12504274 Score: 339
Period size: 138 Copynumber: 2.4 Consensus size: 137
12503933 GGTTTAAGAT
* *** * * *
12503943 ATAAGACAATAGCTTGGCTATGACAACCAATAGCA-TCTACCAGAATAGTAAACACGAGGATTAT
1 ATAAGACCATAGCTTAAATATGACAACCAATAG-AGTCT-GCAGGACAGTAAACACGAGGATTAT
*
12504007 AAAGTGTAAGACCATAGCTAGGCTATGACAACCAATGGAGTTTGCCAGGATAGTAAACATAGAAA
64 AAAGTGTAAGACCATAGCTAGACTATGACAACCAATGGAGTTTGCCAGGATAGTAAACATAGAAA
*
12504072 ATATAAGGT
129 ATATAAGGC
* * * * * * * **
12504081 GTAAGACCATAGCTCAATTATGGCAACCAATGGAGCCCGTCAGGACAGTAAACATTAGGATTATA
1 ATAAGACCATAGCTTAAATATGACAACCAATAGAGTCTG-CAGGACAGTAAACACGAGGATTATA
* * * **
12504146 AGGTGTAAGACCATAGCTCGACTATGGA-AACTAATGGA-TTCTGTTAGGATAGTAAACAT-GAG
65 AAGTGTAAGACCATAGCTAGACTAT-GACAACCAATGGAGTT-TGCCAGGATAGTAAACATAGA-
* *
12504208 GATTATAAGGC
127 AAATATAAGGC
*
12504219 ATAAGACCATAGCTTAAATATGACAACCAATAGAGTCTGCAAGGACAATAAACACG
1 ATAAGACCATAGCTTAAATATGACAACCAATAGAGTCTGC-AGGACAGTAAACACG
12504275 GGGAAGTCCG
Statistics
Matches: 154, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
137 6 0.04
138 146 0.95
139 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (137 bp):
ATAAGACCATAGCTTAAATATGACAACCAATAGAGTCTGCAGGACAGTAAACACGAGGATTATAA
AGTGTAAGACCATAGCTAGACTATGACAACCAATGGAGTTTGCCAGGATAGTAAACATAGAAAAT
ATAAGGC
Found at i:12515284 original size:19 final size:19
Alignment explanation
Indices: 12515260--12515298 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12515250 ATATATGCTC
12515260 ATAAAAACCTAAAAAAAAT
1 ATAAAAACCTAAAAAAAAT
* *
12515279 ATAAAAACTTAAAAAGAAT
1 ATAAAAACCTAAAAAAAAT
12515298 A
1 A
12515299 AGTTAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (19 bp):
ATAAAAACCTAAAAAAAAT
Found at i:12526484 original size:27 final size:27
Alignment explanation
Indices: 12526454--12526524 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
12526444 CTGCCAAAAT
***
12526454 AGTAAACACAGGGTAGTCTGTTGGGAC
1 AGTAAACACAGGGTAGTCCACTGGGAC
*
12526481 AGTAAACAC-GGGCTAGTCCACTGGGAG
1 AGTAAACACAGGG-TAGTCCACTGGGAC
*
12526508 AGTAAACACAGGATAGT
1 AGTAAACACAGGGTAGT
12526525 TTACCAAGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.08
27 32 0.86
28 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (27 bp):
AGTAAACACAGGGTAGTCCACTGGGAC
Found at i:12537254 original size:39 final size:40
Alignment explanation
Indices: 12537126--12537260 Score: 163
Period size: 40 Copynumber: 3.4 Consensus size: 40
12537116 CGTTTGAATA
* * *
12537126 AAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTATCTA-
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCT-TTTAC
* *
12537166 AAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTTT-C
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTTAC
12537205 TAAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-TTTTAC
1 -AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTTAC
12537244 AAAAAGCGCCGC-AAAAA
1 AAAAA-CGCCGCTAAAAA
12537261 CCTAAACCTA
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
38 14 0.17
39 22 0.26
40 48 0.57
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTTAC
Found at i:12537363 original size:41 final size:41
Alignment explanation
Indices: 12537300--12537412 Score: 190
Period size: 41 Copynumber: 2.8 Consensus size: 41
12537290 TTTTTAGGGA
*
12537300 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCACTAATGCTCTAGTC
* * *
12537341 TTTAGCGGCGTTTTTGATGAAGCGCCACTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCACTAATGCTCTAGTC
12537382 TTTAGCGGCGTTTTTTAAGAAGCGCCACTAA
1 TTTAGCGGCGTTTTTTAAGAAGCGCCACTAA
12537413 AAGCCTTTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAAGAAGCGCCACTAATGCTCTAGTC
Found at i:12538004 original size:15 final size:15
Alignment explanation
Indices: 12537984--12538015 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12537974 TATTTTAAGG
12537984 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
12537999 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
12538014 TT
1 TT
12538016 AGCGATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:12538022 original size:14 final size:15
Alignment explanation
Indices: 12537993--12538030 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
12537983 GTTTAGGGAG
*
12537993 TATGGATTTAGGGAT
1 TATGGATTTAGCGAT
12538008 TATGGA-TTAGCGAT
1 TATGGATTTAGCGAT
12538022 TATGG-TTTA
1 TATGGATTTA
12538031 AGGGTTGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGCGAT
Found at i:12541702 original size:15 final size:17
Alignment explanation
Indices: 12541668--12541705 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
12541658 TAATTTATTT
12541668 ATTTTTATTATTTTAGA
1 ATTTTTATTATTTTAGA
*
12541685 ATTTTTA-TA-TTTATA
1 ATTTTTATTATTTTAGA
12541700 ATTTTT
1 ATTTTT
12541706 TTTCCTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTTATTATTTTAGA
Found at i:12542842 original size:27 final size:25
Alignment explanation
Indices: 12542812--12542884 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 25
12542802 AATTTCGAGG
*
12542812 TTTATAATTTTTAATTTTTATTAATT
1 TTTAT-ATTTTTAACTTTTATTAATT
* *
12542838 ATTTATGTTTTCTCACTTTTATTAATT
1 -TTTATATTTT-TAACTTTTATTAATT
12542865 TTTATTATTATTTAAACTTT
1 TTTA-TATT-TTT-AACTTT
12542885 CTTTATTTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 8 0.22
27 22 0.59
28 7 0.19
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.66
Consensus pattern (25 bp):
TTTATATTTTTAACTTTTATTAATT
Found at i:12543122 original size:43 final size:43
Alignment explanation
Indices: 12543073--12543366 Score: 169
Period size: 43 Copynumber: 6.8 Consensus size: 43
12543063 TTTTTGCGAG
* * *
12543073 AAGCGTCGCTAAAGGT-TTGTTCTATAGCGGCGTTTGAGATAAA
1 AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTTGAGAT-AA
* * *
12543116 AAGCGTCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGTAA
1 AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTTGAGATAA
* * * * * * **
12543159 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGTGTTTGTGGGAA
1 AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTTGAGATAA
* * * * * * * **
12543202 AAGAGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGGGAA
1 AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTTGAGATAA
* * * * * * *
12543245 AAGCGCCGCTAAAGAACATGGTTTTTAGCGCCGTTTGTCG-GAA
1 AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTTG-AGATAA
* * * * * * ** *
12543288 AAGCGCCGCTAAAGAACATGGTCTTTAGAGGAGTTTGTGGGAG
1 AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTTGAGATAA
* * * *
12543331 AAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTT
1 AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTT
12543367 ATTTCCAAAA
Statistics
Matches: 218, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
42 1 0.00
43 197 0.90
44 20 0.09
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (43 bp):
AAGCGTCGCTAAAGATCATGGTCTATAGCGGCGTTTGAGATAA
Found at i:12543172 original size:86 final size:84
Alignment explanation
Indices: 12543053--12543344 Score: 266
Period size: 86 Copynumber: 3.4 Consensus size: 84
12543043 ATGATATGTT
* * * * * * *
12543053 TTTAGCGGCATTTTTGCGAGAAGCGTCGCTAAAG-GTTTGTTCTATAGCGGCGTTTGAGATAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACTTTGTTCTTTAGCGGCGTTTGAG--AAAA
*
12543117 AGCGTCGCTAAAGATCATGGTC
64 AGCG-CGCTAAAGAACATGGTC
* ** * *
12543139 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGTGTTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACTTTGTTCTTTAGCGGCG-TT-TGAGAAAA
* *
12543204 GAGC-CGCTAAAGACCATGTTC
64 -AGCGCGCTAAAGAACATGGTC
* * * * * *
12543225 TTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGTT-TTTAGCGCCGTTTGTCGGAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG-ACTTTGTTCTTTAGCGGCGTTTG-AGAAAA
12543289 AGCGCCGCTAAAGAACATGGTC
64 AGCG-CGCTAAAGAACATGGTC
* * *
12543311 TTTAGAGGAGTTTGTGGGAGAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
12543345 GTCATGGTCT
Statistics
Matches: 169, Mismatches: 29, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
84 5 0.03
85 6 0.04
86 128 0.76
87 22 0.13
88 5 0.03
89 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (84 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACTTTGTTCTTTAGCGGCGTTTGAGAAAAAG
CGCGCTAAAGAACATGGTC
Found at i:12543366 original size:86 final size:85
Alignment explanation
Indices: 12543114--12543366 Score: 317
Period size: 86 Copynumber: 2.9 Consensus size: 85
12543104 GTTTGAGATA
* * * * *
12543114 AAAAGCGTCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACCATG
1 AAAAGCGCCGCTAAAGAACATGGTCTTTAG-GGAGTTTGTGGGAAAAGCGCCGCTAAAGAACATG
* * *
12543179 TTCTTTAGCGGTGTTTGTGGG
65 GTCTTTAGCGGCGTTTGTCGG
* * * *
12543200 AAAAGAGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGAACATG
1 AAAAGCGCCGCTAAAGAACATGGTCTTTAGGGA-GTTTGTGGGAAAAGCGCCGCTAAAGAACATG
* *
12543265 GTTTTTAGCGCCGTTTGTCGG
65 GTCTTTAGCGGCGTTTGTCGG
* **
12543286 AAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGAGTTTGTGGGAGAAGCGCCGCTAAAGGTCATG
1 AAAAGCGCCGCTAAAGAACATGGTCTTTAG-GGAGTTTGTGGGAAAAGCGCCGCTAAAGAACATG
*
12543351 GTCTTTAGTGGCGTTT
65 GTCTTTAGCGGCGTTT
12543367 ATTTCCAAAA
Statistics
Matches: 142, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
85 1 0.01
86 139 0.98
87 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (85 bp):
AAAAGCGCCGCTAAAGAACATGGTCTTTAGGGAGTTTGTGGGAAAAGCGCCGCTAAAGAACATGG
TCTTTAGCGGCGTTTGTCGG
Found at i:12543366 original size:129 final size:130
Alignment explanation
Indices: 12543070--12543366 Score: 375
Period size: 129 Copynumber: 2.3 Consensus size: 130
12543060 GCATTTTTGC
* * * * * *
12543070 GAGAAGCGTCGCTAAAGGT-TTGTTCTATAGCGGCGTTTGAGATAAAAAGCGTCGCTAAAGATCA
1 GAGAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGAGAGAAAAAGCGCCGCTAAAGAACA
* * * * *
12543134 TGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGTGTTTGTGG
66 TGGTCTTTAGCGCCGTTTGTGGTAAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGAGTTTGTGG
* * ** * * *
12543199 GAAAAGAGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTG-GGAAAAGCGCCGCTAAAGAACA
1 GAGAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGAGAGAAAAAGCGCCGCTAAAGAACA
*
12543263 TGGTTTTTAGCGCCGTTTGTCGG-AAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGAGTTTGTG
66 TGGTCTTTAGCGCCGTTTGT-GGTAAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGAGTTTGTG
12543327 G
130 G
* *
12543328 GAGAAGCGCCGCTAAAGGTCATGGTCTTTAGTGGCGTTT
1 GAGAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTT
12543367 ATTTCCAAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
129 120 0.86
130 20 0.14
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (130 bp):
GAGAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGAGAGAAAAAGCGCCGCTAAAGAACA
TGGTCTTTAGCGCCGTTTGTGGTAAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGAGTTTGTGG
Found at i:12547689 original size:91 final size:91
Alignment explanation
Indices: 12547534--12547743 Score: 278
Period size: 91 Copynumber: 2.3 Consensus size: 91
12547524 CAAGTAATAT
* * * * **
12547534 AATAATACACAGATTGATAGTTTAAGTACCACATTGAACATTTTTAAATTATAAGTATTACATTA
1 AATAATACACAAATTGATAGTTTAGGTACCACATTGAACATTTTTAAAGTACAAGTACCACATTA
* * *
12547599 GACGTTTTATGAAAGTACAGGTACCG
66 GACATTTTATGAAAGTACAAGTACCA
* *
12547625 AATAATACTCAAATTGATAGTTTAGGTATCACATT-AGACATTTTTAAAGTACAAGTACCACATT
1 AATAATACACAAATTGATAGTTTAGGTACCACATTGA-ACATTTTTAAAGTACAAGTACCACATT
12547689 AGACATTTTATGAAAGTACAAGTACCA
65 AGACATTTTATGAAAGTACAAGTACCA
* *
12547716 AATAATACACAATTTGATTAGTTCAGGT
1 AATAATACACAAATTGA-TAGTTTAGGT
12547744 TAGAGGTGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
90 1 0.01
91 93 0.90
92 9 0.09
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (91 bp):
AATAATACACAAATTGATAGTTTAGGTACCACATTGAACATTTTTAAAGTACAAGTACCACATTA
GACATTTTATGAAAGTACAAGTACCA
Found at i:12547696 original size:29 final size:31
Alignment explanation
Indices: 12547654--12547715 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 31
12547644 GTTTAGGTAT
12547654 CACATTAGACATTTT-T-AAAGTACAAGTAC
1 CACATTAGACATTTTATGAAAGTACAAGTAC
12547683 CACATTAGACATTTTATGAAAGTACAAGTAC
1 CACATTAGACATTTTATGAAAGTACAAGTAC
12547714 CA
1 CA
12547716 AATAATACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 15 0.48
30 1 0.03
31 15 0.48
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (31 bp):
CACATTAGACATTTTATGAAAGTACAAGTAC
Found at i:12547977 original size:30 final size:31
Alignment explanation
Indices: 12547942--12548028 Score: 131
Period size: 31 Copynumber: 2.7 Consensus size: 31
12547932 TAAATATATA
12547942 TTTTTTATTTTTAAAA-ATATTTTAAAATACT
1 TTTTTTATTTTTAAAATAT-TTTTAAAATACT
12547973 TTTTTTATTTTTAAAATATTTTTAAAATACT
1 TTTTTTATTTTTAAAATATTTTTAAAATACT
*
12548004 TTTTTTAATTTTCTAAAATTTTTTT
1 TTTTTT-ATTTT-TAAAATATTTTT
12548029 TGGTGTTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
31 34 0.65
32 7 0.13
33 11 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTTTTATTTTTAAAATATTTTTAAAATACT
Found at i:12548015 original size:21 final size:20
Alignment explanation
Indices: 12547990--12548029 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
12547980 TTTTTAAAAT
12547990 ATTTT-TAAAATACTTTTTTTA
1 ATTTTCTAAAAT--TTTTTTTA
12548011 ATTTTCTAAAATTTTTTTT
1 ATTTTCTAAAATTTTTTTT
12548030 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTCTAAAATTTTTTTTA
Found at i:12548269 original size:29 final size:29
Alignment explanation
Indices: 12548223--12548346 Score: 106
Period size: 29 Copynumber: 4.1 Consensus size: 29
12548213 TCTAGTTCAG
*
12548223 GTACCACATTGGACATTTTTAAAGTACAA
1 GTACCACATTAGACATTTTTAAAGTACAA
* * *
12548252 GTAGCACATCAGACATTTTATGAAAGTACAG
1 GTACCACATTAGACATTTT-T-AAAGTACAA
* * ** *
12548283 GTACCAAATAATATACA-AATTAACAGTTCAA
1 GTACCACAT--TAGACATTTTTAA-AGTACAA
*
12548314 GTATCACATTAGACATTTTTAAAGTACAA
1 GTACCACATTAGACATTTTTAAAGTACAA
12548343 GTAC
1 GTAC
12548347 ATTATCCAAA
Statistics
Matches: 70, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
29 30 0.43
30 7 0.10
31 28 0.40
32 1 0.01
33 4 0.06
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (29 bp):
GTACCACATTAGACATTTTTAAAGTACAA
Found at i:12549142 original size:3 final size:3
Alignment explanation
Indices: 12549134--12549178 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12549124 TGATTTTTTA
12549134 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12549179 GCTTAAGGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12549539 original size:28 final size:29
Alignment explanation
Indices: 12549487--12549552 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
12549477 CAATAAATGT
*
12549487 TATAAAAATTATTAAATTTTAATTAAAAA
1 TATAAAAATTATTAAAATTTAATTAAAAA
12549516 TATAAAAA-TATTAAAAATTT-ATTAAAAA
1 TATAAAAATTATT-AAAATTTAATTAAAAA
*
12549544 T-TAGAAATT
1 TATAAAAATT
12549553 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 5 0.15
28 14 0.42
29 14 0.42
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
TATAAAAATTATTAAAATTTAATTAAAAA
Found at i:12549540 original size:11 final size:10
Alignment explanation
Indices: 12549489--12549546 Score: 59
Period size: 11 Copynumber: 5.9 Consensus size: 10
12549479 ATAAATGTTA
12549489 TAAAAATTAT
1 TAAAAATTAT
**
12549499 TAAATTTTAAT
1 TAAAAATT-AT
12549510 TAAAAA-TA-
1 TAAAAATTAT
12549518 TAAAAA-TAT
1 TAAAAATTAT
12549527 TAAAAATTTAT
1 TAAAAA-TTAT
12549538 TAAAAATTA
1 TAAAAATTA
12549547 GAAATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 8 0.20
9 7 0.17
10 10 0.25
11 15 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:12549546 original size:18 final size:18
Alignment explanation
Indices: 12549507--12549553 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12549497 ATTAAATTTT
12549507 AATTAAAAA--TATAAAA
1 AATTAAAAATTTATAAAA
*
12549523 ATATTAAAAATTTATTAAA
1 A-ATTAAAAATTTATAAAA
*
12549542 AATTAGAAATTT
1 AATTAAAAATTT
12549554 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 8 0.31
18 10 0.38
19 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATTAAAAATTTATAAAA
Found at i:12549576 original size:22 final size:21
Alignment explanation
Indices: 12549537--12549593 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
12549527 TAAAAATTTA
12549537 TTAAAAATTAG-AAATTTTTTT
1 TTAAAAATT-GTAAATTTTTTT
12549558 TTAAAAATTGTAAATTTTTTT
1 TTAAAAATTGTAAATTTTTTT
*
12549579 ATAAAATATTGTAAA
1 TTAAAA-ATTGTAAA
12549594 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 1 0.03
21 24 0.73
22 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TTAAAAATTGTAAATTTTTTT
Found at i:12549981 original size:21 final size:22
Alignment explanation
Indices: 12549945--12549987 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
12549935 TTAGAAAAAA
12549945 TTACAATTTGTTATAATTTTTT
1 TTACAATTTGTTATAATTTTTT
12549967 TTACAATTT-TTATAATTTTTT
1 TTACAATTTGTTATAATTTTTT
12549988 CTAGTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
TTACAATTTGTTATAATTTTTT
Found at i:12552043 original size:25 final size:24
Alignment explanation
Indices: 12552014--12552060 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12552004 AAAATATCAT
*
12552014 TAAAATAATAATAGTAGTCATTTAA
1 TAAAAGAAT-ATAGTAGTCATTTAA
* *
12552039 TAAAAGGATATATTAGTCATTT
1 TAAAAGAATATAGTAGTCATTT
12552061 CCTAACTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (24 bp):
TAAAAGAATATAGTAGTCATTTAA
Found at i:12553022 original size:37 final size:37
Alignment explanation
Indices: 12552979--12553108 Score: 115
Period size: 36 Copynumber: 3.5 Consensus size: 37
12552969 CCACCTTCAT
**
12552979 CCGATTTGCTTCCTTGTTTCATTTCTTTTCTTTTCTG
1 CCGATTTGCTTCCCAGTTTCATTTCTTTTCTTTTCTG
* **
12553016 CCGATTTG-GTCCCAGTTT-ATTTTCTTGCCTTTTCTG
1 CCGATTTGCTTCCCAGTTTCA-TTTCTTTTCTTTTCTG
* * * *
12553052 CCGATTTGCTCCCCCGATTCTTTTCTTTTCTATTTC-G
1 CCGATTTGCTTCCCAGTTTCATTTCTTTTCT-TTTCTG
*
12553089 ACCGATTTGC-TCACAGTTTC
1 -CCGATTTGCTTCCCAGTTTC
12553109 TGCCGATTTG
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
35 1 0.01
36 29 0.40
37 29 0.40
38 13 0.18
ACGTcount: A:0.09, C:0.28, G:0.13, T:0.50
Consensus pattern (37 bp):
CCGATTTGCTTCCCAGTTTCATTTCTTTTCTTTTCTG
Found at i:12561595 original size:27 final size:27
Alignment explanation
Indices: 12561544--12561629 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
12561534 ATCCTAATAT
12561544 TTAAAATTTATTATAAATAAAAAAACA
1 TTAAAATTTATTATAAATAAAAAAACA
*
12561571 TTAATATTTA-TA-AAATTAAACAAAACA
1 TTAAAATTTATTATAAA-TAAA-AAAACA
**
12561598 TTATGA-TTA--ATAAATAATAAAAA-A
1 TTAAAATTTATTATAAATAA-AAAAACA
12561622 TTAAAATT
1 TTAAAATT
12561630 AAAAAAACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
24 5 0.10
25 12 0.24
26 13 0.27
27 19 0.39
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
TTAAAATTTATTATAAATAAAAAAACA
Found at i:12562645 original size:13 final size:13
Alignment explanation
Indices: 12562622--12562654 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12562612 TTGGGCTAGG
12562622 TGTAA-TTGGGTC
1 TGTAATTTGGGTC
*
12562634 TGTAATTTGGGTT
1 TGTAATTTGGGTC
12562647 TGTAATTT
1 TGTAATTT
12562655 TTGGCTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (13 bp):
TGTAATTTGGGTC
Found at i:12568675 original size:44 final size:44
Alignment explanation
Indices: 12568612--12568706 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
12568602 TAAAATTCCT
*
12568612 CCATATCTATCACCCCCATCTCTAGTCCTATTTATGGAAGCTAG
1 CCATATCTATCACCCCCATCTCTAGTCCCATTTATGGAAGCTAG
*
12568656 CCATATCTATCGCCCCCATCTCTAGTCCCATTTATGGAAGCTAG
1 CCATATCTATCACCCCCATCTCTAGTCCCATTTATGGAAGCTAG
12568700 CCA-ATCT
1 CCATATCT
12568707 TAATGAAAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 4 0.08
44 45 0.92
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.31
Consensus pattern (44 bp):
CCATATCTATCACCCCCATCTCTAGTCCCATTTATGGAAGCTAG
Found at i:12583418 original size:12 final size:12
Alignment explanation
Indices: 12583401--12583429 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
12583391 GATTAAAAAC
12583401 ATAAAAATGAGT
1 ATAAAAATGAGT
12583413 AT-AAAATGAGT
1 ATAAAAATGAGT
12583424 ATAAAA
1 ATAAAA
12583430 TACCTACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (12 bp):
ATAAAAATGAGT
Found at i:12583420 original size:11 final size:11
Alignment explanation
Indices: 12583404--12583430 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12583394 TAAAAACATA
12583404 AAAATGAGTAT
1 AAAATGAGTAT
12583415 AAAATGAGTAT
1 AAAATGAGTAT
12583426 AAAAT
1 AAAAT
12583431 ACCTACTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (11 bp):
AAAATGAGTAT
Found at i:12583841 original size:19 final size:19
Alignment explanation
Indices: 12583817--12583854 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12583807 CTAAAAATAT
*
12583817 TAAATAATTAATATTTATG
1 TAAATAACTAATATTTATG
12583836 TAAATAACTAATATTTATG
1 TAAATAACTAATATTTATG
12583855 GACCGACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (19 bp):
TAAATAACTAATATTTATG
Found at i:12599589 original size:17 final size:17
Alignment explanation
Indices: 12599567--12599600 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12599557 ATTGTTAGTT
12599567 TAAATTTCATTTTTCAC
1 TAAATTTCATTTTTCAC
12599584 TAAATTTCATTTTTCAC
1 TAAATTTCATTTTTCAC
12599601 ACACTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTCATTTTTCAC
Found at i:12601374 original size:25 final size:25
Alignment explanation
Indices: 12601310--12601375 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
12601300 TCCTGTACAT
* * * *
12601310 GTATGCTAATACGAACTGTGAATCG
1 GTATGCTCACACGAGCTGTAAATCG
*
12601335 GTATGCTCACTCGAGCTGTAAATCG
1 GTATGCTCACACGAGCTGTAAATCG
*
12601360 GTATGCTCTCACGAGC
1 GTATGCTCACACGAGC
12601376 CGTGGGTTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCG
Found at i:12606054 original size:20 final size:20
Alignment explanation
Indices: 12606021--12606058 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12606011 AGTTTTTACG
* *
12606021 ATTGGGTTGGGTTTATATAT
1 ATTGGATTGAGTTTATATAT
12606041 ATTGGATTGAGTTTATAT
1 ATTGGATTGAGTTTATAT
12606059 TGGGTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (20 bp):
ATTGGATTGAGTTTATATAT
Found at i:12606924 original size:26 final size:26
Alignment explanation
Indices: 12606888--12606944 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
12606878 GATGTAATTT
*
12606888 GTTATGCCTCCAATTATTACAAGGTA
1 GTTATGCCTCCAATTAGTACAAGGTA
12606914 GTTATGCCTCCAATTAGTACAAGGTA
1 GTTATGCCTCCAATTAGTACAAGGTA
12606940 GTTAT
1 GTTAT
12606945 TCCTGAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (26 bp):
GTTATGCCTCCAATTAGTACAAGGTA
Found at i:12610113 original size:30 final size:30
Alignment explanation
Indices: 12610055--12610113 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
12610045 ATTTTACGAG
* * *
12610055 TCTAGGGGCAAAATTGTAATTTTGTCAAAC
1 TCTAAGGGCAAAAATGTAAATTTGTCAAAC
12610085 TCTAAGGGCAAAAATGTAAAATTT-TCAAA
1 TCTAAGGGCAAAAATGT-AAATTTGTCAAA
12610114 GTGTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (30 bp):
TCTAAGGGCAAAAATGTAAATTTGTCAAAC
Found at i:12610474 original size:51 final size:50
Alignment explanation
Indices: 12610347--12610480 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
12610337 AAAGTGATGG
* * * *
12610347 TCACGTGTGTAGTACTATGTACAGGCTACTACGTGTACCAGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
* * * * *
12610397 TCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCAG-ATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAAT-G-ATAGA
12610448 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
12610481 TGAACCGGTA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.03
50 36 0.51
51 32 0.46
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGATAGA
Found at i:12610583 original size:27 final size:27
Alignment explanation
Indices: 12610545--12610596 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
12610535 TTTAAATGTG
12610545 AAGGGGTTGCTAAGTGCTGATTCCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCCC
*
12610572 AAGGGGTTGCTAAGTGTTGATTCCC
1 AAGGGGTTGCTAAGTGCTGATTCCC
12610597 TGATTCATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (27 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:12610688 original size:102 final size:101
Alignment explanation
Indices: 12610508--12610775 Score: 455
Period size: 102 Copynumber: 2.6 Consensus size: 101
12610498 ATATAAAGGG
12610508 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCCCA
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCCCA
* *
12610573 AGGGGTTGCTAAGTGTTGATTCCCTGATTCATTGGT
66 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
12610609 GGTTACTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAA-GGGGTTGCTAAGTGCTGATTCCCCC
12610674 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
65 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
12610711 GGTTGCTAAGTGCTGATTCCACCGTATCATTGAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTTAAATGTG-AAGGGGTTGCTAAGTGCTGATTCCCC
12610776 GAATCACTGG
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
101 38 0.24
102 86 0.55
103 31 0.20
104 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (101 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCCCA
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:12610715 original size:33 final size:32
Alignment explanation
Indices: 12610651--12610742 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 32
12610641 ATGTGAAGGG
*
12610651 GGTTGCTAAGTGCTGATTCCCC---CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGTTCATTGGT
12610678 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCG-TTCATTGGT
12610711 GGTTGCTAAGTGCTGATTCCACCGTATCATTG
1 GGTTGCTAAGTGCTGATTCC-CCGT-TCATTG
12610743 AATGTGAAAG
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
27 22 0.39
31 2 0.04
32 2 0.04
33 21 0.38
34 9 0.16
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCGTTCATTGGT
Found at i:12613110 original size:8 final size:8
Alignment explanation
Indices: 12613097--12613121 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12613087 TTTTAAATAA
12613097 TATTTTAT
1 TATTTTAT
12613105 TATTTTAT
1 TATTTTAT
12613113 TATTTTAT
1 TATTTTAT
12613121 T
1 T
12613122 GTTTAGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:12622315 original size:14 final size:14
Alignment explanation
Indices: 12622292--12622334 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
12622282 TCAAGAGACC
12622292 ATTAATTAATTTAA
1 ATTAATTAATTTAA
*
12622306 ATTGATTAATTTAA
1 ATTAATTAATTTAA
*
12622320 TTTAATTTAATTTAA
1 ATTAA-TTAATTTAA
12622335 TTCGATTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
ATTAATTAATTTAA
Found at i:12622319 original size:5 final size:5
Alignment explanation
Indices: 12622293--12622336 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
12622283 CAAGAGACCA
* *
12622293 TTAA- TTAAT TTAAA TTGA- TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
12622337 CGATTTAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
4 7 0.20
5 28 0.80
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TTAAT
Found at i:12622342 original size:15 final size:14
Alignment explanation
Indices: 12622297--12622343 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
12622287 AGACCATTAA
12622297 TTAATTTAAATTGA-
1 TTAATTT-AATTGAT
*
12622311 TTAATTTAATTTAAT
1 TTAATTTAA-TTGAT
12622326 TTAATTTAATTCGAT
1 TTAATTTAATT-GAT
12622341 TTA
1 TTA
12622344 GTTGGTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 12 0.43
15 14 0.50
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (14 bp):
TTAATTTAATTGAT
Found at i:12625931 original size:237 final size:237
Alignment explanation
Indices: 12625512--12625979 Score: 785
Period size: 237 Copynumber: 2.0 Consensus size: 237
12625502 CTCACCCTGT
* *
12625512 TTTTTCCAGTCTAATTGATAAATCTATTCCAATTGATCTCTCAATGAGTCTTCTGAAACTTTTTC
1 TTTTTCCAGTCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCTTC
** *
12625577 CTTTGTTATTTTCCCCAAATCGAAAATGTAAGAATCACCATCACTTGAAAGTGCCTCACTCTTTT
66 CTTTGTTATTTTCCCCAAATAAAAAATGTAAGAATCACCATCACTTGAAACTGCCTCACTCTTTT
*
12625642 TTGGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCGTTAGCTCAGTCACCACTTT
131 TTGGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCATTAGCTCAGTCACCACTTT
12625707 TGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTTACTTAG
196 TGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTTACTTAG
12625749 TTTTTCCAGTCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCTTC
1 TTTTTCCAGTCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCTTC
* * *
12625814 CTTTGTTA-TTTCGTCCAAATAAAAAATGTAAGAATCACCATCGCTTGAAACTTCCTCACTCTTT
66 CTTTGTTATTTTC-CCCAAATAAAAAATGTAAGAATCACCATCACTTGAAACTGCCTCACTCTTT
* * * *
12625878 TTTTGAATTATCCTCATCATCTATTGATTCTTGTTTAGTGACATTCATTAGCTCAGTCACCACTT
130 TTTGGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCATTAGCTCAGTCACCACTT
* *
12625943 TTGGTTCTCTAATCAGTCCTTAAGCGTGATCGTTGTT
195 TTGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTT
12625980 GCTTGCTTTT
Statistics
Matches: 215, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
236 4 0.02
237 211 0.98
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.41
Consensus pattern (237 bp):
TTTTTCCAGTCTAATTGATAAATCTATTACAATTGATCTCTCAATGAGTCTTCTGAAACTTCTTC
CTTTGTTATTTTCCCCAAATAAAAAATGTAAGAATCACCATCACTTGAAACTGCCTCACTCTTTT
TTGGAATTATCCTCATCAACCATTGATTCTTGTTTAGTAACATTCATTAGCTCAGTCACCACTTT
TGGTTCTCTAATCAATCCTCAAGCGTGATCGTTGTTACTTAG
Found at i:12629912 original size:19 final size:17
Alignment explanation
Indices: 12629888--12629931 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
12629878 AAAAACATAA
12629888 AAGGAAATTAAACAAACT
1 AAGGAAATTAAACAAA-T
* *
12629906 AATGGAAAGTAATCAAAT
1 AA-GGAAATTAAACAAAT
12629924 AAGGAAAT
1 AAGGAAAT
12629932 ACATATATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 5 0.23
18 5 0.23
19 12 0.55
ACGTcount: A:0.59, C:0.07, G:0.16, T:0.18
Consensus pattern (17 bp):
AAGGAAATTAAACAAAT
Found at i:12632375 original size:20 final size:20
Alignment explanation
Indices: 12632350--12632392 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12632340 TTATTACATC
12632350 TTTTAAATATGACTTAAAAG
1 TTTTAAATATGACTTAAAAG
* * *
12632370 TTTTAATTGTGTCTTAAAAG
1 TTTTAAATATGACTTAAAAG
12632390 TTT
1 TTT
12632393 GCTTGAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (20 bp):
TTTTAAATATGACTTAAAAG
Found at i:12634549 original size:12 final size:12
Alignment explanation
Indices: 12634534--12634591 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
12634524 AAATGATATA
12634534 GAAAAAGAGTGT
1 GAAAAAGAGTGT
*
12634546 GAAAAAGAATGT
1 GAAAAAGAGTGT
**
12634558 GAAAGGGAGTGT
1 GAAAAAGAGTGT
*
12634570 GAAAAAAAGTGT
1 GAAAAAGAGTGT
12634582 GAAACAAGAG
1 GAAA-AAGAG
12634592 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
12 33 0.89
13 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.33, T:0.14
Consensus pattern (12 bp):
GAAAAAGAGTGT
Found at i:12636911 original size:32 final size:32
Alignment explanation
Indices: 12636865--12636935 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
12636855 CATCACAAGA
12636865 GACCATTGATGGAGGTCGT-TGGTATTATCTAGG
1 GACC-TTGATGGAGGTCGTAT-GTATTATCTAGG
* * *
12636898 GACCTTGATGGAGGTTGTATGTCTTATTTAGG
1 GACCTTGATGGAGGTCGTATGTATTATCTAGG
12636930 GACCTT
1 GACCTT
12636936 CTCCCACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.37
Consensus pattern (32 bp):
GACCTTGATGGAGGTCGTATGTATTATCTAGG
Found at i:12638757 original size:56 final size:57
Alignment explanation
Indices: 12638669--12638807 Score: 198
Period size: 56 Copynumber: 2.5 Consensus size: 57
12638659 TTCAAGTCAG
* * *
12638669 TTTCATTT-TC-ATTTTCA-TTTCATTTTGGAGAAAACCATAATCATTTCCA-ATGT
1 TTTCATTTCTCTATTTTCATTTTCATTTTGGAGAAAAACATAACCATTTCCATATGA
12638722 TTTCATTTCTCTATTTTCATTTTCATTTTGGAGAAAAACATAACCATTTCCATATGA
1 TTTCATTTCTCTATTTTCATTTTCATTTTGGAGAAAAACATAACCATTTCCATATGA
*
12638779 TTTCGTTTCT-TCATTTTCATTTTCATTTT
1 TTTCATTTCTCT-ATTTTCATTTTCATTTT
12638808 CATTTTCATT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
53 8 0.10
54 2 0.03
55 7 0.09
56 31 0.40
57 29 0.38
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.51
Consensus pattern (57 bp):
TTTCATTTCTCTATTTTCATTTTCATTTTGGAGAAAAACATAACCATTTCCATATGA
Found at i:12638799 original size:6 final size:6
Alignment explanation
Indices: 12638788--12638819 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
12638778 ATTTCGTTTC
12638788 TTCATT TTCATT TTCATT TTCATT TTCATT TT
1 TTCATT TTCATT TTCATT TTCATT TTCATT TT
12638820 GGAGAAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCATT
Found at i:12647144 original size:60 final size:54
Alignment explanation
Indices: 12647072--12647219 Score: 190
Period size: 54 Copynumber: 2.6 Consensus size: 54
12647062 CATCTTCAGA
* * *
12647072 TGAAGTGTTTTCTTCATCAGAATTATGACTAGTGACTTTTATATCTTCATCCTGATCTGT
1 TGAAGTTTTTTCTTCATCAGAATTATAACTAGTAAC-TTT-TA---T-ATCCTGATCTGT
12647132 TGAAGTTTTTTCTTCATCAG-ATTGATAACTAGTAACTTTTATATCCTGATCTGT
1 TGAAGTTTTTTCTTCATCAGAATT-ATAACTAGTAACTTTTATATCCTGATCTGT
*
12647186 TGAAGTTTTTTCTTCATCAGATTTATAACTAGTA
1 TGAAGTTTTTTCTTCATCAGAATTATAACTAGTA
12647220 GCTTATAAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 10
0.85 0.04 0.10
Matches are distributed among these distances:
54 42 0.51
55 3 0.04
58 2 0.02
59 6 0.07
60 29 0.35
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (54 bp):
TGAAGTTTTTTCTTCATCAGAATTATAACTAGTAACTTTTATATCCTGATCTGT
Found at i:12647459 original size:18 final size:19
Alignment explanation
Indices: 12647436--12647483 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
12647426 GGACTGGAAA
12647436 TCATATTTTTGTT-GTTTT
1 TCATATTTTTGTTCGTTTT
*
12647454 TCATATTTTTTTTCGTTTT
1 TCATATTTTTGTTCGTTTT
*
12647473 TTATGATTTTT
1 TCAT-ATTTTT
12647484 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
19 8 0.31
20 6 0.23
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.73
Consensus pattern (19 bp):
TCATATTTTTGTTCGTTTT
Found at i:12647704 original size:18 final size:19
Alignment explanation
Indices: 12647681--12647717 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12647671 CTATTTAAAT
12647681 CTAAATT-TTTAATTTCTC
1 CTAAATTATTTAATTTCTC
*
12647699 CTAAATTATTTATTTTCTC
1 CTAAATTATTTAATTTCTC
12647718 TTCTGCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (19 bp):
CTAAATTATTTAATTTCTC
Found at i:12649363 original size:32 final size:32
Alignment explanation
Indices: 12649326--12649389 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
12649316 TTTTACAAGA
12649326 TTGAAAGATTCTTTTAATAAAGTATTTTAGAC
1 TTGAAAGATTCTTTTAATAAAGTATTTTAGAC
12649358 TTGAAAGATTCTTTTAATAAAGTATTTTAGAC
1 TTGAAAGATTCTTTTAATAAAGTATTTTAGAC
12649390 CTTATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (32 bp):
TTGAAAGATTCTTTTAATAAAGTATTTTAGAC
Found at i:12649965 original size:24 final size:24
Alignment explanation
Indices: 12649938--12649984 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12649928 ATAGATATAG
12649938 ATTAAAGAAAATCTATATTTTAAA
1 ATTAAAGAAAATCTATATTTTAAA
* * *
12649962 ATTATAGTAATTCTATATTTTAA
1 ATTAAAGAAAATCTATATTTTAA
12649985 TATACTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTAAAGAAAATCTATATTTTAAA
Found at i:12652566 original size:23 final size:23
Alignment explanation
Indices: 12652521--12652572 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
12652511 TTATTTTTAA
* *
12652521 ATTTTGAATTATTTACAGGTAAT
1 ATTTAGAATTATTTACAGATAAT
**
12652544 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTACAGATAAT
12652567 ATTTAG
1 ATTTAG
12652573 TGATAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (23 bp):
ATTTAGAATTATTTACAGATAAT
Found at i:12652571 original size:13 final size:13
Alignment explanation
Indices: 12652553--12652608 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
12652543 TATTTAGAAT
12652553 TATTTAGTGATAA
1 TATTTAGTGATAA
12652566 TATTTAGTGATAA
1 TATTTAGTGATAA
12652579 TATTTAG-GAT--
1 TATTTAGTGATAA
*
12652589 TCTTTAGTGATAA
1 TATTTAGTGATAA
12652602 TATTTAG
1 TATTTAG
12652609 AAAAAATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 6 0.16
11 3 0.08
12 3 0.08
13 26 0.68
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:12652580 original size:36 final size:36
Alignment explanation
Indices: 12652540--12652608 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
12652530 TATTTACAGG
12652540 TAATATTTAGAATTATTTAGTGATAATATTTAGTGA
1 TAATATTTAGAATTATTTAGTGATAATATTTAGTGA
* *
12652576 TAATATTTAGGATTCTTTAGTGATAATATTTAG
1 TAATATTTAGAATTATTTAGTGATAATATTTAG
12652609 AAAAAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.48
Consensus pattern (36 bp):
TAATATTTAGAATTATTTAGTGATAATATTTAGTGA
Found at i:12653341 original size:69 final size:69
Alignment explanation
Indices: 12653261--12653398 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
12653251 GTACCACGTG
12653261 GTTGGAAATTCGACAAGGGTTGATTTGCAAGTGATACTAGGATCAACTACAAGAGGAAGAGTTGG
1 GTTGGAAATTCGACAAGGGTTGATTTGCAAGTGATACTAGGATCAACTACAAGAGGAAGAGTTGG
12653326 CGGT
66 CGGT
12653330 GTTGGAAATTCGACAAGGGTTGATTTGCAAGTGATACTAGGATCAACTACAAGAGGAAGAGTTGG
1 GTTGGAAATTCGACAAGGGTTGATTTGCAAGTGATACTAGGATCAACTACAAGAGGAAGAGTTGG
12653395 CGGT
66 CGGT
12653399 TTGAAGGATC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.25
Consensus pattern (69 bp):
GTTGGAAATTCGACAAGGGTTGATTTGCAAGTGATACTAGGATCAACTACAAGAGGAAGAGTTGG
CGGT
Found at i:12660750 original size:13 final size:13
Alignment explanation
Indices: 12660734--12660778 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
12660724 TAAATTTTGA
12660734 AATATTTAGTGAT
1 AATATTTAGTGAT
12660747 AATATTTAG-GAT
1 AATATTTAGTGAT
12660759 --TATTTAGTGAT
1 AATATTTAGTGAT
12660770 AATATTTAG
1 AATATTTAG
12660779 GAAAAATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.24
11 3 0.10
12 3 0.10
13 16 0.55
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (13 bp):
AATATTTAGTGAT
Found at i:12660753 original size:23 final size:23
Alignment explanation
Indices: 12660727--12660778 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
12660717 TTATTTTTAA
*
12660727 ATTTTGAAATATTTAGTGATAAT
1 ATTTAGAAATATTTAGTGATAAT
* *
12660750 ATTTAGGATTATTTAGTGATAAT
1 ATTTAGAAATATTTAGTGATAAT
12660773 ATTTAG
1 ATTTAG
12660779 GAAAAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (23 bp):
ATTTAGAAATATTTAGTGATAAT
Found at i:12660779 original size:23 final size:23
Alignment explanation
Indices: 12660736--12660780 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
12660726 AATTTTGAAA
12660736 TATTTAGTGATAATATTTAGGAT
1 TATTTAGTGATAATATTTAGGAT
12660759 TATTTAGTGATAATATTTAGGA
1 TATTTAGTGATAATATTTAGGA
12660781 AAAATCTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (23 bp):
TATTTAGTGATAATATTTAGGAT
Found at i:12662186 original size:6 final size:6
Alignment explanation
Indices: 12662177--12662204 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12662167 ATAAAAAGTT
12662177 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
12662205 ATAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:12669107 original size:22 final size:22
Alignment explanation
Indices: 12669037--12669107 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
12669027 AAATTCAATA
*
12669037 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
12669059 TC-AATTCCGTTCAAAAATTCTC
1 TCAAATTCC-TTCAAAAATTCTC
* *
12669081 TCAAATTCCTTCCAAAATTCCC
1 TCAAATTCCTTCAAAAATTCTC
12669103 TCAAA
1 TCAAA
12669108 CTCTCAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 5 0.11
22 33 0.75
23 6 0.14
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.35
Consensus pattern (22 bp):
TCAAATTCCTTCAAAAATTCTC
Found at i:12669113 original size:30 final size:30
Alignment explanation
Indices: 12669078--12669136 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
12669068 TTCAAAAATT
12669078 CTCTCAAATTCCTTCCAAAATTCC-CTCAAA
1 CTCTCAAATTCCTTCCAAAA-TCCTCTCAAA
12669108 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
12669137 TTTCCTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.32, C:0.37, G:0.00, T:0.31
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:12669147 original size:21 final size:22
Alignment explanation
Indices: 12669108--12669149 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12669098 TTCCCTCAAA
12669108 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
12669130 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
12669150 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:12669376 original size:14 final size:15
Alignment explanation
Indices: 12669347--12669380 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12669337 AAAATTTAAA
12669347 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
12669362 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
12669376 TTTTA
1 TTTTA
12669381 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:12671802 original size:124 final size:123
Alignment explanation
Indices: 12671583--12671847 Score: 379
Period size: 124 Copynumber: 2.1 Consensus size: 123
12671573 CCACTATGGC
* * *
12671583 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAATTATTTCCTACATGACTAATTGTAGCGA
1 GCGATTTGACACTATTTGCTAAGAAACGTCAAAAAAAGTATTTCCTACATGACTAACTGTAGCGA
* * * **
12671648 AATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * * *
12671706 GCGATTTTATACTATTTGCTAAGAAAACGTCAAAAAAAAGTATTTCTTACATGAC-CACTGTAGC
1 GCGATTTGACACTATTTGCTAAG-AAACGTC-AAAAAAAGTATTTCCTACATGACTAACTGTAGC
12671770 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
64 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
**
12671830 GCGATTTCCCACTATTTG
1 GCGATTTGACACTATTTG
12671848 ACCAGATACG
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
123 20 0.16
124 84 0.67
125 21 0.17
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (123 bp):
GCGATTTGACACTATTTGCTAAGAAACGTCAAAAAAAGTATTTCCTACATGACTAACTGTAGCGA
AATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:12674836 original size:20 final size:20
Alignment explanation
Indices: 12674790--12674850 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
12674780 CTATAAATCT
12674790 ATGATATGATATGATAT-GA
1 ATGATATGATATGATATAGA
12674809 TATGATATGATATGATATAGA
1 -ATGATATGATATGATATAGA
* * *
12674830 ATTATATAATATAATATAGA
1 ATGATATGATATGATATAGA
12674850 A
1 A
12674851 GGGCTAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 35 0.95
21 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGATATGATATGATATAGA
Found at i:12674846 original size:5 final size:5
Alignment explanation
Indices: 12674789--12674826 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
12674779 ACTATAAATC
12674789 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TAT
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TAT
12674827 AGAATTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (5 bp):
TATGA
Done.