Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 27 of 32
Found at i:13204125 original size:50 final size:52
Alignment explanation
Indices: 13204014--13204145 Score: 128
Period size: 50 Copynumber: 2.6 Consensus size: 52
13204004 CAATAACCCT
* * **
13204014 TACATAATTCACAAAAAGGATTGTTGTTTTTTCATGGGATCAAGTGATAACC
1 TACATAATCCACAAAAAGGATTCTTGCCTTTTCATGGGATCAAGTGATAACC
** * * * *
13204066 TTTACAATCCACAAAAA-GATTCTTGCCTTTT-ATGGGATTAAGTGGTAATC
1 TACATAATCCACAAAAAGGATTCTTGCCTTTTCATGGGATCAAGTGATAACC
* *
13204116 TACATAATCCAC--AAGGGATTCTTGCGTTTT
1 TACATAATCCACAAAAAGGATTCTTGCCTTTT
13204146 GATAGGAAGC
Statistics
Matches: 64, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
48 2 0.03
49 13 0.20
50 25 0.39
51 11 0.17
52 13 0.20
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (52 bp):
TACATAATCCACAAAAAGGATTCTTGCCTTTTCATGGGATCAAGTGATAACC
Found at i:13204366 original size:27 final size:27
Alignment explanation
Indices: 13204336--13204388 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
13204326 TGATGAAAGG
13204336 TTAAAAATATGCTAGAGAGTGAAGATA
1 TTAAAAATATGCTAGAGAGTGAAGATA
13204363 TTAAAAATATGCTAGAGAGTGAAGAT
1 TTAAAAATATGCTAGAGAGTGAAGAT
13204389 GAGCTTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.04, G:0.23, T:0.26
Consensus pattern (27 bp):
TTAAAAATATGCTAGAGAGTGAAGATA
Found at i:13205315 original size:24 final size:24
Alignment explanation
Indices: 13205288--13205335 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
13205278 AAGGTCTTAT
*
13205288 ATTACAAGCAGAAATTGCATTCAA
1 ATTACAAGCAAAAATTGCATTCAA
*
13205312 ATTATAAGCAAAAATTGCATTCAA
1 ATTACAAGCAAAAATTGCATTCAA
13205336 CTACAATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (24 bp):
ATTACAAGCAAAAATTGCATTCAA
Found at i:13206534 original size:59 final size:59
Alignment explanation
Indices: 13206471--13206585 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
13206461 TAATTAAGAC
* * * * * * *
13206471 AAAAATATTTTATTTTGTAT-AAATTGAGACAAATATGTTTTCTTGTCCAGATTAAGGTA
1 AAAAATATTTT-TCTTGTATAAAATTAAAACAAACATATTTTCTTATCCAAATTAAGGTA
*
13206530 AAAAATATTTTTCTTGTTTAAAATTAAAACAAACATATTTTCTTATCCAAATTAAG
1 AAAAATATTTTTCTTGTATAAAATTAAAACAAACATATTTTCTTATCCAAATTAAG
13206586 ACCAAACATG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
58 6 0.13
59 41 0.87
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (59 bp):
AAAAATATTTTTCTTGTATAAAATTAAAACAAACATATTTTCTTATCCAAATTAAGGTA
Found at i:13206584 original size:28 final size:28
Alignment explanation
Indices: 13206550--13206622 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
13206540 TTCTTGTTTA
* *
13206550 AAATTAAAACAAACATATTTTCTTATCC-
1 AAATTAAAACAAACATATTTTATT-GCCT
* *
13206578 AAATTAAGACCAAACATGTTTTATTGCCT
1 AAATTAA-AACAAACATATTTTATTGCCT
*
13206607 AAATTAATACAAACAT
1 AAATTAAAACAAACAT
13206623 GTTAAAGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 16 0.43
29 21 0.57
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (28 bp):
AAATTAAAACAAACATATTTTATTGCCT
Found at i:13206633 original size:29 final size:29
Alignment explanation
Indices: 13206578--13206634 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
13206568 TTTCTTATCC
**
13206578 AAATTAAGACCAAACATGTTTTATTGCCT
1 AAATTAAGACCAAACATGTTAAATTGCCT
*
13206607 AAATTAATA-CAAACATGTTAAAGTTGCC
1 AAATTAAGACCAAACATGTTAAA-TTGCC
13206635 ATTTTTGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (29 bp):
AAATTAAGACCAAACATGTTAAATTGCCT
Found at i:13210773 original size:2 final size:2
Alignment explanation
Indices: 13210768--13210803 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
13210758 ATAACACACA
* *
13210768 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13210804 CATGGAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13212809 original size:32 final size:30
Alignment explanation
Indices: 13212773--13212831 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
13212763 TATTGATAAA
13212773 AAAAACAAGGAGCATTTTAAAAAATAACCCTT
1 AAAAACAAGGAG--TTTTAAAAAATAACCCTT
* * *
13212805 AAAAATAAGGTGTTTTCAAAAATAACC
1 AAAAACAAGGAGTTTTAAAAAATAACC
13212832 TCCTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
32 10 0.42
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.24
Consensus pattern (30 bp):
AAAAACAAGGAGTTTTAAAAAATAACCCTT
Found at i:13212984 original size:45 final size:45
Alignment explanation
Indices: 13212901--13213049 Score: 199
Period size: 45 Copynumber: 3.3 Consensus size: 45
13212891 CACGCTATGA
* * * ** *
13212901 TGTTACACACCATGTACAGAAACATGTTACACATCATGGTTAGAT
1 TGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGT
* *
13212946 TGTTACACGCCATATACAAAAATATGTGACACGCCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGT
* *
13212991 TGTTACACGTCATGTACAAAAACATGTGACACGCCATTGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGT
*
13213036 TGTTACACGTCATG
1 TGTTACACGCCATG
13213050 GTTAACTTGT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGT
Found at i:13213044 original size:21 final size:21
Alignment explanation
Indices: 13213019--13213136 Score: 103
Period size: 21 Copynumber: 5.5 Consensus size: 21
13213009 AAAACATGTG
*
13213019 ACACGCCATTGTTAGGTTGTT
1 ACACGCCATGGTTAGGTTGTT
* **
13213040 ACACGTCATGGTTAACTTGTT
1 ACACGCCATGGTTAGGTTGTT
* **
13213061 ACACGCCAT-GTACAAAAATATGTT
1 ACACGCCATGGT---TAGGT-TGTT
*
13213085 ACACGTCATGGTTAGGTTGTT
1 ACACGCCATGGTTAGGTTGTT
*
13213106 ACACGTCATGGTTAGGTTGTT
1 ACACGCCATGGTTAGGTTGTT
*
13213127 ACATGCCATG
1 ACACGCCATG
13213137 TTAAAAAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.03
21 58 0.73
22 2 0.03
23 3 0.04
24 12 0.15
25 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (21 bp):
ACACGCCATGGTTAGGTTGTT
Found at i:13213144 original size:66 final size:66
Alignment explanation
Indices: 13212974--13213137 Score: 247
Period size: 66 Copynumber: 2.5 Consensus size: 66
13212964 AAAATATGTG
* * *
13212974 ACACGCCATGGTTAGGTTGTTACACGTCATGTACAAAAACATGTGACACGCCATTGTTAGGTTGT
1 ACACGTCATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGTTGT
13213039 T
66 T
** * * *
13213040 ACACGTCATGGTTAACTTGTTACACGCCATGTACAAAAATATGTTACACGTCATGGTTAGGTTGT
1 ACACGTCATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGTTGT
13213105 T
66 T
*
13213106 ACACGTCATGGTTAGGTTGTTACATGCCATGT
1 ACACGTCATGGTTAGGTTGTTACACGCCATGT
13213138 TAAAAAAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 87 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (66 bp):
ACACGTCATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACACGCCATGGTTAGGTTGT
T
Found at i:13213197 original size:24 final size:24
Alignment explanation
Indices: 13213153--13213223 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
13213143 AAAATACTGT
* *
13213153 TGTTACACGCTATG-TACAAAAACA
1 TGTTACACGCCATGTTA-AAAATCA
**
13213177 TGTTACACGCCATAGTTAAAAATGT
1 TGTTACACGCCAT-GTTAAAAATCA
13213202 TGTTACACGCCATGTTGAAAAA
1 TGTTACACGCCATGTT-AAAAA
13213224 AAAAACAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 15 0.38
25 23 0.57
26 2 0.05
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (24 bp):
TGTTACACGCCATGTTAAAAATCA
Found at i:13223552 original size:16 final size:18
Alignment explanation
Indices: 13223525--13223559 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13223515 TCACAAATAA
13223525 AGTTTTTAAGG-AAAGCC
1 AGTTTTTAAGGAAAAGCC
13223542 AGTTTTT-AGGAAAAGCC
1 AGTTTTTAAGGAAAAGCC
13223559 A
1 A
13223560 CCTTACTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (18 bp):
AGTTTTTAAGGAAAAGCC
Found at i:13237969 original size:31 final size:30
Alignment explanation
Indices: 13237898--13238001 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 30
13237888 GACCCGACTT
*** *
13237898 GATTCCCCCCGGCTCCCCCTCCCACTCCTACC
1 GATTCCCCCCGG--CCCCCTCCCACGAGTCCC
13237930 GATT-CCCCCGGCCCCCTTCCCACGAGTCCC
1 GATTCCCCCCGGCCCCC-TCCCACGAGTCCC
* *
13237960 GATTCCCCCCTGCCCCCCCGCCACGAGTCCGC
1 GATTCCCCCCGGCCCCCTC-CCACGAGTCC-C
13237992 GATTCCCCCC
1 GATTCCCCCC
13238002 TGCCGGCCTG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
29 5 0.08
30 14 0.23
31 28 0.45
32 15 0.24
ACGTcount: A:0.10, C:0.60, G:0.14, T:0.16
Consensus pattern (30 bp):
GATTCCCCCCGGCCCCCTCCCACGAGTCCC
Found at i:13238138 original size:10 final size:10
Alignment explanation
Indices: 13238123--13238150 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
13238113 TTATCATAAA
13238123 AAACCGACCG
1 AAACCGACCG
13238133 AAACCGACCG
1 AAACCGACCG
13238143 AAACCGAC
1 AAACCGAC
13238151 TTTATACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.39, G:0.18, T:0.00
Consensus pattern (10 bp):
AAACCGACCG
Found at i:13247801 original size:3 final size:3
Alignment explanation
Indices: 13247793--13247823 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
13247783 TATGTCGTAC
*
13247793 AGA AGA AGA AGA AGG AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
13247824 CAGGGGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:13254867 original size:18 final size:18
Alignment explanation
Indices: 13254841--13254885 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
13254831 GCTTGTTGAG
*
13254841 TTATTCAAGGCCAAACTT
1 TTATACAAGGCCAAACTT
13254859 TTATACAAGGCCAAACTT
1 TTATACAAGGCCAAACTT
13254877 TTATACAAG
1 TTATACAAG
13254886 TACGTTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (18 bp):
TTATACAAGGCCAAACTT
Found at i:13262675 original size:46 final size:45
Alignment explanation
Indices: 13262577--13262676 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 45
13262567 TGTCGTTGAT
* * *
13262577 GAAATCATCGATAGAAACAATTGGAATGATTAATAACTATACTGA
1 GAAATCACCGATAGAAACAATTGGAATGATTAATAACTACACTAA
* * * * *
13262622 TATAATCACCGATGGAGACGATTGGAATGATTAATAAGTACACTAA
1 GA-AATCACCGATAGAAACAATTGGAATGATTAATAACTACACTAA
13262668 CGAAATCAC
1 -GAAATCAC
13262677 TGACAAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
45 1 0.02
46 42 0.95
47 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (45 bp):
GAAATCACCGATAGAAACAATTGGAATGATTAATAACTACACTAA
Found at i:13263059 original size:3 final size:3
Alignment explanation
Indices: 13263051--13263080 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
13263041 TTTCATACAA
*
13263051 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13263081 TGTGGGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13264067 original size:20 final size:19
Alignment explanation
Indices: 13264024--13264078 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
13264014 ATGAGAACAT
* *
13264024 TTAGATTAATTTAAAATTTG
1 TTAGATTAA-TTAAAGTTTA
13264044 TTAGATTAATTAAAGTTGTA
1 TTAGATTAATTAAAGTT-TA
**
13264064 TTAGGCTAATTAAAG
1 TTAGATTAATTAAAG
13264079 AATTTAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.44
Consensus pattern (19 bp):
TTAGATTAATTAAAGTTTA
Found at i:13264192 original size:17 final size:17
Alignment explanation
Indices: 13264142--13264192 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
13264132 TACTTAAAGA
**
13264142 ATTTAAATTAATTATTT
1 ATTTAAATTAATTAAAT
*
13264159 ATTTAGCAATGAATTAAAT
1 ATTTA--AATTAATTAAAT
13264178 ATTTAAATTAATTAA
1 ATTTAAATTAATTAA
13264193 GGGTTTAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.50
19 14 0.50
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
ATTTAAATTAATTAAAT
Found at i:13264472 original size:68 final size:67
Alignment explanation
Indices: 13264394--13264520 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 67
13264384 TAGTAATTAA
* * * *
13264394 TCAATAAATTAAATTATTAAATTTTAGA-AAAAATTAAAATTATTTAACTTAATTAAGGTTTAGG
1 TCAATAAATTAAATGAGTAAA-TTTA-ATAAAAATTAAAATTAGTTAAATTAATTAAGGTTTAGG
13264458 GTAC
64 GTAC
* * *
13264462 TCAATTAATTAAATGAGTAAATTTAATAAAATTTAAAATTAGTTAAATTATTTAAGGTT
1 TCAATAAATTAAATGAGTAAATTTAATAAAAATTAAAATTAGTTAAATTAATTAAGGTT
13264521 GCTTTAGGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 1 0.02
67 32 0.63
68 18 0.35
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (67 bp):
TCAATAAATTAAATGAGTAAATTTAATAAAAATTAAAATTAGTTAAATTAATTAAGGTTTAGGGT
AC
Found at i:13272783 original size:224 final size:224
Alignment explanation
Indices: 13272384--13272823 Score: 643
Period size: 224 Copynumber: 2.0 Consensus size: 224
13272374 AAAGTTCTAG
* * *
13272384 ACTTTGAGAATGACATAACGAACCGATAACTCAGGGATAAAGAATCGATTCTCCGAGTACGACAA
1 ACTTTGAGAATGACATAACGAACCGATAACTCAAGGACAAAGAATCGATTCTCCAAGTACGACAA
* * *
13272449 ACCAGATCAAGCTAGCTAGAAAATACAAAAATTCATTTCAAACTTACCCCAACGGGCAAGAAATC
66 ACCAGATCAAGCTAGCCAGAAAATACAAAAATTCATTTCAAACTTACCCCAACAGGCAAGAAATA
*
13272514 ATAAAGCTTATAAATACCCATCTTGGAAAGCAAAAATGAAAGTTTTTGAAGAATTTGAAGATTTG
131 ATAAAGCTTATAAATACCCATATTGGAAAGCAAAAATGAAAGTTTTTGAAGAATTTGAAGATTTG
* *
13272579 AAAAAGAGAGAAGAACAAGAAGTCGAAGA
196 AAAAAGAAAGAAGAAAAAGAAGTCGAAGA
* *
13272608 ACTTTGAGAATGACATGAA-TAACCGATAACTCAAGGACAAAGAATCGATTCTCCAAGTATGACA
1 ACTTTGAGAATGACAT-AACGAACCGATAACTCAAGGACAAAGAATCGATTCTCCAAGTACGACA
* ** * *
13272672 GACTTGATCAAGCTAGCCA-AAATATA-AGAAAATTCATTTCAAACTTACTCCAATAGGCAAGAA
65 AACCAGATCAAGCTAGCCAGAAA-ATACA-AAAATTCATTTCAAACTTACCCCAACAGGCAAGAA
* * * * *
13272735 ATAATAGAGCTTATAAGTACCCATATTGGAGAGCCAAAATGTAAGTTTTTGAAGAATTTGAAGAT
128 ATAATAAAGCTTATAAATACCCATATTGGAAAGCAAAAATGAAAGTTTTTGAAGAATTTGAAGAT
13272800 TTGAAAAAGAAAGAAGAAAAAGAA
193 TTGAAAAAGAAAGAAGAAAAAGAA
13272824 AAAGAATAAG
Statistics
Matches: 192, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
223 4 0.02
224 186 0.97
225 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.22
Consensus pattern (224 bp):
ACTTTGAGAATGACATAACGAACCGATAACTCAAGGACAAAGAATCGATTCTCCAAGTACGACAA
ACCAGATCAAGCTAGCCAGAAAATACAAAAATTCATTTCAAACTTACCCCAACAGGCAAGAAATA
ATAAAGCTTATAAATACCCATATTGGAAAGCAAAAATGAAAGTTTTTGAAGAATTTGAAGATTTG
AAAAAGAAAGAAGAAAAAGAAGTCGAAGA
Found at i:13272822 original size:6 final size:6
Alignment explanation
Indices: 13272802--13272835 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
13272792 TTGAAGATTT
*
13272802 GAAAAA GAAAGAA GAAAAA GAAAAA GAATAA GAA
1 GAAAAA GAAA-AA GAAAAA GAAAAA GAAAAA GAA
13272836 GAAAAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:13275245 original size:25 final size:25
Alignment explanation
Indices: 13275216--13275263 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
13275206 ATATATAATT
13275216 AACTAACAATTAAAAACTATTCCGC
1 AACTAACAATTAAAAACTATTCCGC
*
13275241 AACTAACAATTGAAAACTATTCC
1 AACTAACAATTAAAAACTATTCC
13275264 ACAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (25 bp):
AACTAACAATTAAAAACTATTCCGC
Found at i:13275735 original size:86 final size:86
Alignment explanation
Indices: 13275634--13276228 Score: 837
Period size: 86 Copynumber: 7.0 Consensus size: 86
13275624 TGATATGTTA
* * * *
13275634 TTAAGTTTGCATCATAGTTCAAGAAATATAAATTAATTTTATATTTTTTAATTTACAAGTTCAAT
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACAAGTTCAAC
13275699 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * *
13275720 TTAAGTTTGCATCATATTTCAAGTAATATAAATTAATTTCACATTTGTTT-GCTTACAAGTTCAA
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTT-TTTAGTTTACAAGTTCAA
*
13275784 TTAATATAAAAATTTTATATAT
65 CTAATATAAAAATTTTATATAT
*
13275806 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTT-GCTTACAAGTTCAA
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTT-TTTAGTTTACAAGTTCAA
13275870 CTAATATAAAAATTTTATATAT
65 CTAATATAAAAATTTTATATAT
* * * * *
13275892 TTAAAGATTACACCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTAAA
1 TT-AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACAAGTTCAA
*
13275957 CTAACATAAAAATTTTATATAT
65 CTAATATAAAAATTTTATATAT
* * * *
13275979 TCATGTTTGCATCATTGTTCAAGTAATATAAATTAATTTTACATTTGTTT-GCTTACAAGTTCAA
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTT-TTTAGTTTACAAGTTCAA
*
13276043 CTAACATAAAAATTTTATATAT
65 CTAATATAAAAATTTTATATAT
* * * * *
13276065 TTAAGTTGGCATCATAGTTCAAGAAATATAAATTAATTTTACATTTGTTAGTTTAGAAATTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACAAGTTCAAC
13276130 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * * *
13276151 TTAAGTTTTCATCATA--T---GTAATATAAATTACTTTTACATTTGTTAGTTTACAAATTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACAAGTTCAAC
13276211 TAATATAAAAATTTTATA
66 TAATATAAAAATTTTATA
13276229 AGTAGTATAA
Statistics
Matches: 464, Mismatches: 40, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
81 58 0.12
84 1 0.00
85 2 0.00
86 323 0.70
87 80 0.17
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (86 bp):
TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACAAGTTCAAC
TAATATAAAAATTTTATATAT
Found at i:13276105 original size:259 final size:258
Alignment explanation
Indices: 13275646--13276228 Score: 899
Period size: 259 Copynumber: 2.3 Consensus size: 258
13275636 AAGTTTGCAT
* * * * *
13275646 CATAGTTCAAGAAATATAAATTAATTTTATATTTTTTAATTTACAAGTTCAATTAATATAAAAAT
1 CATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAAT
*
13275711 TTTATATATTTAAGTTTGCATCATATTTCAAGTAATATAAATTAATTTCACATTTGTTTGCTTAC
66 TTTATATATTCAAGTTTGCATCATATTTCAAGTAATATAAATTAATTTCACATTTGTTTGCTTAC
* * * *
13275776 AAGTTCAATTAATATAAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTA
131 AAGTTCAACTAACATAAAAATTTTATATATTTAAGTTGGCATCATAGTTCAAGAAATATAAATTA
* *
13275841 ATTTTACATTTGTTTGCTTACAAGTTCAACTAATATAAAAATTTTATATATTTAAAGATTACAC
196 ATTTTACATTTGTTAGCTTACAAATTCAACTAATATAAAAATTTTATATATTT-AAGATTACAC
* *
13275905 CATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTAAACTAACATAAAAAT
1 CATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAAT
* *
13275970 TTTATATATTCATGTTTGCATCAT-TGTTCAAGTAATATAAATTAATTTTACATTTGTTTGCTTA
66 TTTATATATTCAAGTTTGCATCATAT-TTCAAGTAATATAAATTAATTTCACATTTGTTTGCTTA
13276034 CAAGTTCAACTAACATAAAAATTTTATATATTTAAGTTGGCATCATAGTTCAAGAAATATAAATT
130 CAAGTTCAACTAACATAAAAATTTTATATATTTAAGTTGGCATCATAGTTCAAGAAATATAAATT
* * * * *
13276099 AATTTTACATTTGTTAGTTTAGAAATTCAACTAATATAAAAATTTTATATATTTAAGTTTTCAT
195 AATTTTACATTTGTTAGCTTACAAATTCAACTAATATAAAAATTTTATATATTTAAGATTACAC
* *
13276163 CATA--T---GTAATATAAATTACTTTTACATTTGTTAGTTTACAAATTCAACTAATATAAAAAT
1 CATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAAT
13276223 TTTATA
66 TTTATA
13276229 AGTAGTATAA
Statistics
Matches: 298, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
253 57 0.19
256 1 0.00
258 12 0.04
259 228 0.77
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (258 bp):
CATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAAT
TTTATATATTCAAGTTTGCATCATATTTCAAGTAATATAAATTAATTTCACATTTGTTTGCTTAC
AAGTTCAACTAACATAAAAATTTTATATATTTAAGTTGGCATCATAGTTCAAGAAATATAAATTA
ATTTTACATTTGTTAGCTTACAAATTCAACTAATATAAAAATTTTATATATTTAAGATTACAC
Found at i:13281459 original size:206 final size:206
Alignment explanation
Indices: 13281099--13281514 Score: 760
Period size: 206 Copynumber: 2.0 Consensus size: 206
13281089 TGATCATGCA
* *
13281099 AGTGAGGCAGTTTAGATACTCTCACTTATTGGAGAAGTAGACTTTAGCTATATTTTGATAAATTT
1 AGTGAAGCAGTTTAGATACTCTCACTTACTGGAGAAGTAGACTTTAGCTATATTTTGATAAATTT
* * * *
13281164 GAAGACCAGAATTTTTTAAAGGGTAAAGAATGTAGAACCTTAATTTTTACATAAAGGTAAATTGG
66 GAAGACCAGAAATTTTTAAAAGGCAAAGAATGTAGAACCTTAAGTTTTACATAAAGGTAAATTGG
13281229 TAATTTGACCCAAAGGCATAATAGTCATTTTCTTGGTGAGTATCATCTATCATCCATAATTTCAT
131 TAATTTGACCCAAAGGCATAATAGTCATTTTCTTGGTGAGTATCATCTATCATCCATAATTTCAT
13281294 TTATTAATTAT
196 TTATTAATTAT
13281305 AGTGAAGCAGTTTAGATACTCTCACTTACTGGAGAAGTAGACTTTAGCTATATTTTGATAAATTT
1 AGTGAAGCAGTTTAGATACTCTCACTTACTGGAGAAGTAGACTTTAGCTATATTTTGATAAATTT
*
13281370 GAAGACCAGAAATTTTTAAAAGGCAGAGAATGTAGAACCTTAAGTTTTACATAAAGGTAAATTGG
66 GAAGACCAGAAATTTTTAAAAGGCAAAGAATGTAGAACCTTAAGTTTTACATAAAGGTAAATTGG
*
13281435 TAATTTGACTCAAAGGCATAATAGTCATTTTCTTGGTGAGTATCATCTATCATCCATAATTTCAT
131 TAATTTGACCCAAAGGCATAATAGTCATTTTCTTGGTGAGTATCATCTATCATCCATAATTTCAT
13281500 TTATTAATTAT
196 TTATTAATTAT
13281511 AGTG
1 AGTG
13281515 GTTTCAATGT
Statistics
Matches: 202, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
206 202 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (206 bp):
AGTGAAGCAGTTTAGATACTCTCACTTACTGGAGAAGTAGACTTTAGCTATATTTTGATAAATTT
GAAGACCAGAAATTTTTAAAAGGCAAAGAATGTAGAACCTTAAGTTTTACATAAAGGTAAATTGG
TAATTTGACCCAAAGGCATAATAGTCATTTTCTTGGTGAGTATCATCTATCATCCATAATTTCAT
TTATTAATTAT
Found at i:13283069 original size:43 final size:43
Alignment explanation
Indices: 13283015--13283188 Score: 174
Period size: 42 Copynumber: 4.1 Consensus size: 43
13283005 GTGTATCAGT
* * *
13283015 ATTATGTAAATCTTACCCATGATGATAATGTGAATGGGTGTTG
1 ATTATGGAAATCTTACCCTTGATGATAATGTGAATGGGTATTG
* * * *
13283058 ATTATGGAAATCCTACCCTTGATGATAATGTGTATAGGTAATG
1 ATTATGGAAATCTTACCCTTGATGATAATGTGAATGGGTATTG
* * * *
13283101 ATTATGAAAATCTTA-CCTTGA-GCGTAAGGTGACTGGGTATTG
1 ATTATGGAAATCTTACCCTTGATG-ATAATGTGAATGGGTATTG
* * ** *
13283143 ATTGTGGGAATC-TACCCTAAATGATAATGTGAATGGGTATTA
1 ATTATGGAAATCTTACCCTTGATGATAATGTGAATGGGTATTG
13283185 ATTA
1 ATTA
13283189 CATAAATCTA
Statistics
Matches: 103, Mismatches: 25, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
41 3 0.03
42 50 0.49
43 50 0.49
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (43 bp):
ATTATGGAAATCTTACCCTTGATGATAATGTGAATGGGTATTG
Found at i:13283180 original size:42 final size:42
Alignment explanation
Indices: 13283036--13283217 Score: 141
Period size: 42 Copynumber: 4.3 Consensus size: 42
13283026 CTTACCCATG
* **
13283036 ATGATAATGTGAATGGGTGTTGATTATGGAAATCCTACCCTTG
1 ATGATAATGTGAATGGGTATTGATTATGGAAAT-CTACCCTAA
* * * * * *
13283079 ATGATAATGTGTATAGGTAATGATTATGAAAATCTTACCTTGA
1 ATGATAATGTGAATGGGTATTGATTATGGAAATC-TACCCTAA
** * * * *
13283122 GCG-TAAGGTGACTGGGTATTGATTGTGGGAATCTACCCTAA
1 ATGATAATGTGAATGGGTATTGATTATGGAAATCTACCCTAA
* *** *
13283163 ATGATAATGTGAATGGGTATTAATTACATAAATCTACCTTAA
1 ATGATAATGTGAATGGGTATTGATTATGGAAATCTACCCTAA
*
13283205 TATGATTATGTGA
1 -ATGATAATGTGA
13283218 TTATGCTTAA
Statistics
Matches: 104, Mismatches: 32, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
41 7 0.07
42 52 0.50
43 45 0.43
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (42 bp):
ATGATAATGTGAATGGGTATTGATTATGGAAATCTACCCTAA
Found at i:13283523 original size:14 final size:14
Alignment explanation
Indices: 13283506--13283535 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13283496 AGAGAGAAAT
13283506 ATCCCATCCATTGG
1 ATCCCATCCATTGG
13283520 ATCCCATCCATTGG
1 ATCCCATCCATTGG
13283534 AT
1 AT
13283536 TTGGAGTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.30
Consensus pattern (14 bp):
ATCCCATCCATTGG
Found at i:13296569 original size:32 final size:31
Alignment explanation
Indices: 13296494--13296613 Score: 102
Period size: 34 Copynumber: 3.8 Consensus size: 31
13296484 AATTATTTGG
* *
13296494 AGAAGGACTAAATTGAAAAGAAAAAAATGTTAGG
1 AGAAGGACTAAATTG-AAAGAAAAAAAT-ATA-T
*
13296528 AGAAAGACTAAATTGGAAAGAAAAAAATATAT
1 AGAAGGACTAAATT-GAAAGAAAAAAATATAT
* *
13296560 CGAAGGACTAAATTTAAA-AAAAATAA-ATAT
1 AGAAGGACTAAATTGAAAGAAAAA-AATATAT
* * *
13296590 TGGA-GACTAAATTGAAAGGAAAAA
1 AGAAGGACTAAATTGAAAGAAAAAA
13296614 TAAAGAAAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
29 13 0.18
30 15 0.21
31 5 0.07
32 12 0.16
33 2 0.03
34 25 0.34
35 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.18, T:0.19
Consensus pattern (31 bp):
AGAAGGACTAAATTGAAAGAAAAAAATATAT
Found at i:13302358 original size:18 final size:19
Alignment explanation
Indices: 13302326--13302365 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
13302316 AAACTATCAA
13302326 TATCAATATATTATGAAAT
1 TATCAATATATTATGAAAT
13302345 TATCAATA-ATTATGAAAT
1 TATCAATATATTATGAAAT
13302363 TAT
1 TAT
13302366 TAAATCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
TATCAATATATTATGAAAT
Found at i:13304567 original size:75 final size:75
Alignment explanation
Indices: 13304444--13304634 Score: 217
Period size: 75 Copynumber: 2.5 Consensus size: 75
13304434 TTACACTTTG
* * * *
13304444 TTACACACCATGTATAAAAACATGTTACACGCCAT-TATAAGATTGTTACATGTCATGTATAAAA
1 TTACACGCCATATATAAAAACATGTTACACACCATGT-TAAGATTGTTACATATCATGT-TAAAA
**
13304508 A-AATATTATTA
64 ATAATACGATTA
* * *
13304519 TTACACGTCATATATAAAAATATGTTACACTCCATGGTTAAG-TTGTTACATATCATGTTAAAAA
1 TTACACGCCATATATAAAAACATGTTACACACCAT-GTTAAGATTGTTACATATCATGTTAAAAA
* *
13304583 TAATACGGTTG
65 TAATACGATTA
*
13304594 TTACACGCCATATACAAAAACATGTTACACACCATAGTTAA
1 TTACACGCCATATATAAAAACATGTTACACACCAT-GTTAA
13304635 AAAAGTTTGT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
74 6 0.06
75 87 0.89
76 4 0.04
77 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.32
Consensus pattern (75 bp):
TTACACGCCATATATAAAAACATGTTACACACCATGTTAAGATTGTTACATATCATGTTAAAAAT
AATACGATTA
Found at i:13312444 original size:8 final size:8
Alignment explanation
Indices: 13312420--13312461 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
13312410 TAACTTAAGA
*
13312420 ATAAATTT
1 ATAAATAT
13312428 ATAAA-AT
1 ATAAATAT
13312435 ATAAATAT
1 ATAAATAT
*
13312443 ATATATAT
1 ATAAATAT
*
13312451 ATATATAT
1 ATAAATAT
13312459 ATA
1 ATA
13312462 CTTTTAGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 6 0.19
8 25 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATAAATAT
Found at i:13313421 original size:37 final size:36
Alignment explanation
Indices: 13313309--13313422 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 36
13313299 GTTTTCCGCC
* *
13313309 TTTTCTTTTAAACGTGTTAAGAT-AA--AACTAATT
1 TTTTCTTTTAAACATGATAAGATAAACTAACTAATT
* * **
13313342 ACTTTTCTTTTAAAACATGATAAGATTAACTGACTGGTTT
1 --TTTTCTTTT-AAACATGATAAGATAAACTAACT-AATT
*
13313382 TTTTCTTTTAAACATGCTAAGATAAACCTAACTAATT
1 TTTTCTTTTAAACATGATAAGATAAA-CTAACTAATT
13313419 TTTT
1 TTTT
13313423 TTAAAAAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
35 9 0.14
36 12 0.19
37 23 0.37
38 14 0.22
39 3 0.05
40 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (36 bp):
TTTTCTTTTAAACATGATAAGATAAACTAACTAATT
Found at i:13318294 original size:35 final size:35
Alignment explanation
Indices: 13318224--13318316 Score: 105
Period size: 35 Copynumber: 2.7 Consensus size: 35
13318214 CGTGCGATAC
* * * * *
13318224 AACACCCCATATCTAGCCCTTATTATGTGTGGTAT
1 AACACCCTACATCTGGCCCTTATCATGTGAGGTAT
** *
13318259 AATGCCCTACATCTGGCCTTTATCATGTGAGGTAT
1 AACACCCTACATCTGGCCCTTATCATGTGAGGTAT
*
13318294 AACACCTTACATCTGGCCCTTAT
1 AACACCCTACATCTGGCCCTTAT
13318317 TCTCACATAA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (35 bp):
AACACCCTACATCTGGCCCTTATCATGTGAGGTAT
Found at i:13324974 original size:21 final size:21
Alignment explanation
Indices: 13324949--13325024 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
13324939 ACCTTTACCC
13324949 ATATTAATATTTATAACTA-AA
1 ATATTAATATTTA-AACTATAA
*
13324970 ATATTAATGA-TTAAATTATAA
1 ATATTAAT-ATTTAAACTATAA
* *
13324991 AAATTAATATTTAAATTATCAA
1 ATATTAATATTTAAACTAT-AA
*
13325013 CTATTAATATTT
1 ATATTAATATTT
13325025 TAAATAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.11
21 29 0.62
22 13 0.28
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (21 bp):
ATATTAATATTTAAACTATAA
Found at i:13325032 original size:27 final size:26
Alignment explanation
Indices: 13325002--13325058 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
13324992 AATTAATATT
* *
13325002 TAAATTATCAACTATTAATATTTTAAA
1 TAAATTATAAACTATTAA-AATTTAAA
*
13325029 TAAATTATAAATTATTAAAATTTAAA
1 TAAATTATAAACTATTAAAATTTAAA
13325055 -AAAT
1 TAAAT
13325059 AAAATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 7 0.26
27 16 0.59
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATTATAAACTATTAAAATTTAAA
Found at i:13325130 original size:42 final size:41
Alignment explanation
Indices: 13325082--13325262 Score: 152
Period size: 42 Copynumber: 4.3 Consensus size: 41
13325072 ATAATAACAT
* *
13325082 TTAAATTATAGATAAAATAAGAATATTTTATAATATTAATGA
1 TTAAATTATAAATAAAATAATAATATTTTATAATATTAAT-A
* *
13325124 TTAAATTATAAATAAAATATTAATA-TTTA-AATTATCAATTA
1 TTAAATTATAAATAAAATAATAATATTTTATAA-TATTAA-TA
* * ** * * *
13325165 TTAATATTTAAAATATAAAATAAAAATAAATCATTATAATAATA
1 TTAA-A-TTATAA-ATAAAATAATAATATTTTATAATATTAATA
* *
13325209 TTAAAATTATAAATAAAATAATAATATTTTATTATGTTAATCA
1 TT-AAATTATAAATAAAATAATAATATTTTATAATATTAAT-A
13325252 TT-AATTATAAA
1 TTAAATTATAAA
13325263 AATTAATATT
Statistics
Matches: 111, Mismatches: 19, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
40 2 0.02
41 23 0.21
42 47 0.42
43 13 0.12
44 17 0.15
45 8 0.07
46 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (41 bp):
TTAAATTATAAATAAAATAATAATATTTTATAATATTAATA
Found at i:13325192 original size:22 final size:22
Alignment explanation
Indices: 13325135--13325186 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
13325125 TAAATTATAA
*
13325135 ATAAAATATTAATATTTAAATT
1 ATAAAATATTAATATTTAAAAT
* *
13325157 ATCAATTATTAATATTTAAAAT
1 ATAAAATATTAATATTTAAAAT
13325179 ATAAAATA
1 ATAAAATA
13325187 AAAATAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAAATATTAATATTTAAAAT
Found at i:13325225 original size:128 final size:123
Alignment explanation
Indices: 13325004--13325299 Score: 341
Period size: 128 Copynumber: 2.4 Consensus size: 123
13324994 TTAATATTTA
* * * * *
13325004 AATTATCAACTATTAATATTTTAAA-TA--AATTATAAATTATTAAAATTTAAAAAATAAAATTA
1 AATTATAAAATATTAATA-TTTAAATTATCAATTATTAATT-TTAAAATATAAAAAATAAAATAA
* * * *
13325066 ATTATCATAATAACATTTAAATTATAGATAAAATAAGAATATTTTATAATATTAATGATT
64 ATCATCATAATAACATTAAAATTATAAATAAAATAAGAATATTTTATAATATTAATCATT
*
13325126 AAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTAAAATATAAAATA-AAA
1 -AA-T-T--ATAAAATATTAATATTTAAATTATCAATTATTAAT-TTTAAAATATAAAAAATAAA
* * * * *
13325190 ATAAATCATTATAATAATATTAAAATTATAAATAAAATAATAATATTTTATTATGTTAATCATT
60 ATAAATCATCATAATAACATTAAAATTATAAATAAAATAAGAATATTTTATAATATTAATCATT
13325254 AATTATAAAA-ATTAATATTTAAATTATCAATTATTAATTTTTAAAA
1 AATTATAAAATATTAATATTTAAATTATCAATTATTAA-TTTTAAAA
13325300 AAATTATAAT
Statistics
Matches: 149, Mismatches: 15, Indels: 19
0.81 0.08 0.10
Matches are distributed among these distances:
122 34 0.23
123 9 0.06
124 1 0.01
125 2 0.01
126 7 0.05
127 16 0.11
128 57 0.38
129 22 0.15
130 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (123 bp):
AATTATAAAATATTAATATTTAAATTATCAATTATTAATTTTAAAATATAAAAAATAAAATAAAT
CATCATAATAACATTAAAATTATAAATAAAATAAGAATATTTTATAATATTAATCATT
Found at i:13325321 original size:25 final size:26
Alignment explanation
Indices: 13325274--13325325 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
13325264 ATTAATATTT
*
13325274 AAATTATCAATTATTAATTTTTAAAA
1 AAATTATCAATTATTAATATTTAAAA
*
13325300 AAATTAT-AATTATTTATATTTAAAA
1 AAATTATCAATTATTAATATTTAAAA
13325325 A
1 A
13325326 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATTATCAATTATTAATATTTAAAA
Found at i:13325324 original size:22 final size:22
Alignment explanation
Indices: 13325254--13325324 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
13325244 GTTAATCATT
**
13325254 AATTATAAAAATTAATATTT-A
1 AATTATAATTATTAATATTTAA
*
13325275 AATTATCAATTATTAATTTTTAAAAA
1 AATTAT-AATTATTAATATTT---AA
*
13325301 AATTATAATTATTTATATTTAA
1 AATTATAATTATTAATATTTAA
13325323 AA
1 AA
13325325 ATAAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 6 0.15
22 15 0.38
25 12 0.30
26 7 0.17
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTATAATTATTAATATTTAA
Found at i:13325333 original size:25 final size:25
Alignment explanation
Indices: 13325282--13325333 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
13325272 TTAAATTATC
* *
13325282 AATTATTAATTTTTAAAAAAATTAT
1 AATTATTAATATTTAAAAAAATAAT
*
13325307 AATTATTTATATTTAAAAATAA-AAT
1 AATTATTAATATTTAAAAA-AATAAT
13325332 AA
1 AA
13325334 AATAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTATTAATATTTAAAAAAATAAT
Found at i:13330779 original size:2 final size:2
Alignment explanation
Indices: 13330772--13330802 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13330762 TTTATATGTT
*
13330772 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13330803 TTACGGGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:13336870 original size:3 final size:3
Alignment explanation
Indices: 13336864--13336893 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
13336854 ATCATCATCA
*
13336864 TCT TCT TCT TCT TCT TCG TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
13336894 ATGCTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:13345863 original size:6 final size:6
Alignment explanation
Indices: 13345854--13345878 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13345844 GTCCATGATT
13345854 ACGACC ACGACC ACGACC ACGACC A
1 ACGACC ACGACC ACGACC ACGACC A
13345879 GAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:13346739 original size:40 final size:40
Alignment explanation
Indices: 13346677--13346849 Score: 175
Period size: 46 Copynumber: 4.0 Consensus size: 40
13346667 AAATTGAACT
* * *
13346677 TCGACTTTGTGAACCTTAAGGGTGAGAGATTATAAGATCG
1 TCGACTTTGTGAAGCTTGAGGGTGAGAGATTATAGGATCG
*
13346717 TCGACTTTATGAAGCTTGAGGGTGAAGATGAGAGATTATAGGATCG
1 TCGACTTTGTGAAGCTTGA--G-G--G-TGAGAGATTATAGGATCG
*
13346763 TCGAATTTGTGAAGCTTGAGGGTGAAGGCTAGAGATTATAGGATCG
1 TCGACTTTGTGAAGCTTGAGGGT----G--AGAGATTATAGGATCG
* *
13346809 TTGACTTTGTGAAGCTTGAGGGTGAGAGATTAGAGGATCG
1 TCGACTTTGTGAAGCTTGAGGGTGAGAGATTATAGGATCG
13346849 T
1 T
13346850 GCTGATAACG
Statistics
Matches: 112, Mismatches: 9, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
40 33 0.29
41 1 0.01
42 2 0.02
43 2 0.02
44 2 0.02
45 1 0.01
46 71 0.63
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.29
Consensus pattern (40 bp):
TCGACTTTGTGAAGCTTGAGGGTGAGAGATTATAGGATCG
Found at i:13346766 original size:46 final size:46
Alignment explanation
Indices: 13346699--13346843 Score: 211
Period size: 46 Copynumber: 3.1 Consensus size: 46
13346689 ACCTTAAGGG
* *
13346699 TGAGAGATTATAAGATCGTCGACTTTATGAAGCTTGAGGGTGAAGA
1 TGAGAGATTATAGGATCGTCGACTTTGTGAAGCTTGAGGGTGAAGA
* *
13346745 TGAGAGATTATAGGATCGTCGAATTTGTGAAGCTTGAGGGTGAAGGC
1 TGAGAGATTATAGGATCGTCGACTTTGTGAAGCTTGAGGGTGAA-GA
*
13346792 T-AGAGATTATAGGATCGTTGACTTTGTGAAGCTTGAGGGTGAGAGA
1 TGAGAGATTATAGGATCGTCGACTTTGTGAAGCTTGAGGGTGA-AGA
*
13346838 TTAGAG
1 TGAGAG
13346844 GATCGTGCTG
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
46 82 0.92
47 7 0.08
ACGTcount: A:0.30, C:0.08, G:0.34, T:0.29
Consensus pattern (46 bp):
TGAGAGATTATAGGATCGTCGACTTTGTGAAGCTTGAGGGTGAAGA
Found at i:13347669 original size:42 final size:41
Alignment explanation
Indices: 13347583--13347707 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 41
13347573 AAAACTTAAT
* *
13347583 TAAAATTATTAATATTTAAATCATAATAA-CATTTAAATTATAAA
1 TAAAA-TATTAATATTTAAA--ATAACAATTA-TTAAATTATAAA
** *
13347627 TAAAATATTAATATTTTAAAATATTAATTATTAAATTGTAAA
1 TAAAATATTAATA-TTTAAAATAACAATTATTAAATTATAAA
*
13347669 TAAAATATTAATATTTAAATTAACAATTATTAATATTAT
1 TAAAATATTAATATTTAAAATAACAATTATTAA-ATTAT
13347708 TAGAAGCAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
41 17 0.24
42 34 0.48
43 9 0.13
44 11 0.15
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (41 bp):
TAAAATATTAATATTTAAAATAACAATTATTAAATTATAAA
Found at i:13347678 original size:22 final size:22
Alignment explanation
Indices: 13347615--13347678 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
13347605 ATAATAACAT
13347615 TTAAATTATAAATAAAATATTA
1 TTAAATTATAAATAAAATATTA
* ** **
13347637 ATATTTTA-AAATATTA-ATTA
1 TTAAATTATAAATAAAATATTA
*
13347657 TTAAATTGTAAATAAAATATTA
1 TTAAATTATAAATAAAATATTA
13347679 ATATTTAAAT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
20 8 0.28
21 12 0.41
22 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTAAATTATAAATAAAATATTA
Found at i:13347883 original size:40 final size:42
Alignment explanation
Indices: 13347815--13347918 Score: 149
Period size: 40 Copynumber: 2.5 Consensus size: 42
13347805 ATAGCATTTC
13347815 AATTATAAATAAAACATTAATATTTTAAAACATTAATGATTA
1 AATTATAAATAAAACATTAATATTTTAAAACATTAATGATTA
* * **
13347857 AATTATAAA-AAAA-GTTAGTATTTTAAAATGTTAATGATTA
1 AATTATAAATAAAACATTAATATTTTAAAACATTAATGATTA
*
13347897 AATTATAAATAAAATATTAATA
1 AATTATAAATAAAACATTAATA
13347919 GTATTATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
40 32 0.59
41 8 0.15
42 14 0.26
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (42 bp):
AATTATAAATAAAACATTAATATTTTAAAACATTAATGATTA
Found at i:13348166 original size:42 final size:45
Alignment explanation
Indices: 13348118--13348218 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 45
13348108 TTATAATAAC
* * *
13348118 ATTTAAATTATAAATT-AAATATTAATATTTTAAAATATTA-ATT
1 ATTTAAATTATAAATTAAAATATTAATATTTAAAAAAATTAGAAT
*
13348161 A-TTAAATTGT-AATTAAAATATTAATATTTAAAAAAATTATGAAT
1 ATTTAAATTATAAATTAAAATATTAATATTTAAAAAAATTA-GAAT
13348205 ATTTAAATTATAAA
1 ATTTAAATTATAAA
13348219 AAATTAATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
41 4 0.08
42 30 0.62
43 1 0.02
44 3 0.06
45 8 0.17
46 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (45 bp):
ATTTAAATTATAAATTAAAATATTAATATTTAAAAAAATTAGAAT
Found at i:13352471 original size:10 final size:10
Alignment explanation
Indices: 13352446--13352482 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
13352436 AGATCAAATT
13352446 AATATTATATA
1 AATATT-TATA
*
13352457 TATATTTATA
1 AATATTTATA
13352467 AATATTTATA
1 AATATTTATA
13352477 AATATT
1 AATATT
13352483 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AATATTTATA
Found at i:13352510 original size:25 final size:24
Alignment explanation
Indices: 13352456--13352512 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
13352446 AATATTATAT
* *
13352456 ATATATTTATAAATATTTATAAAT
1 ATATATTTTTAAATATTTATAAAC
13352480 AT-TATTTTTAAAT-TTATATAAAAC
1 ATATATTTTTAAATATT-TAT-AAAC
13352504 ATATATTTT
1 ATATATTTT
13352513 CAATATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 13 0.46
24 7 0.25
25 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATATTTTTAAATATTTATAAAC
Found at i:13357202 original size:24 final size:24
Alignment explanation
Indices: 13357175--13357221 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
13357165 TTTTATTAAA
*
13357175 CATTTATGTGAATATATTTGTATG
1 CATTTATGTGAATATATGTGTATG
13357199 CATTTATGTGAATATATGTGTAT
1 CATTTATGTGAATATATGTGTAT
13357222 TTGTTGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (24 bp):
CATTTATGTGAATATATGTGTATG
Found at i:13366072 original size:224 final size:225
Alignment explanation
Indices: 13365661--13366108 Score: 598
Period size: 224 Copynumber: 2.0 Consensus size: 225
13365651 TTTCATACAA
*
13365661 CAAATGAAGGCAAGATCGAGCCCTTCATATTGGGATCAATCCCAAGGTATCCATTACCATTAAGG
1 CAAATGAAGGCAAGATCGAGCCCTTCATATTGGGATCAATCCCAAGGTATCCATTACCAGTAAGG
* *
13365726 ATGGTAGATTTTCAACAAAATAACAACTTTTTCCTTAGTTAATGCTATGCGGCTCCAATGGGATT
66 AAGGTAGATTTTCAACAAAATAACAACTTTTTCCTTAGTTAATGCTATGCGGCTCCAATGAGATT
* * * *
13365791 TGCAAGTTTAAATACACTCTCTTTAGATCATCATTGCAGAACAATAAGAGAAGAAACAAGACATA
131 TGCAAGTGTAAATACACTATCTTTAGATCATCATTGCAGAACAATAAAAGAAGAAACAAGACACA
** *
13365856 AGGTTAGGGCAAG-TATTTTCACATTCTTT
196 AGGTTAAAGCAAGCAATTTTCACATTCTTT
* * * * * * *
13365885 CAAATGAAGGCAGGATCGAGCCTTTCATATTGGGATCGATCTCGAGGTATCCATTAGCAGTAATG
1 CAAATGAAGGCAAGATCGAGCCCTTCATATTGGGATCAATCCCAAGGTATCCATTACCAGTAAGG
* * * * *
13365950 AAGGTAGATTTTCAACAAAGTAACGACTCTTTT-CTTAGTTAATGTTATGTGGCTCTAATGAGAT
66 AAGGTAGATTTTCAACAAAATAACAACT-TTTTCCTTAGTTAATGCTATGCGGCTCCAATGAGAT
* * * *
13366014 TTGTAAGTGTAAATACACTATTTTTGGATCATCATTGTAGAGA-AATAACAAG-AGAAACAAGAC
130 TTGCAAGTGTAAATACACTATCTTTAGATCATCATTGCAGA-ACAATAA-AAGAAGAAACAAGAC
*
13366077 ACAAGTTTAAAGCAAGCAATTTTCACATTCTT
193 ACAAGGTTAAAGCAAGCAATTTTCACATTCTT
13366109 CCCAGTTTTT
Statistics
Matches: 193, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
224 172 0.89
225 21 0.11
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (225 bp):
CAAATGAAGGCAAGATCGAGCCCTTCATATTGGGATCAATCCCAAGGTATCCATTACCAGTAAGG
AAGGTAGATTTTCAACAAAATAACAACTTTTTCCTTAGTTAATGCTATGCGGCTCCAATGAGATT
TGCAAGTGTAAATACACTATCTTTAGATCATCATTGCAGAACAATAAAAGAAGAAACAAGACACA
AGGTTAAAGCAAGCAATTTTCACATTCTTT
Found at i:13369212 original size:28 final size:28
Alignment explanation
Indices: 13369077--13369272 Score: 160
Period size: 28 Copynumber: 6.8 Consensus size: 28
13369067 TTACAACAAC
* * *
13369077 TCTTGTCTTTAATTAAGACAAAACATGTTA
1 TCTTGTC-TAAATTAAGAC-AAATATGTTT
* * *
13369107 ACTTGTCTAAAATTGAGACAAATGTGTTT
1 TCTTGTCT-AAATTAAGACAAATATGTTT
* * * *
13369136 TCTTATTTAGATTAAAACAAAACCTAT-TTT
1 TCTTGTCTAAATTAAGAC-AAA--TATGTTT
* *
13369166 TCTTATTTTAAATTAAGACAAATATGTTT
1 TCTT-GTCTAAATTAAGACAAATATGTTT
* *
13369195 TCTTGTCTAAATAAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGAC-AAATATGTTT
* *
13369224 TCTTGTCTAAATTAAGATAAATATATTT
1 TCTTGTCTAAATTAAGACAAATATGTTT
*
13369252 TCTTGTCTAAATTAGGACAAA
1 TCTTGTCTAAATTAAGACAAA
13369273 CATATAAAAG
Statistics
Matches: 133, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
28 48 0.36
29 48 0.36
30 24 0.18
31 13 0.10
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAATATGTTT
Found at i:13369221 original size:29 final size:29
Alignment explanation
Indices: 13369077--13369272 Score: 157
Period size: 29 Copynumber: 6.7 Consensus size: 29
13369067 TTACAACAAC
* *
13369077 TCTTGTCTTTAATTAAGACAAAACATGTTA
1 TCTTGTC-TAAATTAAGACAAAACATGTTT
* * **
13369107 ACTTGTCTAAAATTGAGAC-AAATGTGTTT
1 TCTTGTCT-AAATTAAGACAAAACATGTTT
* * * *
13369136 TCTTATTTAGATTAAAACAAAACCTAT-TTT
1 TCTTGTCTAAATTAAGACAAAA-C-ATGTTT
* * *
13369166 TCTTATTTTAAATTAAGAC-AAATATGTTT
1 TCTT-GTCTAAATTAAGACAAAACATGTTT
*
13369195 TCTTGTCTAAATAAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* * *
13369224 TCTTGTCTAAATTAAGA-TAAATATATTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
*
13369252 TCTTGTCTAAATTAGGACAAA
1 TCTTGTCTAAATTAAGACAAA
13369273 CATATAAAAG
Statistics
Matches: 130, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
28 44 0.34
29 50 0.38
30 24 0.18
31 12 0.09
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATGTTT
Found at i:13369247 original size:57 final size:57
Alignment explanation
Indices: 13369077--13369272 Score: 189
Period size: 59 Copynumber: 3.4 Consensus size: 57
13369067 TTACAACAAC
* * ** * *
13369077 TCTTGTCTTTAATTAAGACAAAACATGTTAACTTGTCTAAAATTGAGACAAATGTGTTT
1 TCTTGTC-TAAATAAAGACAAAACATGTTTTCTTGTCT-AAATTAAGACAAATATGTTT
* * * * *
13369136 TCTTATTTAGATTAAA-ACAAAACCTAT-TTTTCTTATTTTAAATTAAGACAAATATGTTT
1 TCTTGTCTA-AATAAAGACAAAA-C-ATGTTTTCTT-GTCTAAATTAAGACAAATATGTTT
* *
13369195 TCTTGTCTAAATAAAGACAAAACATGTTTTCTTGTCTAAATTAAGATAAATATATTT
1 TCTTGTCTAAATAAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAATATGTTT
* *
13369252 TCTTGTCTAAATTAGGACAAA
1 TCTTGTCTAAATAAAGACAAA
13369273 CATATAAAAG
Statistics
Matches: 111, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
57 41 0.37
58 20 0.18
59 46 0.41
60 4 0.04
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (57 bp):
TCTTGTCTAAATAAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAATATGTTT
Found at i:13369287 original size:57 final size:57
Alignment explanation
Indices: 13369174--13369280 Score: 135
Period size: 57 Copynumber: 1.9 Consensus size: 57
13369164 TTTCTTATTT
* * ***
13369174 TAAATTAAGACAAATATGTTTTCTTGTCTAAATAAAGACAAAACATGTTTTCTTGTC
1 TAAATTAAGACAAATATATTTTCTTGTCTAAATAAAGACAAAACATATAAACTTGTC
* * *
13369231 TAAATTAAGATAAATATATTTTCTTGTCTAAATTAGGAC-AAACATATAAA
1 TAAATTAAGACAAATATATTTTCTTGTCTAAATAAAGACAAAACATATAAA
13369281 AGTTGTCATT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
56 7 0.17
57 35 0.83
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (57 bp):
TAAATTAAGACAAATATATTTTCTTGTCTAAATAAAGACAAAACATATAAACTTGTC
Found at i:13371340 original size:13 final size:13
Alignment explanation
Indices: 13371322--13371348 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13371312 TGCTACTAGG
13371322 TTAAGGTGAAGAA
1 TTAAGGTGAAGAA
13371335 TTAAGGTGAAGAA
1 TTAAGGTGAAGAA
13371348 T
1 T
13371349 CAGAGGCCCA
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:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (13 bp):
TTAAGGTGAAGAA
Found at i:13374767 original size:100 final size:99
Alignment explanation
Indices: 13374585--13374805 Score: 230
Period size: 100 Copynumber: 2.2 Consensus size: 99
13374575 ATTCGCTTTG
* ***
13374585 AGTTGGGGCGAGCACCACTCAAGTCTGGGTGAAGCTGAATGCCACTCACAGTACGCTCAAGGGAT
1 AGTTGGGGCGAGCACCACTCAAGTCTGGGTGAAGCTGAATGCCACTCACAG-AAGCTCAAAAAAT
13374650 CCAAGACAATGGAGATTTGCCCACTATCTGTTTTA
65 CCAAGACAATGGAGATTTGCCCACTATCTGTTTTA
* * * * *
13374685 AGTTGGGGTGGGCACCACTCAAGATGTGGGTGAGGTTGAATGCCACTCACTA-AAGCTCAAAAAA
1 AGTTGGGGCGAGCACCACTCAAG-TCTGGGTGAAGCTGAATGCCACTCAC-AGAAGCTCAAAAAA
* * * * * ** *
13374749 TCCAAGATAGTGGGGATTTGTCGACTAT-TCACTTTG
64 TCCAAGACAATGGAGATTTGCCCACTATCT-GTTTTA
*
13374785 AGTTGGGGCAAGCACCACTCA
1 AGTTGGGGCGAGCACCACTCA
13374806 TAGTTAGTAA
Statistics
Matches: 98, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
99 1 0.01
100 73 0.74
101 23 0.23
102 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.24
Consensus pattern (99 bp):
AGTTGGGGCGAGCACCACTCAAGTCTGGGTGAAGCTGAATGCCACTCACAGAAGCTCAAAAAATC
CAAGACAATGGAGATTTGCCCACTATCTGTTTTA
Found at i:13381079 original size:17 final size:18
Alignment explanation
Indices: 13381048--13381081 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13381038 GACATGTAAG
*
13381048 ATCACAATATCATACTTA
1 ATCACAATATAATACTTA
13381066 ATCA-AATATAATACTT
1 ATCACAATATAATACTT
13381082 CCACAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
ATCACAATATAATACTTA
Found at i:13394175 original size:34 final size:31
Alignment explanation
Indices: 13394131--13394210 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 31
13394121 ATAGGAGATC
*
13394131 AAATTAAACAAAATTGTAAAGTACAATGTGGACT
1 AAATTAAACAAAATTCTAAAGTACAA---GGACT
* * *
13394165 AAATTGAACAAAACTCTATAGTACAAGGACT
1 AAATTAAACAAAATTCTAAAGTACAAGGACT
*
13394196 AAAATAAACAAAATT
1 AAATTAAACAAAATT
13394211 TTATAGAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 17 0.44
34 22 0.56
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (31 bp):
AAATTAAACAAAATTCTAAAGTACAAGGACT
Found at i:13394198 original size:31 final size:30
Alignment explanation
Indices: 13394160--13394238 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
13394150 AGTACAATGT
13394160 GGACTAAATTGAACAAAACTCTATAGTACA-A
1 GGACTAAATTGAACAAAACTCTATAG-A-ATA
* * * *
13394191 GGACTAAAATAAACAAAATTTTATAGAATA
1 GGACTAAATTGAACAAAACTCTATAGAATA
*
13394221 GAGATTAAATTGAACAAA
1 G-GACTAAATTGAACAAA
13394239 GCTTTGTCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 1 0.03
30 3 0.08
31 35 0.90
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.24
Consensus pattern (30 bp):
GGACTAAATTGAACAAAACTCTATAGAATA
Found at i:13397385 original size:15 final size:15
Alignment explanation
Indices: 13397341--13397385 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
13397331 ATCTTTTAGA
*
13397341 AAATTAATTAAAACT
1 AAATTAATTAACACT
*
13397356 AAATTAACGTAAACACT
1 AAATTAA--TTAACACT
13397373 AAATTAATTAACA
1 AAATTAATTAACA
13397386 TGACTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 12 0.48
17 13 0.52
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATTAATTAACACT
Found at i:13404825 original size:36 final size:36
Alignment explanation
Indices: 13404784--13404863 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
13404774 CGGTATGGGA
*
13404784 GCACATGACGATAATAACTATGTGCAGTGTGGGAGT
1 GCACATGACAATAATAACTATGTGCAGTGTGGGAGT
* *
13404820 GCACATGACAATAATAGCTATGTGCGGTGTGGGAGT
1 GCACATGACAATAATAACTATGTGCAGTGTGGGAGT
13404856 GCACATGA
1 GCACATGA
13404864 ACTGAGTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (36 bp):
GCACATGACAATAATAACTATGTGCAGTGTGGGAGT
Found at i:13411410 original size:21 final size:21
Alignment explanation
Indices: 13411386--13411425 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13411376 CTATTTATAT
13411386 TTTATGCATTAT-AGTTTAATA
1 TTTA-GCATTATAAGTTTAATA
*
13411407 TTTAGTATTATAAGTTTAA
1 TTTAGCATTATAAGTTTAA
13411426 CTAGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTAGCATTATAAGTTTAATA
Found at i:13415298 original size:1 final size:1
Alignment explanation
Indices: 13415292--13415319 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
13415282 ACCCACTGAT
13415292 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
13415320 AACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:13425183 original size:14 final size:14
Alignment explanation
Indices: 13425164--13425190 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13425154 AAAGTTGAGT
13425164 TACTTAGCAAATTG
1 TACTTAGCAAATTG
13425178 TACTTAGCAAATT
1 TACTTAGCAAATT
13425191 ATACACATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
TACTTAGCAAATTG
Found at i:13429816 original size:108 final size:107
Alignment explanation
Indices: 13429671--13429879 Score: 355
Period size: 108 Copynumber: 1.9 Consensus size: 107
13429661 TATAAGAAAT
* * *
13429671 TTTGAGTAAATTTAAATAAAGGTAAATTGGGTAAGAGTTGAATAATTGCAAAAGAATGTGTATTT
1 TTTGAGTAAATTTAAATAAAAGTAAATTGAGTAAGAGTTAAATAATTGCAAAAGAATGTGTATTT
*
13429736 GTAAATTGTGAAAGTTGTAACTAAATCAACATATTTTACTAA
66 GTAAATTATGAAAGTTGTAACTAAATCAACATATTTTACTAA
* *
13429778 TTTGAGTGAATTTAAATAAAAAGTAAATTGAGTAAGAGTTAAATAATTTCAAAAGAATGTGTATT
1 TTTGAGTAAATTTAAAT-AAAAGTAAATTGAGTAAGAGTTAAATAATTGCAAAAGAATGTGTATT
13429843 TGTAAATTATGAAAGTTGTAACTAAATCAACATATTT
65 TGTAAATTATGAAAGTTGTAACTAAATCAACATATTT
13429880 AGTCATTTTG
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 16 0.17
108 79 0.83
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (107 bp):
TTTGAGTAAATTTAAATAAAAGTAAATTGAGTAAGAGTTAAATAATTGCAAAAGAATGTGTATTT
GTAAATTATGAAAGTTGTAACTAAATCAACATATTTTACTAA
Found at i:13431351 original size:19 final size:17
Alignment explanation
Indices: 13431327--13431365 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
13431317 CAATTAGCAT
*
13431327 AAAATAAATTAACTTAATA
1 AAAATAAACTAA-TTAA-A
13431346 AAAATAAACTAATTAAA
1 AAAATAAACTAATTAAA
13431363 AAA
1 AAA
13431366 GTTAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATAAACTAATTAAA
Found at i:13439490 original size:20 final size:20
Alignment explanation
Indices: 13439449--13439492 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13439439 AATAAAAATT
* *
13439449 AATTATTAATTAATTACTAG
1 AATTATTAATTAATGACAAG
13439469 AATTATTAATCTAATGA-AAG
1 AATTATTAAT-TAATGACAAG
13439489 AATT
1 AATT
13439493 TAGTCACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (20 bp):
AATTATTAATTAATGACAAG
Found at i:13439662 original size:16 final size:16
Alignment explanation
Indices: 13439643--13439694 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
13439633 TTGTACATAT
13439643 ATTACATACATTTATC
1 ATTACATACATTTATC
13439659 ATTACATACATTTATC
1 ATTACATACATTTATC
* *
13439675 ATTACATATATTTATT
1 ATTACATACATTTATC
13439691 ATTA
1 ATTA
13439695 TTATTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTACATACATTTATC
Found at i:13442198 original size:21 final size:18
Alignment explanation
Indices: 13442138--13442188 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
13442128 TAGTTAGTTA
* *
13442138 TTTTCTTCATTT-AGTTG
1 TTTTCATCATTTAAATTG
*
13442155 TTTTCATTATTTAAATTG
1 TTTTCATCATTTAAATTG
*
13442173 CTTTCATCATTTAAAT
1 TTTTCATCATTTAAAT
13442189 GTTAGTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTCATCATTTAAATTG
Found at i:13447883 original size:15 final size:16
Alignment explanation
Indices: 13447838--13447883 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
13447828 TACCTCGATA
*
13447838 AATTAATTT-TTTATT
1 AATTAATTTATTAATT
* *
13447853 AATTAATGTATAAATT
1 AATTAATTTATTAATT
13447869 -ATTAATTTATTAATT
1 AATTAATTTATTAATT
13447884 TACAGATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
AATTAATTTATTAATT
Found at i:13453673 original size:39 final size:39
Alignment explanation
Indices: 13453619--13453697 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
13453609 AACACCAATT
13453619 CCATAACAACACAATCTATCTAGTAAGATAAGGGACTTA
1 CCATAACAACACAATCTATCTAGTAAGATAAGGGACTTA
*
13453658 CCATAACAACACAATCTATCTAGTAAGATAGGGGACTTA
1 CCATAACAACACAATCTATCTAGTAAGATAAGGGACTTA
13453697 C
1 C
13453698 TTGAGGATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (39 bp):
CCATAACAACACAATCTATCTAGTAAGATAAGGGACTTA
Found at i:13455450 original size:55 final size:55
Alignment explanation
Indices: 13455357--13455482 Score: 132
Period size: 55 Copynumber: 2.3 Consensus size: 55
13455347 ACTACAACAT
*
13455357 TACAATGTTAGTTTTTTTAAAATTATATATGACACTTTA-CGATATATACCAAACGA
1 TACAATATTAG-TTTTTTAAAATTATATATGACACTTTATC-ATATATACCAAACGA
* ** * * *
13455413 TACAATATTAGTTTTTTAAAATTTTA-ATCGATTCTTTATCATATATATCAAATGC
1 TACAATATTAGTTTTTTAAAATTATATAT-GACACTTTATCATATATACCAAACGA
*
13455468 TATAATATTA-TTTTT
1 TACAATATTAGTTTTT
13455483 CTAGCAATCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
54 7 0.12
55 42 0.70
56 11 0.18
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.46
Consensus pattern (55 bp):
TACAATATTAGTTTTTTAAAATTATATATGACACTTTATCATATATACCAAACGA
Found at i:13463417 original size:22 final size:20
Alignment explanation
Indices: 13463392--13463439 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
13463382 TACTTAAAGT
13463392 AATTAAATTAAAAATAACATAA
1 AATTAAATT-AAAATAAC-TAA
* *
13463414 AATTGAATTAAAATAACTTA
1 AATTAAATTAAAATAACTAA
13463434 AATTAA
1 AATTAA
13463440 TCTAATCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
AATTAAATTAAAATAACTAA
Found at i:13481245 original size:71 final size:73
Alignment explanation
Indices: 13481151--13481323 Score: 251
Period size: 73 Copynumber: 2.4 Consensus size: 73
13481141 ATTTAGTCAT
* * * **
13481151 CTAAGAAGTATGGTTAGTTAACTAAGAGCTCACTACCAAAAACTTCAGTTACAA-A-ACAGATGA
1 CTAAGAAGCAT-GTTAGTCAACTAAGAGCTCACTACCAAAAACTTCAGTTACAAGATAAAGACAA
13481214 CTTAATCGA
65 CTTAATCGA
* * *
13481223 CTAAGTAGCATGTTAGTCAACTAAGAGCTTACTGCCAAAAACTTCAGTTACAAGATAAAGACAAC
1 CTAAGAAGCATGTTAGTCAACTAAGAGCTCACTACCAAAAACTTCAGTTACAAGATAAAGACAAC
13481288 TTAATCGA
66 TTAATCGA
13481296 CTAAGAAGCATGTTAGTCAACTAAGAGC
1 CTAAGAAGCATGTTAGTCAACTAAGAGC
13481324 ACTCTGTCTG
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
71 39 0.43
72 10 0.11
73 41 0.46
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (73 bp):
CTAAGAAGCATGTTAGTCAACTAAGAGCTCACTACCAAAAACTTCAGTTACAAGATAAAGACAAC
TTAATCGA
Found at i:13481796 original size:35 final size:35
Alignment explanation
Indices: 13481750--13481840 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 35
13481740 GTTGATCCCG
*
13481750 TGAAAAACCATTGTTAAAGGTTGTGGTCGAGCTTT
1 TGAAAAACCATTGTTAAAGGTTGTGGTCGAGCTTA
* * * *
13481785 TGAAAAACCATT-TT--GGGTTTTGGTTGATCTTA
1 TGAAAAACCATTGTTAAAGGTTGTGGTCGAGCTTA
13481817 TGAAAAACCATTGTTAAAGGTTGT
1 TGAAAAACCATTGTTAAAGGTTGT
13481841 AGCTGAGCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 25 0.54
33 2 0.04
34 2 0.04
35 17 0.37
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (35 bp):
TGAAAAACCATTGTTAAAGGTTGTGGTCGAGCTTA
Found at i:13481826 original size:32 final size:32
Alignment explanation
Indices: 13481729--13481828 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 32
13481719 AAAAGTTAGA
* ***
13481729 TTTGGGTTTTAGTTGATCCCGTGAAAAACCAT
1 TTTGGGTTTTGGTTGATCTTATGAAAAACCAT
* * * * *
13481761 TGTTAAAGGTTGTGGTCGAGCTTTTGAAAAACCAT
1 T-TT--GGGTTTTGGTTGATCTTATGAAAAACCAT
13481796 TTTGGGTTTTGGTTGATCTTATGAAAAACCAT
1 TTTGGGTTTTGGTTGATCTTATGAAAAACCAT
13481828 T
1 T
13481829 GTTAAAGGTT
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
32 26 0.50
33 2 0.04
34 2 0.04
35 22 0.42
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTGGGTTTTGGTTGATCTTATGAAAAACCAT
Found at i:13481863 original size:67 final size:66
Alignment explanation
Indices: 13481729--13481863 Score: 175
Period size: 67 Copynumber: 2.0 Consensus size: 66
13481719 AAAAGTTAGA
* *
13481729 TTTGGGTTTTAGTTGATCCCGTGAAAAACCATTGTTAAAGGTTGTGGTCGAGCTTTTGAAAAACC
1 TTTGGGTTTTAGTTGATCCCATGAAAAACCATTGTTAAAGGTTGTGCTCGAGC-TTTGAAAAACC
13481794 AT
65 AT
* **
13481796 TTTGGGTTTTGGTTGATCTTATGAAAAACCATTGTTAAAGGTTGTAGCT-GAGC-TTGCAAAAAG
1 TTTGGGTTTTAGTTGATCCCATGAAAAACCATTGTTAAAGGTTGT-GCTCGAGCTTTG-AAAAA-
13481859 CCAT
63 CCAT
13481863 T
1 T
13481864 GTAAAAGCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
65 3 0.05
66 5 0.08
67 50 0.83
68 2 0.03
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (66 bp):
TTTGGGTTTTAGTTGATCCCATGAAAAACCATTGTTAAAGGTTGTGCTCGAGCTTTGAAAAACCA
T
Found at i:13489326 original size:73 final size:73
Alignment explanation
Indices: 13489206--13489366 Score: 241
Period size: 73 Copynumber: 2.2 Consensus size: 73
13489196 GAAGTATGGT
* * * *
13489206 TAGTCAATTAAAAGCTTACTATTAGAAACTTCAGTTACAAGACAAAGACGACTTAATAGACTAAG
1 TAGTCAACTAAGAGCTTACTATCAGAAACTTCAGTTACAAGACAAAGACAACTTAATAGACTAAG
13489271 AAGCATGC
66 AAGCATGC
* * * *
13489279 TAGTCAACTAAGAGCTTATTGTCAGAAACTTCAGTTACAAGATAAAGACAACTTAATTGACTAAG
1 TAGTCAACTAAGAGCTTACTATCAGAAACTTCAGTTACAAGACAAAGACAACTTAATAGACTAAG
*
13489344 AAGCATGT
66 AAGCATGC
13489352 TAGTCAACTAAGAGC
1 TAGTCAACTAAGAGC
13489367 ACTCTGTCTG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (73 bp):
TAGTCAACTAAGAGCTTACTATCAGAAACTTCAGTTACAAGACAAAGACAACTTAATAGACTAAG
AAGCATGC
Found at i:13489834 original size:34 final size:33
Alignment explanation
Indices: 13489796--13489900 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 33
13489786 TTATCTCATG
13489796 AAAAATCATTGTTAAAGGTTGTGGTTGAGTCTTT
1 AAAAA-CATTGTTAAAGGTTGTGGTTGAGTCTTT
* * *
13489830 AAAAACTATT-TT--ATGTTTTTGTTG-GTCCTGTGT
1 AAAAAC-ATTGTTAAAGGTTGTGGTTGAGT-CT-T-T
*
13489863 AAAACCATTGTTAAAGGTTGTGGTTGAGTCTTT
1 AAAAACATTGTTAAAGGTTGTGGTTGAGTCTTT
13489896 AAAAA
1 AAAAA
13489901 ACTATTTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
30 2 0.04
31 11 0.20
32 4 0.07
33 16 0.29
34 9 0.16
35 11 0.20
36 2 0.04
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.42
Consensus pattern (33 bp):
AAAAACATTGTTAAAGGTTGTGGTTGAGTCTTT
Found at i:13489867 original size:32 final size:32
Alignment explanation
Indices: 13489830--13489934 Score: 104
Period size: 32 Copynumber: 3.2 Consensus size: 32
13489820 TTGAGTCTTT
13489830 AAAAACTATTTTATGTTTTTGTTGGTCCTGTG
1 AAAAACTATTTTATGTTTTTGTTGGTCCTGTG
* * * * * * *
13489862 TAAAACCATTGTTAAAGGTTGTGGTTGAGT-CTTTA
1 AAAAACTATT-TT--ATGTTTTTGTTG-GTCCTGTG
13489897 AAAAACTATTTTATGTTTTTGTTGGTCCTGTG
1 AAAAACTATTTTATGTTTTTGTTGGTCCTGTG
13489929 AAAAAC
1 AAAAAC
13489935 CATTGTTAAG
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
31 2 0.04
32 26 0.48
33 2 0.04
34 2 0.04
35 20 0.37
36 2 0.04
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.44
Consensus pattern (32 bp):
AAAAACTATTTTATGTTTTTGTTGGTCCTGTG
Found at i:13489872 original size:66 final size:67
Alignment explanation
Indices: 13489794--13489943 Score: 275
Period size: 67 Copynumber: 2.3 Consensus size: 67
13489784 GTTTATCTCA
*
13489794 TGAAAAATCATTGTTAAAGGTTGTGGTTGAGTCTTT-AAAAACTATTTTATGTTTTTGTTGGTCC
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGTCTTTAAAAAACTATTTTATGTTTTTGTTGGTCC
13489858 TG
66 TG
*
13489860 TGTAAAACCATTGTTAAAGGTTGTGGTTGAGTCTTTAAAAAACTATTTTATGTTTTTGTTGGTCC
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGTCTTTAAAAAACTATTTTATGTTTTTGTTGGTCC
13489925 TG
66 TG
13489927 TGAAAAACCATTGTTAA
1 TGAAAAACCATTGTTAA
13489944 GCTATTGTAA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
66 34 0.43
67 46 0.57
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (67 bp):
TGAAAAACCATTGTTAAAGGTTGTGGTTGAGTCTTTAAAAAACTATTTTATGTTTTTGTTGGTCC
TG
Found at i:13494775 original size:23 final size:22
Alignment explanation
Indices: 13494731--13494776 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
13494721 AATTTGTTAG
* * *
13494731 ATTTAATTTTATTTTTTTAATA
1 ATTTAATTTAATTGTTTGAATA
13494753 ATTTAAATTTAATTGTTTGAATA
1 ATTT-AATTTAATTGTTTGAATA
13494776 A
1 A
13494777 GATTATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTTAATTTAATTGTTTGAATA
Found at i:13497238 original size:16 final size:17
Alignment explanation
Indices: 13497208--13497241 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13497198 TTCTTTCTTA
13497208 TTTTTCATATGTTTTTC
1 TTTTTCATATGTTTTTC
*
13497225 TTTTTCA-ATTTTTTTC
1 TTTTTCATATGTTTTTC
13497241 T
1 T
13497242 CAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTCATATGTTTTTC
Found at i:13497500 original size:57 final size:58
Alignment explanation
Indices: 13497438--13497546 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
13497428 TTTTGATTTG
13497438 TCAAATTCAAATTTTATT-TTTAAATTAATTTAATTTATTTACAGATAAATTAGATAA
1 TCAAATTCAAATTTTATTATTTAAATTAATTTAATTTATTTACAGATAAATTAGATAA
* ** * * **
13497495 TCAAATTTAGTTTTTATTATTTAAATTATTTTCATTTATTTGTAGATAAATT
1 TCAAATTCAAATTTTATTATTTAAATTAATTTAATTTATTTACAGATAAATT
13497547 GGATGACTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 15 0.34
58 29 0.66
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (58 bp):
TCAAATTCAAATTTTATTATTTAAATTAATTTAATTTATTTACAGATAAATTAGATAA
Found at i:13499938 original size:2 final size:2
Alignment explanation
Indices: 13499931--13499959 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13499921 TTTCAAAACA
13499931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13499960 CTTAACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13503169 original size:2 final size:2
Alignment explanation
Indices: 13503162--13503194 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13503152 AGACACAGCC
13503162 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
13503195 GACAAATTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13503266 original size:2 final size:2
Alignment explanation
Indices: 13503259--13503284 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13503249 AGCATCTCCA
13503259 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
13503285 CATATTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:13504961 original size:55 final size:55
Alignment explanation
Indices: 13504896--13505006 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
13504886 CTCCTTCTTG
* * *
13504896 CTCCTTAATCTGCTTGTTGCTTGTTGGTTTTATCTTAGTTTTTAGAAGTTTCATA
1 CTCCTTAATCTGCGTGTTGCATGTTGGTTTTATCTTAGGTTTTAGAAGTTTCATA
*
13504951 CTCCTTAATCTGCGTGTTGCATGTTGGTTTTATTTTAGGTTTTAGAAGTTTCATA
1 CTCCTTAATCTGCGTGTTGCATGTTGGTTTTATCTTAGGTTTTAGAAGTTTCATA
13505006 C
1 C
13505007 ACTTATTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.50
Consensus pattern (55 bp):
CTCCTTAATCTGCGTGTTGCATGTTGGTTTTATCTTAGGTTTTAGAAGTTTCATA
Found at i:13517864 original size:21 final size:21
Alignment explanation
Indices: 13517838--13517895 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
13517828 ACAACTTAAG
* * *
13517838 TTCAAAACTTATTCAAACAAC
1 TTCAAAAATCATTCAAACAAA
13517859 TTCAAAAATCATTCAAACAAA
1 TTCAAAAATCATTCAAACAAA
* *
13517880 TTCAAAGATAATTCAA
1 TTCAAAAATCATTCAA
13517896 GTCATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.28
Consensus pattern (21 bp):
TTCAAAAATCATTCAAACAAA
Found at i:13528353 original size:25 final size:26
Alignment explanation
Indices: 13528306--13528395 Score: 73
Period size: 25 Copynumber: 3.5 Consensus size: 26
13528296 TACTTAAATT
13528306 TTATTTAATCAATTAAACTATTTAAG
1 TTATTTAATCAATTAAACTATTTAAG
*
13528332 TTATTTATTC-ATT-AACTAATTTAA-
1 TTATTTAATCAATTAAACT-ATTTAAG
* * *
13528356 TTAATTT-TTAAATTAAA-TATTATTAG
1 TT-ATTTAATCAATTAAACTATT-TAAG
*
13528382 TTATTTAATTAATT
1 TTATTTAATCAATT
13528396 GTTAACTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
24 11 0.21
25 23 0.44
26 18 0.35
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
TTATTTAATCAATTAAACTATTTAAG
Found at i:13528412 original size:34 final size:32
Alignment explanation
Indices: 13528350--13528427 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 32
13528340 TCATTAACTA
* * *
13528350 ATTTAATTAATTTTTAAATTAAATATTATTAGTT
1 ATTTAATTAATTGTTAAACTAAACATTATT--TT
13528384 ATTTAATTAATTGTT-AACTAATACATTATTTT
1 ATTTAATTAATTGTTAAACTAA-ACATTATTTT
*
13528416 ATTTTATTAATT
1 ATTTAATTAATT
13528428 ACATGATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 13 0.33
33 5 0.13
34 21 0.54
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (32 bp):
ATTTAATTAATTGTTAAACTAAACATTATTTT
Found at i:13529266 original size:35 final size:34
Alignment explanation
Indices: 13529207--13529302 Score: 93
Period size: 35 Copynumber: 2.8 Consensus size: 34
13529197 TTCGGCAATG
* * * *
13529207 GAGTTCTACCATGCAAATTGGTGGAGTCGACGATA
1 GAGTTCTACCATGTAAACTAGTGGAATCGA-GATA
* * * *
13529242 GAGTTCTACTATGTAAACTAGTGGAAATGGAGGTG
1 GAGTTCTACCATGTAAACTAGTGG-AATCGAGATA
*
13529277 GAATTCTACCATGTAAACTAGTGGAA
1 GAGTTCTACCATGTAAACTAGTGGAA
13529303 ACAAGGGCGA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
34 2 0.04
35 44 0.88
36 4 0.08
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (34 bp):
GAGTTCTACCATGTAAACTAGTGGAATCGAGATA
Found at i:13536589 original size:28 final size:25
Alignment explanation
Indices: 13536526--13536590 Score: 60
Period size: 28 Copynumber: 2.5 Consensus size: 25
13536516 AAATATATAT
* * *
13536526 TTTTAATATTACTATTAATTTTATA
1 TTTTAATATTATTATAAATTTTAAA
13536551 TTTT-ATAATTATTAATAAAGTTTATAAA
1 TTTTAAT-ATTATT-ATAAA-TTT-TAAA
13536579 TTTTAATATTAT
1 TTTTAATATTAT
13536591 AATTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 9 0.28
26 4 0.12
27 3 0.09
28 12 0.38
29 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTAATATTATTATAAATTTTAAA
Found at i:13536709 original size:18 final size:18
Alignment explanation
Indices: 13536664--13536709 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
13536654 AAATTTAATA
* * *
13536664 TTTAATTGATTCGGTTTT
1 TTTAATTGATTTGATTAT
13536682 TTTAA-T-ATTTGATTAT
1 TTTAATTGATTTGATTAT
13536698 TTTAATTGATTT
1 TTTAATTGATTT
13536710 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 12 0.52
17 2 0.09
18 9 0.39
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (18 bp):
TTTAATTGATTTGATTAT
Found at i:13537533 original size:17 final size:16
Alignment explanation
Indices: 13537511--13537545 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
13537501 TTTAAATGTG
*
13537511 TAAATATATTTATATTA
1 TAAATATAATTA-ATTA
13537528 TAAATATAATTAATTA
1 TAAATATAATTAATTA
13537544 TA
1 TA
13537546 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATATAATTAATTA
Found at i:13557621 original size:35 final size:35
Alignment explanation
Indices: 13557582--13557710 Score: 177
Period size: 35 Copynumber: 3.7 Consensus size: 35
13557572 TTTTGGGTTT
* * *
13557582 TGGTTGATCTTGAGAAAAACCATTATTGAATGTTG
1 TGGTTGAGCTTGTGAAAAACCATTATTGAAAGTTG
* *
13557617 TGGTTGAGCTTTTGAAAAACCATTATTGAAGGTTG
1 TGGTTGAGCTTGTGAAAAACCATTATTGAAAGTTG
* *
13557652 TGGTTGAGCTTTTGAAAAACCATTGTTGAAAGTTG
1 TGGTTGAGCTTGTGAAAAACCATTATTGAAAGTTG
* *
13557687 TGGCTGAGCCTGTGAAAAACCATT
1 TGGTTGAGCTTGTGAAAAACCATT
13557711 GTAAACATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 85 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (35 bp):
TGGTTGAGCTTGTGAAAAACCATTATTGAAAGTTG
Found at i:13557712 original size:35 final size:35
Alignment explanation
Indices: 13557595--13557710 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
13557585 TTGATCTTGA
*
13557595 GAAAAACCATTATTGAATGTTGTGGTTGAGCTTTT
1 GAAAAACCATTATTGAAAGTTGTGGTTGAGCTTTT
*
13557630 GAAAAACCATTATTGAAGGTTGTGGTTGAGCTTTT
1 GAAAAACCATTATTGAAAGTTGTGGTTGAGCTTTT
* * * *
13557665 GAAAAACCATTGTTGAAAGTTGTGGCTGAGCCTGT
1 GAAAAACCATTATTGAAAGTTGTGGTTGAGCTTTT
13557700 GAAAAACCATT
1 GAAAAACCATT
13557711 GTAAACATTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
GAAAAACCATTATTGAAAGTTGTGGTTGAGCTTTT
Found at i:13558286 original size:22 final size:22
Alignment explanation
Indices: 13558258--13558321 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
13558248 TATCTATTAT
13558258 ATATTATATAAATA-ATAATAAA
1 ATATTATATAAATAGAT-ATAAA
*
13558280 ATATTATATAAATAGGTATAAA
1 ATATTATATAAATAGATATAAA
*
13558302 ATATTATATAAATAGGTATA
1 ATATTATATAAATAGATATA
13558322 GGATTTGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 39 0.98
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (22 bp):
ATATTATATAAATAGATATAAA
Found at i:13558292 original size:11 final size:11
Alignment explanation
Indices: 13558258--13558315 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
13558248 TATCTATTAT
13558258 ATATTATATAA
1 ATATTATATAA
*
13558269 ATAATA-ATAAA
1 ATATTATAT-AA
13558280 ATATTATATAA
1 ATATTATATAA
*
13558291 ATAGGTATA-AA
1 ATA-TTATATAA
13558302 ATATTATATAA
1 ATATTATATAA
13558313 ATA
1 ATA
13558316 GGTATAGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 6 0.15
11 27 0.69
12 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
ATATTATATAA
Found at i:13558299 original size:12 final size:12
Alignment explanation
Indices: 13558284--13558321 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
13558274 AATAAAATAT
13558284 TATATAAATAGG
1 TATATAAATAGG
*
13558296 TATA-AAATA-T
1 TATATAAATAGG
13558306 TATATAAATAGG
1 TATATAAATAGG
13558318 TATA
1 TATA
13558322 GGATTTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.18
11 10 0.45
12 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
TATATAAATAGG
Found at i:13559379 original size:2 final size:2
Alignment explanation
Indices: 13559372--13559396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13559362 TAATTCGAAC
13559372 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 A
13559397 AATTTGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13573129 original size:21 final size:22
Alignment explanation
Indices: 13573087--13573129 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
13573077 CCTATGCTTT
* **
13573087 TTTTCTTTTTATATTTCTAGAA
1 TTTTCTTTTTAGATTTAAAGAA
13573109 TTTT-TTTTTAGATTTAAAGAA
1 TTTTCTTTTTAGATTTAAAGAA
13573130 ATAGAAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTTCTTTTTAGATTTAAAGAA
Found at i:13573686 original size:16 final size:16
Alignment explanation
Indices: 13573661--13573697 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
13573651 AATTACCTAC
*
13573661 AAAATAATCTGAATTT
1 AAAATAATCTAAATTT
*
13573677 AAAATTATCTAAATTT
1 AAAATAATCTAAATTT
13573693 AAAAT
1 AAAAT
13573698 CATTCGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAATAATCTAAATTT
Found at i:13573743 original size:100 final size:101
Alignment explanation
Indices: 13573569--13573763 Score: 295
Period size: 100 Copynumber: 1.9 Consensus size: 101
13573559 TGAAACAATT
* *
13573569 TGAATTTAAAATGATCTAAGTCTAAAATCATTCCGATTTAAAATCATAAAAACTTGAACTTACTA
1 TGAATTTAAAATGATCTAAATCTAAAATCATTCCGATTCAAAATCATAAAAACTTGAACTTACTA
*
13573634 GTAAAAATGTAAACTTTAATTACCTACAAAATAATC
66 GTAAAAATGTAAAATTTAATTACCTACAAAATAATC
* * *
13573670 TGAATTTAAAATTATCTAAATTTAAAATCATT-CGATTCAAAATCATAAAAACTTTAACTTAAC-
1 TGAATTTAAAATGATCTAAATCTAAAATCATTCCGATTCAAAATCATAAAAACTTGAACTT-ACT
* *
13573733 ATTAAAAATGTAAAATTTAATTACTTACAAA
65 AGTAAAAATGTAAAATTTAATTACCTACAAA
13573764 GATTCATTCT
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 54 0.64
101 31 0.36
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.34
Consensus pattern (101 bp):
TGAATTTAAAATGATCTAAATCTAAAATCATTCCGATTCAAAATCATAAAAACTTGAACTTACTA
GTAAAAATGTAAAATTTAATTACCTACAAAATAATC
Found at i:13575184 original size:28 final size:28
Alignment explanation
Indices: 13575140--13575199 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
13575130 TGAAACGTCG
*
13575140 TTCTAGTTTTTTTCTTACTCTAAGTTTT
1 TTCTAGTTTTTTCCTTACTCTAAGTTTT
13575168 TTCTAGTTTTTTCCTTACTCTAAGTTTT
1 TTCTAGTTTTTTCCTTACTCTAAGTTTT
13575196 TTCT
1 TTCT
13575200 TTTCATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (28 bp):
TTCTAGTTTTTTCCTTACTCTAAGTTTT
Found at i:13576257 original size:29 final size:29
Alignment explanation
Indices: 13576198--13576283 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
13576188 TGAATAGGGG
* *
13576198 TTTCCTAAATCCATTCTTTATGAACATGGT
1 TTTCTTAATTCCATTCTTT-TGAACATGGT
* *
13576228 TTTCTTGATTTCATTCCTTTTGAACA-GGT
1 TTTCTTAATTCCATT-CTTTTGAACATGGT
*
13576257 TTTTTTAATTCCATTCTTTTGAGACAT
1 TTTCTTAATTCCATTCTTTTGA-ACAT
13576284 TTTATGGTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.15
29 18 0.39
30 17 0.37
31 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.50
Consensus pattern (29 bp):
TTTCTTAATTCCATTCTTTTGAACATGGT
Found at i:13578030 original size:37 final size:37
Alignment explanation
Indices: 13577969--13578054 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 37
13577959 TTGTAGCGTA
*
13577969 GGTCATAATCATAAACTTCTATTAA-CCTAGTGGCATG
1 GGTCATAATCATAAAC-TCTATTAATCCAAGTGGCATG
*
13578006 GGTCATAATCATAAAC-CATAATTAATTCAAGTGGCATG
1 GGTCATAATCATAAACTC-T-ATTAATCCAAGTGGCATG
*
13578044 GGTGATAATCA
1 GGTCATAATCA
13578055 CATTGAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 1 0.02
36 1 0.02
37 21 0.49
38 20 0.47
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (37 bp):
GGTCATAATCATAAACTCTATTAATCCAAGTGGCATG
Found at i:13582429 original size:14 final size:16
Alignment explanation
Indices: 13582395--13582444 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
13582385 TAAAATAAAA
13582395 TAATCATATTAATATTT
1 TAATCATA-TAATATTT
13582412 TAATCATA-AATA-TT
1 TAATCATATAATATTT
*
13582426 TAAT-ATTTTAATATTT
1 TAATCA-TATAATATTT
13582442 TAA
1 TAA
13582445 AGAATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 1 0.03
14 7 0.24
15 8 0.28
16 5 0.17
17 8 0.28
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATCATATAATATTT
Found at i:13583206 original size:21 final size:22
Alignment explanation
Indices: 13583177--13583220 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
13583167 GAGCAATTAA
13583177 TTTAAGTTATTTTAG-TTAAAT
1 TTTAAGTTATTTTAGTTTAAAT
*
13583198 TTTATGTTATTTTAGTTTAAAT
1 TTTAAGTTATTTTAGTTTAAAT
13583220 T
1 T
13583221 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTAGTTTAAAT
Found at i:13583913 original size:21 final size:21
Alignment explanation
Indices: 13583889--13583930 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13583879 ACCAACCTCG
*
13583889 AAAGCTGTCGAAGGTT-CTGGA
1 AAAGCTG-CGAAAGTTGCTGGA
*
13583910 AAAGGTGCGAAAGTTGCTGGA
1 AAAGCTGCGAAAGTTGCTGGA
13583931 CCAATTACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.12, G:0.36, T:0.21
Consensus pattern (21 bp):
AAAGCTGCGAAAGTTGCTGGA
Found at i:13584985 original size:51 final size:52
Alignment explanation
Indices: 13584926--13585035 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 52
13584916 AAAATATTAA
* * * * *
13584926 AGCA-TTTTAAGCATTTTGGAGTAGTTTTTGATATACGAA-GAAAACTTTTG
1 AGCATTTTTAAGCATTTTAGAATAATTTTTGATATACGAACAAAAAATTTTG
*
13584976 AGCATTTTTAAGCATTTTAGAATAATTTTTGATATATGAACAAAAAATTTTG
1 AGCATTTTTAAGCATTTTAGAATAATTTTTGATATACGAACAAAAAATTTTG
*
13585028 AACATTTT
1 AGCATTTT
13585036 GAGCATTCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 4 0.08
51 31 0.61
52 16 0.31
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (52 bp):
AGCATTTTTAAGCATTTTAGAATAATTTTTGATATACGAACAAAAAATTTTG
Found at i:13585041 original size:51 final size:50
Alignment explanation
Indices: 13584910--13585042 Score: 140
Period size: 51 Copynumber: 2.6 Consensus size: 50
13584900 TTCCTTACCA
* * * * *
13584910 GAAAGAAAAATATTAAAGCATTTTAAGCATTTTGGAGTAGTTTTTGATATAC
1 GAAA-AAAAATTTTGAA-CATTTTAAGCATTTTAGAATAATTTTTGATATAC
* * * *
13584962 GAAGAAAACTTTTGAGCATTTTTAAGCATTTTAGAATAATTTTTGATATAT
1 GAAAAAAAATTTTGAACA-TTTTAAGCATTTTAGAATAATTTTTGATATAC
*
13585013 GAACAAAAAATTTTGAACATTTTGAGCATT
1 GAA-AAAAAATTTTGAACATTTTAAGCATT
13585043 CTTTGTCAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
50 2 0.03
51 49 0.74
52 15 0.23
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (50 bp):
GAAAAAAAATTTTGAACATTTTAAGCATTTTAGAATAATTTTTGATATAC
Done.