Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008610.1 Hibiscus syriacus cultivar Beakdansim tig00111566_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2108335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1903751 original size:134 final size:133
Alignment explanation
Indices: 1903453--1904036 Score: 810
Period size: 134 Copynumber: 4.4 Consensus size: 133
1903443 GTCGTCCAAG
* * * * *
1903453 GGTGGATGACATGGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGG
1 GGTGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACAG
* * * * *
1903518 TTCCTACATGATGAGGACGGCTGGTATCTATGGTTGACACGGCTCCTATGTGATGAAGAGATCTG
66 TTCCTACATGATGAGGACGGCTGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTG
1903583 GTC
131 GTC
* * * *
1903586 GGTGGATAACACGGCTCATACGTGATGAAGAGTTTTGGCCATCTTTAGGAAGGGTGATAACTCAG
1 GGTGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACAG
* * *
1903651 TTCCTACGTGATGAGGACGGCTAGTTATCTATGGTTGACACGACTCCTACGTGATGAAGAGATCT
66 TTCCTACATGATGAGGACGGCT-GTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCT
1903716 GGTC
130 GGTC
* *
1903720 GGTGGATGACACAGCTCATACGTGATGAAGAGTTATGGCCATCTTTAGGAAGGGCGATAACACAG
1 GGTGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACAG
* * *
1903785 TTCCTACATGATGAGGACGGTTGATTATCTAGGGGTGACACGACTCCTACGCGATGAGGAGATCT
66 TTCCTACATGATGAGGACGGCTG-TTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCT
*
1903850 AGTC
130 GGTC
* * * *
1903854 GGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAAGAAGGGCGGTAACACGG
1 GGTGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACAG
* * ** *
1903919 TTCCTACGTGATGAGGATGTTTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCT
66 TTCCTACATGATGAGGACGGCT-GTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCT
1903984 GGTC
130 GGTC
* * *
1903988 AGG-AGATGACACGACTCATACGTGAGGAAGAGTTCTGGCCATCTTTAGG
1 -GGTGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGG
1904037 GATAATGATT
Statistics
Matches: 409, Mismatches: 38, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
133 82 0.20
134 324 0.79
135 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (133 bp):
GGTGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACAG
TTCCTACATGATGAGGACGGCTGTTATCTAGGGGTGACACGACTCCTACGTGATGAAGAGATCTG
GTC
Found at i:1904080 original size:29 final size:30
Alignment explanation
Indices: 1904037--1904098 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
1904027 CATCTTTAGG
*
1904037 GATAATGATTTCAAAAGAAACCGACTCAAA
1 GATAATGATTTCAAAAGAAACAGACTCAAA
*
1904067 GATAATG-TTTCAAAAGAAATAGACTCAAA
1 GATAATGATTTCAAAAGAAACAGACTCAAA
1904096 GAT
1 GAT
1904099 TGTAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.23
Consensus pattern (30 bp):
GATAATGATTTCAAAAGAAACAGACTCAAA
Found at i:1904382 original size:29 final size:30
Alignment explanation
Indices: 1904325--1904382 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1904315 ACAAAACTTT
1904325 GTTTCAAAAGAAACAAACTCAAAGATTTTA
1 GTTTCAAAAGAAACAAACTCAAAGATTTTA
**
1904355 GTTTCAAAAGAAA-TGACTCAAAGATTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTT
1904383 TCACGAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTA
Found at i:1904406 original size:90 final size:88
Alignment explanation
Indices: 1904259--1904471 Score: 268
Period size: 90 Copynumber: 2.3 Consensus size: 88
1904249 ATCCCAAAGA
1904259 TTTTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAATTGTTTCAAGAGAGACAAAACTT
1 TTTTTCAAAA-GAA-AGACTCAAAGA-TTTT-TCAAG-AAAATTGTTTCAAGAGAGACAAAACTT
* *
1904324 TGTTTCAAAAGAAACAAACTCAAAGATT
61 TGGTTCAAAAGAAACAAACTCAAAGAAT
*
1904352 TTAGTTTCAAAAGAAATGACTCAAAGATTTTTCACG-AAATTGTCTT-AAGAGAGACAAAACTTT
1 TT--TTTCAAAAGAAA-GACTCAAAGATTTTTCAAGAAAATTGT-TTCAAGAGAGACAAAACTTT
* *
1904415 GGTTCAAAAGAAACAGACTCAATGAAT
62 GGTTCAAAAGAAACAAACTCAAAGAAT
*
1904442 TTTTTCAAAAGAAACAACTCAAAGATTTTT
1 TTTTTCAAAAGAAA-GACTCAAAGATTTTT
1904472 ATTTAACTCA
Statistics
Matches: 109, Mismatches: 7, Indels: 13
0.84 0.05 0.10
Matches are distributed among these distances:
88 26 0.24
90 49 0.45
91 2 0.02
92 4 0.04
93 7 0.06
94 13 0.12
95 8 0.07
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (88 bp):
TTTTTCAAAAGAAAGACTCAAAGATTTTTCAAGAAAATTGTTTCAAGAGAGACAAAACTTTGGTT
CAAAAGAAACAAACTCAAAGAAT
Found at i:1904471 original size:27 final size:28
Alignment explanation
Indices: 1904417--1904471 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1904407 AAAACTTTGG
*
1904417 TTCAAAAGAAACAGACTCAATGAATTTT
1 TTCAAAAGAAACAGACTCAAAGAATTTT
1904445 TTCAAAAGAAACA-ACTCAAAG-ATTTT
1 TTCAAAAGAAACAGACTCAAAGAATTTT
1904471 T
1 T
1904472 ATTTAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 6 0.23
27 7 0.27
28 13 0.50
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (28 bp):
TTCAAAAGAAACAGACTCAAAGAATTTT
Found at i:1904557 original size:30 final size:32
Alignment explanation
Indices: 1904487--1904566 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 32
1904477 ACTCACAGAC
1904487 TTTTGTTTCAAGAGAAACAAACTCAAAGATAGG
1 TTTTGTTTCAAGAGAAACAAACTCAAAGATA-G
* *
1904520 TTTTGTTTCAAGGGAAACAATCTCAAAGAT-G
1 TTTTGTTTCAAGAGAAACAAACTCAAAGATAG
*
1904551 -TTTGTTTTAAGAGAAA
1 TTTTGTTTCAAGAGAAA
1904567 TTGTCTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 14 0.33
31 1 0.02
33 28 0.65
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (32 bp):
TTTTGTTTCAAGAGAAACAAACTCAAAGATAG
Found at i:1904658 original size:66 final size:64
Alignment explanation
Indices: 1904541--1904750 Score: 235
Period size: 66 Copynumber: 3.2 Consensus size: 64
1904531 GGGAAACAAT
* * * * **
1904541 CTCAAAGATGTTTGTTTTAAGAGAAATTGTCTCAAAAGAAACAAACCTTTGTTTTCATAAAAACA
1 CTCAAAGAT-TTT-TTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCA-AAAAACA
1904606 TA
63 TA
* * *
1904608 CTTAAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAAAAACAT
1 CTCAAAGATTTTT-TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTC-AAAAAACAT
1904673 A
64 A
* * * *
1904674 CTCAAATA-TTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAA-ATA
1 CTCAAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAA-AAACATA
1904737 CTCAAAGATTTTTT
1 CTCAAAGATTTTTT
1904751 CATTTTGTTT
Statistics
Matches: 121, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
63 13 0.11
64 44 0.36
65 4 0.03
66 51 0.42
67 9 0.07
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (64 bp):
CTCAAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAAAACATA
Found at i:1904707 original size:64 final size:63
Alignment explanation
Indices: 1904562--1904752 Score: 224
Period size: 64 Copynumber: 3.0 Consensus size: 63
1904552 TTGTTTTAAG
* ** * *
1904562 AGAAA-TTGTCTCAAAAGAAACAAACCTTTGTTTTCATAAAAACATACTTAAAGATTTTTCTTCA
1 AGAAACTT-TCTCAAAAGAGACAAAATTTTG-TTTCAAAAAAACATACTCAAAGA-TTTT-TTCA
1904626 AA
62 AA
* * * *
1904628 AGGAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAAAAACATACTCAAATATTCTTTCAAA
1 AGAAACTTTCTCAAAAGAGACAAAATTTTGTTT-CAAAAAAACATACTCAAAGATTTTTTCAAA
*
1904692 AGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAA-ATACTCAAAGATTTTTTCA
1 AGAAACTTTCTCAAAAGAGACAAAATTTTGTT-TCAAAAAAACATACTCAAAGATTTTTTCA
1904753 TTTTGTTTTA
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
63 17 0.16
64 43 0.40
65 7 0.06
66 40 0.37
67 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (63 bp):
AGAAACTTTCTCAAAAGAGACAAAATTTTGTTTCAAAAAAACATACTCAAAGATTTTTTCAAA
Found at i:1904756 original size:36 final size:37
Alignment explanation
Indices: 1904716--1904786 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1904706 AAGAGACAAA
*
1904716 ATTTTGTTATCAA-AGAAA-ATACTCAAAGATTTTTTC
1 ATTTTGTT-TCAAGAGAAACAGACTCAAAGATTTTTTC
* *
1904752 ATTTTGTTTTAAGTGAAACAGACTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACAGACTCAAAGATTTTT
1904787 CAAGAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 3 0.10
36 12 0.40
37 15 0.50
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (37 bp):
ATTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTC
Found at i:1904871 original size:30 final size:31
Alignment explanation
Indices: 1904817--1904875 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1904807 GAGACAAAGT
*
1904817 TTTGTTTAAAAATAAATAGACTCAAAGATCC
1 TTTGTTTAAAAAGAAATAGACTCAAAGATCC
* *
1904848 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTAAAAAGAAATAGACTCAAAGAT
1904876 GATGTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.31
Consensus pattern (31 bp):
TTTGTTTAAAAAGAAATAGACTCAAAGATCC
Found at i:1905005 original size:37 final size:36
Alignment explanation
Indices: 1904913--1905005 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
1904903 ATAATTAGGA
** * *
1904913 AAATTGTCTCAAGTAAGACAACATTTATTTTCAGAG
1 AAATTGTCTCAAGCGAGACAAAAATTATTTTCAGAG
* * *
1904949 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAAAAATTATTTTCAGAG
1904985 AAATTGATCTCAAGCGAGACA
1 AAATTG-TCTCAAGCGAGACA
1905006 GTTTGTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 35 0.73
37 13 0.27
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAAAAATTATTTTCAGAG
Found at i:1905021 original size:35 final size:36
Alignment explanation
Indices: 1904913--1905038 Score: 107
Period size: 35 Copynumber: 3.5 Consensus size: 36
1904903 ATAATTAGGA
** *
1904913 AAATTG-TCTCAAGTAAGACAACATT-TATTTTCAGAG
1 AAATTGATCTCAAGCGAGACAAAATTGT-TTTT-AGAG
*
1904949 AAATTG-TCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGATCTCAAGCGAGAC-AAAATTGTTTTTAGAG
** *
1904985 AAATTGATCTCAAGCGAGAC-AGTTTGTTTTTTGAG
1 AAATTGATCTCAAGCGAGACAAAATTGTTTTTAGAG
** *
1905020 AAAACGATCTCAAGTGAGA
1 AAATTGATCTCAAGCGAGA
1905039 TCAACTTTGT
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
35 28 0.37
36 26 0.34
37 21 0.28
38 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (36 bp):
AAATTGATCTCAAGCGAGACAAAATTGTTTTTAGAG
Found at i:1905142 original size:105 final size:104
Alignment explanation
Indices: 1905018--1905307 Score: 281
Period size: 105 Copynumber: 2.8 Consensus size: 104
1905008 TTGTTTTTTG
* *
1905018 AGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAATAAATTCGAAATTTGTATTCTCA
1 AGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTC-AAATTTGTATTCTCA
1905083 AAGGAAAAATGTCTCAAAAGAGAC-A-TAATTGTTTTGAA
65 AAGGAAAAATGTCTCAAAAGAGACAATTAATTGTTTTGAA
* * * * * *
1905121 AGAAATAACAATCTCAAGTGAGAT-AATTTTGTTTCAGGT-ACAACAAATTTAAGTTTTTATT-T
1 AG-AA-AACAATCTCAAGTGAGATCAACTTTGTTTAATGTGA-AACAAATTCAAATTTGTATTCT
* ** ** ***
1905183 CATA-GAAAAATGTCTCAAGTGAGACGAAGTTTGTTTGTTTTTTT
63 CAAAGGAAAAATGTCTCAAAAGAGAC-AA--TTAATTGTTTTGAA
* *
1905227 AGAAAGCGATCTCGAA-TGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTA-TCTC
1 AGAAAACAATCTC-AAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAA-TTTGTATTCTC
1905290 AAAGGAAAAATGTCTCAA
64 AAAGGAAAAATGTCTCAA
1905308 GTGAGATGAA
Statistics
Matches: 148, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
101 19 0.13
102 4 0.03
103 13 0.09
104 34 0.23
105 44 0.30
106 20 0.14
107 14 0.09
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (104 bp):
AGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTGTATTCTCAA
AGGAAAAATGTCTCAAAAGAGACAATTAATTGTTTTGAA
Found at i:1905385 original size:35 final size:34
Alignment explanation
Indices: 1905294--1905398 Score: 95
Period size: 36 Copynumber: 3.0 Consensus size: 34
1905284 TATCTCAAAG
** *
1905294 GAAAAATGTCTCAAGTGAGATGAAATTTATTTT-
1 GAAAAATGTCTCAAGTGAGACAAAATTTTTTTTA
* **
1905327 GAAAGAAATTATCTCAAACGAGACAAAATTTGTTTTTA
1 G-AA-AAA-TGTCTCAAGTGAGACAAAATTT-TTTTTA
*
1905365 GAAAACTGTCTCAAGTGAGACAAAAATTTTTTTT
1 GAAAAATGTCTCAAGTGAGAC-AAAATTTTTTTT
1905399 CAAAAGAAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
33 1 0.02
34 2 0.04
35 20 0.36
36 26 0.46
37 6 0.11
38 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (34 bp):
GAAAAATGTCTCAAGTGAGACAAAATTTTTTTTA
Found at i:1905740 original size:4 final size:4
Alignment explanation
Indices: 1905733--1906184 Score: 904
Period size: 4 Copynumber: 113.0 Consensus size: 4
1905723 TTTATATATA
1905733 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1905781 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1905829 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1905877 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1905925 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1905973 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1906021 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1906069 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1906117 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1906165 ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT
1906185 TTTTCTCGAT
Statistics
Matches: 448, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 448 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1912366 original size:3 final size:3
Alignment explanation
Indices: 1912358--1912398 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1912348 TACAAAAGTG
*
1912358 TAA TAA TAA TAT TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1912399 ATTAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1912383 original size:20 final size:20
Alignment explanation
Indices: 1912358--1912395 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1912348 TACAAAAGTG
*
1912358 TAATAATAATATTAATAAAA
1 TAATAATAATAATAATAAAA
1912378 TAATAATAATAATAATAA
1 TAATAATAATAATAATAA
1912396 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAATAATAATAATAATAAAA
Found at i:1912417 original size:23 final size:23
Alignment explanation
Indices: 1912358--1912408 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1912348 TACAAAAGTG
*
1912358 TAATAATAATATTAATAAAATAA
1 TAATAATAATAATAATAAAATAA
*
1912381 TAATAATAATAATAATAAATTAA
1 TAATAATAATAATAATAAAATAA
1912404 -AATAA
1 TAATAA
1912409 AATTAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAATAATAATAATAATAAAATAA
Found at i:1917392 original size:18 final size:18
Alignment explanation
Indices: 1917369--1917414 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1917359 ACCGGTCACA
*
1917369 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1917387 ACCCGACCCGATCCGTTG
1 ACCCGACCCGACCCGTTG
1917405 ACCCGACCCG
1 ACCCGACCCG
1917415 TTGACCGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1917394 original size:13 final size:13
Alignment explanation
Indices: 1917391--1917420 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1917381 CCGTTGACCC
*
1917391 GACCCGATCCGTT
1 GACCCGACCCGTT
1917404 GACCCGACCCGTT
1 GACCCGACCCGTT
1917417 GACC
1 GACC
1917421 GGCGTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1918278 original size:17 final size:18
Alignment explanation
Indices: 1918256--1918291 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1918246 TTTTACAGAC
1918256 ATATTGATCTG-ATAAAA
1 ATATTGATCTGCATAAAA
*
1918273 ATATTGATGTGCATAAAA
1 ATATTGATCTGCATAAAA
1918291 A
1 A
1918292 ATGTTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (18 bp):
ATATTGATCTGCATAAAA
Found at i:1919850 original size:24 final size:24
Alignment explanation
Indices: 1919823--1919938 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
1919813 TTCGATTTGA
1919823 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
1919847 ATTCTGATATGATA-TATGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
1919871 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * * *
1919895 ATTTTGATCTGTTACTTGACCT-G
1 ATTCTGATATGATACTTGACATGG
1919918 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
1919939 TTGAATTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1919955 original size:24 final size:24
Alignment explanation
Indices: 1919819--1919948 Score: 118
Period size: 24 Copynumber: 5.4 Consensus size: 24
1919809 GATTTTCGAT
*
1919819 TTGAATTCTGATATGATACTTGAC
1 TTGAATTATGATATGATACTTGAC
* * *
1919843 ATGGATTCTGATATGATA-TATGAC
1 TTGAATTATGATATGATACT-TGAC
* * *
1919867 ATGGATTCTGATATGATACTTGAC
1 TTGAATTATGATATGATACTTGAC
* * * *
1919891 TTGGATTTTGATCTGTTACTTGAC
1 TTGAATTATGATATGATACTTGAC
* * *
1919915 CTGATTTCTGATATGATACTTGAC
1 TTGAATTATGATATGATACTTGAC
1919939 TTGAATTATG
1 TTGAATTATG
1919949 TTTTGATTTT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
23 1 0.01
24 87 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (24 bp):
TTGAATTATGATATGATACTTGAC
Found at i:1928999 original size:29 final size:29
Alignment explanation
Indices: 1928922--1929002 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
1928912 AGTGTTGGCC
* * *
1928922 GTAGGTCGTCATGCCTTCCAGGCGACCTT
1 GTAGGTCGCCATGCCTTCCGGGCAACCTT
1928951 GTAGGTCGCCATGCCTTCCGGGCAACCTT
1 GTAGGTCGCCATGCCTTCCGGGCAACCTT
1928980 GTAGGTCGCCATGCAC-TCCGGGC
1 GTAGGTCGCCATGC-CTTCCGGGC
1929003 GATCTACCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
29 47 0.98
30 1 0.02
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGCCTTCCGGGCAACCTT
Found at i:1929104 original size:33 final size:33
Alignment explanation
Indices: 1929067--1929136 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1929057 ATGTAGGTCA
*
1929067 CTCGGATGCCCTCACATAGCTCGCTTGGCTGCC
1 CTCGGATGCCCTCACATAGCTCGCTTGGCTACC
* *
1929100 CTCGGATTCCCTCGCATAGCTCGCTTGGCTACC
1 CTCGGATGCCCTCACATAGCTCGCTTGGCTACC
1929133 CTCG
1 CTCG
1929137 CATAGCTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.40, G:0.23, T:0.26
Consensus pattern (33 bp):
CTCGGATGCCCTCACATAGCTCGCTTGGCTACC
Found at i:1929188 original size:33 final size:33
Alignment explanation
Indices: 1929133--1929195 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1929123 CTTGGCTACC
* *
1929133 CTCGCATAGCTCGTTCGGATGGCCTCGGATACT
1 CTCGCATAGCTCGGTCGAATGGCCTCGGATACT
*
1929166 CTCGCATATCTCGGTCGAATGGCCTCGGAT
1 CTCGCATAGCTCGGTCGAATGGCCTCGGAT
1929196 GCCCAGCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (33 bp):
CTCGCATAGCTCGGTCGAATGGCCTCGGATACT
Found at i:1931328 original size:23 final size:23
Alignment explanation
Indices: 1931302--1931349 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1931292 ATAAAGTACA
*
1931302 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1931325 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1931348 AT
1 AT
1931350 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1931865 original size:23 final size:23
Alignment explanation
Indices: 1931839--1931899 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1931829 ATAACCACTG
1931839 CCTATTACATTATATAAACGATA
1 CCTATTACATTATATAAACGATA
* *
1931862 CCTATTACATTATATAAGCGCTA
1 CCTATTACATTATATAAACGATA
*
1931885 CCTATTACATCATAT
1 CCTATTACATTATAT
1931900 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
CCTATTACATTATATAAACGATA
Found at i:1932290 original size:23 final size:23
Alignment explanation
Indices: 1932253--1932325 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
1932243 ATACTTTACA
* *
1932253 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
1932276 ATATAAACGAC-ACCTATTACATT
1 ATATAAACG-CTACCTATTACATT
* *
1932299 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1932322 ATAT
1 ATAT
1932326 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 42 0.95
24 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1932689 original size:431 final size:430
Alignment explanation
Indices: 1931661--1933473 Score: 3424
Period size: 431 Copynumber: 4.2 Consensus size: 430
1931651 ATGTTTATTG
1931661 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1931726 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
1931791 TATATACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTGCCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
1931856 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1931921 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
1931986 TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
326 TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
1932051 TATTTGATTGTTTTGATATTTTAT-AAATAATATTTAGAA
391 TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
1932090 TTTTTAA-TT--TAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
*
1932152 AAATTAATATCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1932217 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
1932282 ACGACACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
* *
1932347 TGTTCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTCATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TT
1932412 TTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
325 TTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
1932477 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
390 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
*
1932518 TTTTTTATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1932583 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1932648 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
* *
1932713 ACGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATTTTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1932778 TGTCCATACTTTTTATAAAAAGGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTCT-TTTAAAGTTATGTAATTTATGTTTCAA-T
* * *
1932842 TTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACTCAATAA
324 TTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
1932907 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
389 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
*
1932949 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACACCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1933014 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1933078 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
1933143 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1933208 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
1933273 TTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
326 TTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
1933337 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
390 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
1933378 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1933443 AAATTAATATCTTAAAACTCACTCAAAAGAT
66 AAATTAATATCTTAAAACTCACTCAAAAGAT
1933474 GTATATACCT
Statistics
Matches: 1352, Mismatches: 24, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
426 304 0.22
427 92 0.07
428 25 0.02
429 206 0.15
430 195 0.14
431 530 0.39
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (430 bp):
TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
Found at i:1932724 original size:23 final size:23
Alignment explanation
Indices: 1932698--1932756 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1932688 AACCACTACC
1932698 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
1932721 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
1932744 TATTACATCATAT
1 TATTACATTATAT
1932757 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:1933150 original size:23 final size:23
Alignment explanation
Indices: 1933124--1933186 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1933114 ATATAACCAC
1933124 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1933147 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1933170 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1933187 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1933393 original size:857 final size:857
Alignment explanation
Indices: 1931661--1933473 Score: 3386
Period size: 857 Copynumber: 2.1 Consensus size: 857
1931651 ATGTTTATTG
1931661 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTT-ATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1931726 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
65 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
1931791 TATATACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTGCCTATTACATTATATAA
130 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
1931856 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
195 ACGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1931921 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
260 TGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
*
1931986 TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
325 TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
1932051 TATTTGATTGTTTTGATATTTTATAAATAATATTTAGAATTTTTAATTTAATAATATATATCGTA
390 TATTTGATTGTTTTGATATTTTATAAATAATATTTAGAATTTTTAATTTAATAATATATATCGTA
* *
1932116 ACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAT
455 ACGTAAAAAAGAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAG
1932181 ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATA
520 ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATA
1932246 CTTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACATTATATAAGCGCTA
585 CTTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACATTATATAAGCGCTA
*
1932311 CCTATTACATCATATTTTTACCTATTATATTGAAAGTGTTCATACTTTTTATAAAAAGGATCGAT
650 CCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGAT
*
1932376 ACTTCTTTTAAAGTTATGTCATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCT
715 ACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCT
1932441 ACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAA
780 ACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAA
1932506 TAATATTTAGAAT
845 TAATATTTAGAAT
1932519 TTTTT-ATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTT-ATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1932583 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
65 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1932648 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
130 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
1932713 ACGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATTTTGAAAG
195 ACGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1932778 TGTCCATACTTTTTATAAAAAGGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATT
260 TGTCCATACTTTTTATAAAAAGGATCGATACTTCT-TTTAAAGTTATGTAATTTATGTTTCAA-T
* *
1932842 TTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACTCAATAA
323 TTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
1932907 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATAT
388 ATTATTTGATTGTTTTGATATTTTAT-AAATAATATTTAGAATTTTTAA-TT--TAATAATATAT
1932972 ATCGTAACGTAAAAAAGAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACT
449 ATCGTAACGTAAAAAAGAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACT
1933037 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATAGACACTTTTATAAAAAGGA
514 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGA
*
1933101 TAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
579 TAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACATTATATAA
1933166 GCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGG
644 GCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGG
1933231 ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAA-TAGTGTTTCATGTTT
709 ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAAGTA-TGTTTCATGTTT
1933294 TCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTT
773 TCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTT
1933359 TATAAAATAATATTTAGAA-
838 TATAAAATAATATTTAGAAT
1933378 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTT-ATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1933443 AAATTAATATCTTAAAACTCACTCAAAAGAT
65 AAATTAATATCTTAAAACTCACTCAAAAGAT
1933474 GTATATACCT
Statistics
Matches: 935, Mismatches: 12, Indels: 14
0.97 0.01 0.01
Matches are distributed among these distances:
856 1 0.00
857 310 0.33
858 94 0.10
859 29 0.03
860 197 0.21
861 195 0.21
862 109 0.12
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (857 bp):
TTTTTAATTTATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTA
AATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGT
ATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAA
CGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGT
GTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
TTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAATAATATTTAGAATTTTTAATTTAATAATATATATCGTAA
CGTAAAAAAGAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATAC
TTTACAATATAACCACTACCTATTACATTATATAAACGACACCTATTACATTATATAAGCGCTAC
CTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
CTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTA
CAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAAT
AATATTTAGAAT
Found at i:1933501 original size:25 final size:25
Alignment explanation
Indices: 1933473--1933537 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
1933463 ACTCAAAAGA
*
1933473 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
1933498 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
1933523 TGTACATACCTAAAT
1 TGTACATACCTAAAT
1933538 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:1936545 original size:23 final size:23
Alignment explanation
Indices: 1936519--1936581 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1936509 ATATAACCAG
1936519 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1936542 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1936565 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1936582 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1936969 original size:16 final size:16
Alignment explanation
Indices: 1936944--1936977 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1936934 ATCTATTACA
*
1936944 TTTTTCAATCGACACT
1 TTTTTAAATCGACACT
1936960 TTTTTAAATCGACACT
1 TTTTTAAATCGACACT
1936976 TT
1 TT
1936978 GTTGTGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTTTAAATCGACACT
Found at i:1938178 original size:3 final size:3
Alignment explanation
Indices: 1938170--1938244 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
1938160 ACTTGTTTGG
* * * * *
1938170 ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1938218 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1938245 GTCAGCTTCA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1938227 original size:36 final size:36
Alignment explanation
Indices: 1938180--1938261 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
1938170 ATCATCATCA
*
1938180 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
1938216 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
*
1938252 TCATCTTCAT
1 TCATCATCAT
1938262 TGACCGCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.38
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:1938245 original size:12 final size:12
Alignment explanation
Indices: 1938174--1938261 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
1938164 GTTTGGATCA
* *
1938174 TCATCATCATCA
1 TCATCTTCATCG
* * *
1938186 TCATCATCGTCA
1 TCATCTTCATCG
1938198 TCATCTTCATCG
1 TCATCTTCATCG
*
1938210 TCAGCTTCATCG
1 TCATCTTCATCG
*
1938222 TCATCATCATCG
1 TCATCTTCATCG
1938234 TCATCTTCATCG
1 TCATCTTCATCG
* *
1938246 TCAGCTTCATCT
1 TCATCTTCATCG
1938258 TCAT
1 TCAT
1938262 TGACCGCTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1938270 original size:18 final size:18
Alignment explanation
Indices: 1938198--1938261 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
1938188 ATCATCGTCA
*
1938198 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
* * *
1938216 TCATCGTCATC-ATCATCG
1 TCATCTTCATCGA-CAGCT
*
1938234 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
1938252 TCATCTTCAT
1 TCATCTTCAT
1938262 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGACAGCT
Found at i:1940422 original size:199 final size:199
Alignment explanation
Indices: 1939739--1940883 Score: 2040
Period size: 199 Copynumber: 5.7 Consensus size: 199
1939729 CACAAACGAA
1939739 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
* *
1939804 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATTGCCACTTTTTATATATGGATCGACACT
66 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
* *
1939869 TTATGGTTGCACCCTGTTTTCCATTAATTCTGGACCAAAAATATCGACACAAACTAAACAAGTGT
131 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
1939934 CGAC
196 CGAC
1939938 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
*
1940003 TATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCAACAC
66 TATTACATTATACTTTTGGG-TTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACAC
* * * * *
1940068 CTTATGGTTGCACACTGTTTTCCATTCATTCTGGACTAAAAATATCGACACAAAATAAAAAAAGT
130 TTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACAC-AAATTAAACAAGT
* *
1940133 GCCGAT
194 GTCGAC
*
1940139 ACATTATTTAGACATATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1940204 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
66 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
**
1940269 TTATGGTTGCACCCTGTTGGCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
131 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
1940334 CGAC
196 CGAC
1940338 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
*
1940403 TATTACATTATAATTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
66 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
*
1940468 TTATGGTTGCA-CCTGTTTTCCATTAATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
131 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
1940532 CGAC
196 CGAC
*
1940536 ACATTATTTAGACATATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
*
1940601 TATTACATTATACTTTTGGGTTTGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
66 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
*
1940666 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCAACACAAATTAAACAAGTGT
131 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
1940731 CGAC
196 CGAC
* *
1940735 ATATTATTTAGACATATTCTATCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
* *
1940800 TATTACATTATACTTTTGGGTTTCAATGTTTTTGGGATCGACACTTTTTATATATGGTTCGACAC
66 TATTACATTATACTTTTGGG-TTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACAC
1940865 TTTATGGTTGCACCCTGTT
130 TTTATGGTTGCACCCTGTT
1940884 GGCCATATTG
Statistics
Matches: 903, Mismatches: 39, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
198 192 0.21
199 376 0.42
200 237 0.26
201 98 0.11
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (199 bp):
ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
CGAC
Found at i:1940692 original size:397 final size:398
Alignment explanation
Indices: 1939739--1940883 Score: 2042
Period size: 397 Copynumber: 2.9 Consensus size: 398
1939729 CACAAACGAA
1939739 ACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAA-CGGTATACTTGTACCGGTTAGATTGAAAAATTACA
* *
1939804 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATTGCCACTTTTTATATATGGATCGACACT
65 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
* *
1939869 TTATGGTTGCACCCTGTTTTCCATTAATTCTGGACCAAAAATATCGACACAAACTAAACAAGTGT
130 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
1939934 CGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
195 CGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
*
1939999 TACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCA
260 TACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCG
* * *
1940064 ACACCTTATGGTTGCACACTGTTTTCCATTCATTCTGGACTAAAAATATCGACACAAAATAAAAA
325 ACACTTTATGGTTGCAC-CTGTTTTCCATTAATTCTGGACCAAAAATATCGACACAAAATAAAAA
*
1940129 AAGTGCCGAT
389 AAGTGCCGAC
1940139 ACATTATTTAGACATATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAAC-GGTATACTTGTACCGGTTAGATTGAAAAATTACA
1940204 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
65 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
**
1940269 TTATGGTTGCACCCTGTTGGCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
130 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
1940334 CGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
195 CGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
*
1940399 TACATATTACATTATAATTTTGGG-TTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCG
260 TACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCG
* *
1940463 ACACTTTATGGTTGCACCTGTTTTCCATTAATTCTGGACCAAAAATATCGACAC-AAATTAAACA
325 ACACTTTATGGTTGCACCTGTTTTCCATTAATTCTGGACCAAAAATATCGACACAAAATAAAAAA
*
1940527 AGTGTCGAC
390 AGTGCCGAC
1940536 ACATTATTTAGACATATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTACA
1 ACATTATTTAGACATATTCTCTCATAAAA-CGGTATACTTGTACCGGTTAGATTGAAAAATTACA
*
1940601 TATTACATTATACTTTTGGGTTTGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
65 TATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACT
*
1940666 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCAACACAAATTAAACAAGTGT
130 TTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGT
* *
1940731 CGACATATTATTTAGACATATTCTATCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
195 CGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAAT
* *
1940796 TACATATTACATTATACTTTTGGGTTTCAATGTTTTTGGGATCGACACTTTTTATATATGGTTCG
260 TACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCG
1940861 ACACTTTATGGTTGCACCCTGTT
325 ACACTTTATGGTTGCA-CCTGTT
1940884 GGCCATATTG
Statistics
Matches: 717, Mismatches: 24, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
397 290 0.40
398 90 0.13
399 62 0.09
400 275 0.38
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (398 bp):
ACATTATTTAGACATATTCTCTCATAAAACGGTATACTTGTACCGGTTAGATTGAAAAATTACAT
ATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACACTT
TATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAATTAAACAAGTGTC
GACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATT
ACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGA
CACTTTATGGTTGCACCTGTTTTCCATTAATTCTGGACCAAAAATATCGACACAAAATAAAAAAA
GTGCCGAC
Found at i:1941048 original size:19 final size:19
Alignment explanation
Indices: 1941002--1941050 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1940992 TTATATTCAC
*
1941002 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1941021 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1941040 ATACAAAATTA
1 ATACAAAATTA
1941051 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1942878 original size:33 final size:33
Alignment explanation
Indices: 1942841--1942906 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1942831 CATCTTAATA
* *
1942841 TCACCCCTTAACACCCCAACTTTTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1942874 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1942907 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1942965 original size:21 final size:21
Alignment explanation
Indices: 1942940--1942983 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1942930 CCCCTTATGC
1942940 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
1942961 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
1942982 CT
1 CT
1942984 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:1945046 original size:24 final size:24
Alignment explanation
Indices: 1945009--1945061 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1944999 CTGTTCTATC
1945009 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1945033 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1945057 TATTT
1 TATTT
1945062 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1945223 original size:17 final size:18
Alignment explanation
Indices: 1945201--1945243 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1945191 ATATATCCGG
1945201 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1945218 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1945238 TATCAT
1 TATCAT
1945244 ATTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1945433 original size:20 final size:19
Alignment explanation
Indices: 1945387--1945433 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1945377 TCCGGTAACC
*
1945387 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
1945406 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
1945427 TTTTACC
1 TTTTACC
1945434 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:1945477 original size:181 final size:183
Alignment explanation
Indices: 1945173--1945646 Score: 677
Period size: 181 Copynumber: 2.6 Consensus size: 183
1945163 CGTACTTACG
* *
1945173 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCCTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1945238 TATCATATTTTTACTTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACATGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
* *
1945303 AGGCGCTAAAACTGTTTCTC-TTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
1945354 AAAGTATCGACACTTTTAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCCTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1945419 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACATGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
** *
1945484 AGGATTTAAAACTGCTTCTCTTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * *
1945537 AAAGTACCGACACTTTAAATGTATCCGGTAGTGC-TTTACCGGTTTTATCATTTAT-ATATCGGT
1 AAAGTATCGACACTTTAAATATATCCGGTA-TCCTTTTACCGGTTTTATCATTT-TGATACCGGT
* * * * *
1945600 TTTGTCATAGTTTTACATGTTATATCATTTTGGATCGACACATTTTT
64 TTTATCATATTTTTACATGTTATATCGTTTTGGATCGATATATTTTT
1945647 AATTTGGATC
Statistics
Matches: 261, Mismatches: 28, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
181 137 0.52
182 29 0.11
183 93 0.36
184 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (183 bp):
AAAGTATCGACACTTTAAATATATCCGGTATCCTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACATGTTATATCGTTTTGGATCGATATATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:1951369 original size:90 final size:89
Alignment explanation
Indices: 1951216--1951390 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 89
1951206 CCTAACACAC
** * *
1951216 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTATTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAACCATATCAGGGTTATTATTATTTCAAATTAATTAAATCTAT
*
1951281 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
*
1951306 CCTTTTATATCCAAGTTACCCTAACCATATCAGGGATT-TTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAACCATATCAGGG-TTATTATTATTTCAAATTAATTAAATCTA
1951370 TATTTAATTAATTGAAATTAA
65 TATTTAATTAATTGAAATTAA
1951391 ATATTCGGGA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 7 0.09
90 69 0.88
91 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAACCATATCAGGGTTATTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:1958243 original size:90 final size:89
Alignment explanation
Indices: 1958090--1958264 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
1958080 CCTAACACAC
* * *
1958090 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
1958155 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
* *
1958180 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCGAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1958245 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
1958265 ATATTCGGGG
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:1960166 original size:13 final size:13
Alignment explanation
Indices: 1960148--1960173 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1960138 ATAGTTGAAT
1960148 AGTCTTCATATGC
1 AGTCTTCATATGC
1960161 AGTCTTCATATGC
1 AGTCTTCATATGC
1960174 GCGTCTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
AGTCTTCATATGC
Found at i:1962198 original size:6 final size:6
Alignment explanation
Indices: 1962187--1962213 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1962177 TGCTAGGCTG
1962187 CAGCCT CAGCCT CAGCCT CAGCCT CAG
1 CAGCCT CAGCCT CAGCCT CAGCCT CAG
1962214 GTTTACAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.15
Consensus pattern (6 bp):
CAGCCT
Found at i:1964750 original size:22 final size:24
Alignment explanation
Indices: 1964724--1964776 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1964714 TTTGTGTTAG
* *
1964724 GAAGAT-GAATTTCTAAAATTTTA
1 GAAGATCGAACTTATAAAATTTTA
1964747 -AAGAATCGAACTTATAAAATTTTA
1 GAAG-ATCGAACTTATAAAATTTTA
1964771 GAAGAT
1 GAAGAT
1964777 AAAAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 2 0.08
24 17 0.68
25 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (24 bp):
GAAGATCGAACTTATAAAATTTTA
Found at i:1972588 original size:20 final size:20
Alignment explanation
Indices: 1972565--1972602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1972555 AATCAATATT
*
1972565 AATAAAAATAAAATAATTTG
1 AATAAAAATAAAACAATTTG
*
1972585 AATAAAACTAAAACAATT
1 AATAAAAATAAAACAATT
1972603 ATATATATAT
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:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAAAAATAAAACAATTTG
Found at i:1974075 original size:3 final size:3
Alignment explanation
Indices: 1974067--1974108 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1974057 ATTCGGGCCT
*
1974067 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1974109 AAACGGGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1974722 original size:177 final size:176
Alignment explanation
Indices: 1974426--1974965 Score: 846
Period size: 177 Copynumber: 3.1 Consensus size: 176
1974416 TAAATTGTTT
* *
1974426 TTTGAAAACATCCTACACTGAAGGTCTTCTGGATGGCACGTAGGACTTACAAATCAAGAAACCCC
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCACGTAGGACTTACAAATCAAGAAACCCC
* * * * * *
1974491 CGAAGACTTAGTTTCTTAGTTATCAAGGAACCCATTTGTTAGTCTTAGCTTCCTTTAACAGCTCT
66 CGAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCT
* * *
1974556 TTTGAGATAATTACTAAACCCCCGAAAACTTGGTTTCTAAAATCTCA
131 TTTGAGATAATTAGTAAACCCCTGAAGA-TTGGTTTCTAAAATCTCA
* * *
1974603 TTTGAAAACATCCTGCATTGAAGGTCTTATGGATGCCCCGTAGGACTTACAAATCAAGAAACCCC
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCACGTAGGACTTACAAATCAAGAAACCCC
*
1974668 CGAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTTT
66 CGAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCT
*
1974733 TTTGAGATAATTGGTAAACCCCTGAAGGATTGGTTTCTAAAATCTCA
131 TTTGAGATAATTAGTAAACCCCTGAA-GATTGGTTTCTAAAATCTCA
* * * *
1974780 TTTGAAAATATCCTGAACTAAAGGTCTTATGGATGGCTCGTAGGACTTACAAATCAAGAAACCCC
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCACGTAGGACTTACAAATCAAGAAACCCC
*
1974845 CGAAGGCTTGGTTTCTTAGTTGTTAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCT
66 CGAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCT
* *
1974910 TTTGAGATAATTTGTAAACCCCTGAAGGTTTGGTTTCTAAAATCTCA
131 TTTGAGATAATTAGTAAACCCCTGAA-GATTGGTTTCTAAAATCTCA
1974957 TTTGAAAAC
1 TTTGAAAAC
1974966 CTGTAAAACT
Statistics
Matches: 335, Mismatches: 27, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
177 334 1.00
178 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (176 bp):
TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCACGTAGGACTTACAAATCAAGAAACCCC
CGAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCT
TTTGAGATAATTAGTAAACCCCTGAAGATTGGTTTCTAAAATCTCA
Found at i:1975342 original size:22 final size:22
Alignment explanation
Indices: 1975332--1975442 Score: 197
Period size: 22 Copynumber: 5.0 Consensus size: 22
1975322 TGTGAAAAGA
1975332 GAATCTATCATCTTTGAAGAGA-
1 GAATCTATCATCTTTGAAGA-AT
1975354 GAATCTATCATCTTTGAAGAAT
1 GAATCTATCATCTTTGAAGAAT
1975376 GAATCTATCATCTTTGAAGAAT
1 GAATCTATCATCTTTGAAGAAT
*
1975398 GAATTTATCATCTTTGAAGAAT
1 GAATCTATCATCTTTGAAGAAT
1975420 GAATCTATCATCTTTGAAGAAT
1 GAATCTATCATCTTTGAAGAAT
1975442 G
1 G
1975443 TAGATGTAGA
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
21 1 0.01
22 85 0.99
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
GAATCTATCATCTTTGAAGAAT
Found at i:1975891 original size:54 final size:54
Alignment explanation
Indices: 1975801--1976017 Score: 299
Period size: 54 Copynumber: 4.0 Consensus size: 54
1975791 CATAATCACT
* * * * *
1975801 TGTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCACAGA
1 TGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTACCCAGA
* * * *
1975855 TGTTTGTAAATCATTTGACAACACATTCATCCTTTCTTGTGGCCTCTACCCAGA
1 TGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTACCCAGA
* * *
1975909 TGTTCGTAAAACATTTTACAATACATTCATCCTTTCCTATGGCTTCTACCCAGA
1 TGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTACCCAGA
* * *
1975963 TGTTCGTAAAACATTTGACAATACATTCATCCTTTCCTGTGGGTTTTACCCAGA
1 TGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTACCCAGA
1976017 T
1 T
1976018 TTCTCAATCA
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 145 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (54 bp):
TGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTACCCAGA
Found at i:1977473 original size:90 final size:90
Alignment explanation
Indices: 1977318--1977482 Score: 249
Period size: 90 Copynumber: 1.8 Consensus size: 90
1977308 CATTTGAAAC
* * **
1977318 TTATCCATAAAGCCGGGGCGATTAACCAATTGCTCTAGAGTGACAACTCAATTTTTATTGCATAT
1 TTATCCATAAAGCCGGGGCGATTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGCATAT
*
1977383 AATAGTATAACATGCTAGCTTAATA
66 AATAATATAACATGCTAGCTTAATA
* * * *
1977408 TTATCCATAAAGCCGGGGCGATTAACCAATTACTTTAGGGGGATAACTCAAGCTTTATTGTATAT
1 TTATCCATAAAGCCGGGGCGATTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGCATAT
1977473 AATAATATAA
66 AATAATATAA
1977483 TATGAGTATA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 66 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (90 bp):
TTATCCATAAAGCCGGGGCGATTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGCATAT
AATAATATAACATGCTAGCTTAATA
Found at i:1981032 original size:32 final size:32
Alignment explanation
Indices: 1980982--1981150 Score: 187
Period size: 32 Copynumber: 5.3 Consensus size: 32
1980972 GTGTATGGGT
* * * *
1980982 CACAATAGTATCAGTATTGCATCCAGATACTG
1 CACAATAGAATCAATATTGCATTCAGATAATG
* * *
1981014 CACAGTAGAATCAATATTGTATTAAGATAATG
1 CACAATAGAATCAATATTGCATTCAGATAATG
1981046 CACAATAGAATCAATATTGCATTCAGATAATG
1 CACAATAGAATCAATATTGCATTCAGATAATG
* * * *
1981078 CACAGTAGAATAAATATTACATTCAAATAATG
1 CACAATAGAATCAATATTGCATTCAGATAATG
* * *
1981110 CACAATAGAGTTAGTA-TGTCATTCAGATAATG
1 CACAATAGAATCAATATTG-CATTCAGATAATG
*
1981142 CACAGTAGA
1 CACAATAGA
1981151 GTCAGTATCA
Statistics
Matches: 115, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
31 1 0.01
32 114 0.99
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (32 bp):
CACAATAGAATCAATATTGCATTCAGATAATG
Found at i:1981083 original size:64 final size:64
Alignment explanation
Indices: 1980982--1981150 Score: 225
Period size: 64 Copynumber: 2.6 Consensus size: 64
1980972 GTGTATGGGT
* * * * **
1980982 CACAATAGTATCAGTATTGCATCCAGATACTGCACAGTAGAATCAATATTGTATT-AAGATAATG
1 CACAATAGAATCAGTATTGCATTCAGATAATGCACAGTAGAATAAATATTACATTCAA-ATAATG
*
1981046 CACAATAGAATCAATATTGCATTCAGATAATGCACAGTAGAATAAATATTACATTCAAATAATG
1 CACAATAGAATCAGTATTGCATTCAGATAATGCACAGTAGAATAAATATTACATTCAAATAATG
* *
1981110 CACAATAGAGTTAGTA-TGTCATTCAGATAATGCACAGTAGA
1 CACAATAGAATCAGTATTG-CATTCAGATAATGCACAGTAGA
1981151 GTCAGTATCA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 2 0.02
64 89 0.96
65 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (64 bp):
CACAATAGAATCAGTATTGCATTCAGATAATGCACAGTAGAATAAATATTACATTCAAATAATG
Found at i:1981151 original size:32 final size:32
Alignment explanation
Indices: 1980982--1981173 Score: 172
Period size: 32 Copynumber: 6.0 Consensus size: 32
1980972 GTGTATGGGT
* * * * * *
1980982 CACAATAGTATCAGTATTGCATCCAGATACTG
1 CACAGTAGAATCAATATTACATTCAGATAATG
** *
1981014 CACAGTAGAATCAATATTGTATTAAGATAATG
1 CACAGTAGAATCAATATTACATTCAGATAATG
* *
1981046 CACAATAGAATCAATATTGCATTCAGATAATG
1 CACAGTAGAATCAATATTACATTCAGATAATG
* *
1981078 CACAGTAGAATAAATATTACATTCAAATAATG
1 CACAGTAGAATCAATATTACATTCAGATAATG
* * * *
1981110 CACAATAGAGTTAGTATGT-CATTCAGATAATG
1 CACAGTAGAATCAATAT-TACATTCAGATAATG
* * *
1981142 CACAGTAGAGTCAGTATCACATAT-AGATAATG
1 CACAGTAGAATCAATATTACAT-TCAGATAATG
1981174 TCTAGCAGAT
Statistics
Matches: 135, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
32 133 0.99
33 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (32 bp):
CACAGTAGAATCAATATTACATTCAGATAATG
Found at i:1981172 original size:64 final size:64
Alignment explanation
Indices: 1980982--1981173 Score: 199
Period size: 64 Copynumber: 3.0 Consensus size: 64
1980972 GTGTATGGGT
* * * * * *** *
1980982 CACAATAGTATCAGTATTGCATCCAGATACTGCACAGTAGAATCAATATTGTATTAAGATAATG
1 CACAATAGAATCAATATTGCATTCAGATAATGCACAGTAGAATAAATATCACATTCAGATAATG
* *
1981046 CACAATAGAATCAATATTGCATTCAGATAATGCACAGTAGAATAAATATTACATTCAAATAATG
1 CACAATAGAATCAATATTGCATTCAGATAATGCACAGTAGAATAAATATCACATTCAGATAATG
* * * * * *
1981110 CACAATAGAGTTAGTA-TGTCATTCAGATAATGCACAGTAGAGTCAGTATCACATAT-AGATAAT
1 CACAATAGAATCAATATTG-CATTCAGATAATGCACAGTAGAATAAATATCACAT-TCAGATAAT
1981173 G
64 G
1981174 TCTAGCAGAT
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
63 2 0.02
64 106 0.97
65 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (64 bp):
CACAATAGAATCAATATTGCATTCAGATAATGCACAGTAGAATAAATATCACATTCAGATAATG
Found at i:1982049 original size:13 final size:13
Alignment explanation
Indices: 1982031--1982056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1982021 TGTATACATC
1982031 TATCCATTTTATA
1 TATCCATTTTATA
1982044 TATCCATTTTATA
1 TATCCATTTTATA
1982057 CATACATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TATCCATTTTATA
Found at i:1982472 original size:8 final size:8
Alignment explanation
Indices: 1982055--1982469 Score: 506
Period size: 8 Copynumber: 51.9 Consensus size: 8
1982045 ATCCATTTTA
*
1982055 TACATACA
1 TACATACG
*
1982063 TACATACA
1 TACATACG
*
1982071 TACATACA
1 TACATACG
*
1982079 TACATACA
1 TACATACG
*
1982087 TACATACA
1 TACATACG
*
1982095 TACATACA
1 TACATACG
*
1982103 TACATACA
1 TACATACG
*
1982111 TACATACA
1 TACATACG
1982119 TACATACG
1 TACATACG
1982127 TACATACG
1 TACATACG
1982135 TACATACG
1 TACATACG
1982143 TACATACG
1 TACATACG
1982151 TACATACG
1 TACATACG
1982159 TACATACG
1 TACATACG
1982167 TACATACG
1 TACATACG
1982175 TACATACG
1 TACATACG
*
1982183 TTCATACG
1 TACATACG
*
1982191 TTCATACG
1 TACATACG
*
1982199 TTCATACG
1 TACATACG
*
1982207 TTCATACG
1 TACATACG
*
1982215 TTCATACG
1 TACATACG
*
1982223 TTCATACG
1 TACATACG
*
1982231 TTCATACG
1 TACATACG
*
1982239 TTCATACG
1 TACATACG
*
1982247 TTCATACG
1 TACATACG
*
1982255 TTCATACG
1 TACATACG
*
1982263 TTCATACG
1 TACATACG
*
1982271 TTCATACG
1 TACATACG
*
1982279 TTCATACG
1 TACATACG
*
1982287 TTCATACG
1 TACATACG
*
1982295 TTCATACG
1 TACATACG
*
1982303 TTCATACG
1 TACATACG
*
1982311 TTCATACG
1 TACATACG
*
1982319 TTCATACG
1 TACATACG
*
1982327 TTCATACG
1 TACATACG
1982335 TACATACG
1 TACATACG
1982343 TACATACG
1 TACATACG
1982351 TACATACG
1 TACATACG
1982359 TACATACG
1 TACATACG
1982367 TACATACG
1 TACATACG
*
1982375 TTCATACG
1 TACATACG
*
1982383 TTCATACG
1 TACATACG
*
1982391 TTCATACG
1 TACATACG
1982399 TACATACG
1 TACATACG
1982407 TACATACG
1 TACATACG
*
1982415 TATATACG
1 TACATACG
*
1982423 TTCATACG
1 TACATACG
*
1982431 TTCATACG
1 TACATACG
*
1982439 TTCATACG
1 TACATACG
*
1982447 TTCATACG
1 TACATACG
*
1982455 TACATACA
1 TACATACG
1982463 TACATAC
1 TACATAC
1982470 ATATATTTTA
Statistics
Matches: 397, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 397 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (8 bp):
TACATACG
Found at i:1983406 original size:19 final size:19
Alignment explanation
Indices: 1983374--1983415 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1983364 ATAACTTCAG
*
1983374 AGATTTCTAGAAAC-TACAA
1 AGATTTCGAGAAACAT-CAA
*
1983393 AGATTTCGATAAACATCAA
1 AGATTTCGAGAAACATCAA
1983412 AGAT
1 AGAT
1983416 ACACTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (19 bp):
AGATTTCGAGAAACATCAA
Found at i:1990310 original size:19 final size:17
Alignment explanation
Indices: 1990270--1990330 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
1990260 TTTTTTATTT
*
1990270 TATTTTTAT-TGTTTTAA
1 TATTTTTATCT-TTATAA
1990287 TATTTTTATCTTTATGACA
1 TATTTTTATCTTTAT-A-A
*
1990306 TATTTTTTATTTTTATAA
1 TA-TTTTTATCTTTATAA
1990324 TATTTTT
1 TATTTTT
1990331 TTTTGCCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 17 0.45
18 5 0.13
19 4 0.11
20 12 0.32
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTTTTATCTTTATAA
Found at i:1990332 original size:19 final size:18
Alignment explanation
Indices: 1990272--1990331 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 18
1990262 TTTTATTTTA
1990272 TTTTTATTGTTT-TAATA-
1 TTTTTATT-TTTATAATAT
*
1990289 TTTTTATCTTTATGACATAT
1 TTTTTATTTTTAT-A-ATAT
1990309 TTTTTATTTTTATAATAT
1 TTTTTATTTTTATAATAT
1990327 TTTTT
1 TTTTT
1990332 TTTGCCTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 3 0.08
17 8 0.22
18 10 0.27
19 4 0.11
20 12 0.32
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTATTTTTATAATAT
Found at i:1991114 original size:12 final size:10
Alignment explanation
Indices: 1991082--1991160 Score: 72
Period size: 12 Copynumber: 7.3 Consensus size: 10
1991072 TGAAAATGTT
1991082 AAATAAAA-A
1 AAATAAAATA
1991091 TAAAT-AAATA
1 -AAATAAAATA
1991101 AACATAATAATA
1 AA-ATAA-AATA
1991113 AATATAAAATA
1 AA-ATAAAATA
1991124 AAATAAAAAATA
1 AAAT--AAAATA
1991136 AAATAAAATA
1 AAATAAAATA
1991146 AAATTAAAATGA
1 AAA-TAAAAT-A
1991158 AAA
1 AAA
1991161 AAGTACTAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
9 5 0.08
10 18 0.30
11 13 0.22
12 24 0.40
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (10 bp):
AAATAAAATA
Found at i:1991124 original size:17 final size:16
Alignment explanation
Indices: 1991081--1991174 Score: 81
Period size: 17 Copynumber: 5.9 Consensus size: 16
1991071 TTGAAAATGT
1991081 TAAATA-AAAAT-AAA
1 TAAATATAAAATAAAA
*
1991095 TAAATA-AACATAATAA
1 TAAATATAAAATAA-AA
1991111 TAAATATAAAATAAAA
1 TAAATATAAAATAAAA
*
1991127 TAAAAAATAAAATAAAA
1 T-AAATATAAAATAAAA
1991144 TAAA-ATTAAAATGAAAA
1 TAAATA-TAAAAT-AAAA
*
1991161 -AAGTACTAAAATAA
1 TAAATA-TAAAATAA
1991175 TAAATCAAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
16 24 0.35
17 32 0.47
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
TAAATATAAAATAAAA
Found at i:1991126 original size:5 final size:5
Alignment explanation
Indices: 1991082--1991160 Score: 72
Period size: 5 Copynumber: 14.6 Consensus size: 5
1991072 TGAAAATGTT
1991082 AAATA AAA-A TAAAT- AAATA AACATA ATAATA AATATA AAATA AAATAAA
1 AAATA AAATA -AAATA AAATA AA-ATA A-AATA AA-ATA AAATA AAAT--A
1991131 AAATA AAATA AAATA AAATTA AAATGA AAA
1 AAATA AAATA AAATA AAA-TA AAAT-A AAA
1991161 AAGTACTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 19
0.77 0.00 0.23
Matches are distributed among these distances:
4 5 0.08
5 31 0.48
6 22 0.34
7 6 0.09
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:1991160 original size:22 final size:21
Alignment explanation
Indices: 1991082--1991160 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
1991072 TGAAAATGTT
*
1991082 AAATAAAAAT-AAAT-AAATA
1 AAATTAAAATAAAATAAAATA
1991101 AACA-TAATAATAAATATAAAATA
1 AA-ATTAA-AATAAA-ATAAAATA
*
1991124 AAATAAAAAATAAAATAAAATA
1 AAAT-TAAAATAAAATAAAATA
1991146 AAATTAAAATGAAAA
1 AAATTAAAAT-AAAA
1991161 AAGTACTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 4 0.08
20 4 0.08
21 7 0.14
22 19 0.39
23 13 0.27
24 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (21 bp):
AAATTAAAATAAAATAAAATA
Found at i:1991233 original size:37 final size:37
Alignment explanation
Indices: 1991192--1991269 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
1991182 AAGGAAGGAA
*
1991192 AAAATATAAATATAAACAAATAAA-T-AAATAATAAAAT
1 AAAATATAAACA-AAACAAA-AAACTAAAATAATAAAAT
* *
1991229 AAAATATTAACACAACAAAAAACTAAAATAATAAAAT
1 AAAATATAAACAAAACAAAAAACTAAAATAATAAAAT
1991266 AAAA
1 AAAA
1991270 AATCAAAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 3 0.08
36 7 0.19
37 26 0.72
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (37 bp):
AAAATATAAACAAAACAAAAAACTAAAATAATAAAAT
Found at i:1991296 original size:24 final size:22
Alignment explanation
Indices: 1991261--1991318 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
1991251 CTAAAATAAT
*
1991261 AAAATAAAAAATCAAAGGGAAAA
1 AAAATAAAAAAT-AAAAGGAAAA
*
1991284 TAAATAAATAAATAAAAGGAAAA
1 AAAATAAA-AAATAAAAGGAAAA
1991307 AATAATAAAAAA
1 AA-AATAAAAAA
1991319 ATATCAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.14
Consensus pattern (22 bp):
AAAATAAAAAATAAAAGGAAAA
Found at i:1991320 original size:24 final size:24
Alignment explanation
Indices: 1991262--1991321 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1991252 TAAAATAATA
* *
1991262 AAAT-AAAAAATCAAAGGGAAAAT
1 AAATAAAAAAATAAAAGGAAAAAT
*
1991285 AAATAAATAAATAAAAGGAAAAA-
1 AAATAAAAAAATAAAAGGAAAAAT
1991308 ATAATAAAAAAATA
1 A-AATAAAAAAATA
1991322 TCAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AAATAAAAAAATAAAAGGAAAAAT
Found at i:1992425 original size:15 final size:14
Alignment explanation
Indices: 1992405--1992451 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1992395 TAACAAATAA
1992405 ATAATAATAATAATG
1 ATAATAAT-ATAATG
*
1992420 ATAATACTATAATAG
1 ATAATAATATAAT-G
*
1992435 TTAATAATATAAT-
1 ATAATAATATAATG
1992448 ATAA
1 ATAA
1992452 ACTATATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 5 0.19
15 19 0.70
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (14 bp):
ATAATAATATAATG
Found at i:1992431 original size:27 final size:24
Alignment explanation
Indices: 1992401--1992462 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 24
1992391 TTAATAACAA
1992401 ATAAATAATAATAATAATGATAATACT
1 ATAAATAATAAT-ATAAT-ATAA-ACT
1992428 ATAATAGTTAATAATATAATATAAACT
1 ATAA-A--TAATAATATAATATAAACT
1992455 ATATAATA
1 ATA-AATA
1992463 TATATATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
25 2 0.06
27 11 0.35
28 6 0.19
29 5 0.16
30 7 0.23
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (24 bp):
ATAAATAATAATATAATATAAACT
Found at i:1992502 original size:33 final size:33
Alignment explanation
Indices: 1992460--1992605 Score: 120
Period size: 33 Copynumber: 4.3 Consensus size: 33
1992450 AAACTATATA
*
1992460 ATATA-TATATTTCAAAAAAATATTTTTAAACT
1 ATATATTATATTTCAAAAAAATATTTTAAAACT
* * *
1992492 ATATATTATATTTTTAAAAAAGT-TTTCAAAACT
1 ATATATTATA-TTTCAAAAAAATATTTTAAAACT
* *
1992525 ATATATTATATAGTT-ATCAAAAATGATTTTAAAAAT
1 ATATATTATAT--TTCA-AAAAAAT-ATTTTAAAACT
* * *
1992561 ATTATATAAGT-TTTCAAAAAAAAAATTTAAAACT
1 A-TATATTA-TATTTCAAAAAAATATTTTAAAACT
1992595 ATATATTATAT
1 ATATATTATAT
1992606 AAGTTTTTCA
Statistics
Matches: 89, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
32 7 0.08
33 30 0.34
34 27 0.30
35 7 0.08
36 10 0.11
37 7 0.08
38 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (33 bp):
ATATATTATATTTCAAAAAAATATTTTAAAACT
Found at i:1992567 original size:70 final size:68
Alignment explanation
Indices: 1992450--1992646 Score: 170
Period size: 70 Copynumber: 2.8 Consensus size: 68
1992440 AATATAATAT
* * *
1992450 AAACTATATAATATATATA-TTTCAAAAAAAT-ATTTTTAAACTATATATTATATTTT-TAAAAA
1 AAACTATAT-AT-TATATAGTTTC--AAAAATGATTTTAAAAATATATATTATATTTTAAAAAAA
**
1992512 AGTTTTCA
62 AAATTT-A
1992520 AAACTATATATTATATAGTTATCAAAAATGATTTTAAAAATAT-TA-TATAAGTTTTCAAAAAAA
1 AAACTATATATTATATAGTT-TCAAAAATGATTTTAAAAATATATATTAT-A-TTTT-AAAAAAA
1992583 AAATTTA
62 AAATTTA
*
1992590 AAACTATATATTATATAAGTTTTTCAAAAATGTTTTTTTAAAAACTATATATTATAT
1 AAACTATATATTATAT-AG--TTTCAAAAATG--ATTTTAAAAA-TATATATTATAT
1992647 AAGTTTTCAA
Statistics
Matches: 106, Mismatches: 6, Indels: 25
0.77 0.04 0.18
Matches are distributed among these distances:
67 3 0.03
68 15 0.14
69 19 0.18
70 28 0.26
71 11 0.10
72 9 0.08
73 2 0.02
74 9 0.08
75 4 0.04
76 3 0.03
77 3 0.03
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (68 bp):
AAACTATATATTATATAGTTTCAAAAATGATTTTAAAAATATATATTATATTTTAAAAAAAAAAT
TTA
Found at i:1992590 original size:34 final size:37
Alignment explanation
Indices: 1992519--1992658 Score: 110
Period size: 41 Copynumber: 3.8 Consensus size: 37
1992509 AAAAGTTTTC
* **
1992519 AAAACTATATATTATAT-AGTTATC--AAAAATGATTT
1 AAAAC-ATATATTATATAAGTTTTCAAAAAAAAAATTT
*
1992554 TAAA-A-ATATTATATAAGTTTTCAAAAAAAAAATTT
1 AAAACATATATTATATAAGTTTTCAAAAAAAAAATTT
*****
1992589 AAAACTATATATTATATAAGTTTTTCAAAAATGTTTTTTT
1 AAAAC-ATATATTATATAAG-TTTTCAAAAA-AAAAATTT
1992629 AAAAACTATATATTATATAAGTTTTCAAAA
1 -AAAAC-ATATATTATATAAGTTTTCAAAA
1992659 TGTTTAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
32 9 0.10
33 7 0.08
35 15 0.17
37 1 0.01
38 12 0.14
39 10 0.12
40 12 0.14
41 20 0.23
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (37 bp):
AAAACATATATTATATAAGTTTTCAAAAAAAAAATTT
Found at i:1992672 original size:39 final size:39
Alignment explanation
Indices: 1992589--1992697 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 39
1992579 AAAAAAATTT
****
1992589 AAAACTATATATTATATAAGTTTTTCAAAAATGTTTTTTTA
1 AAAACTATATATTATATAAG-TTTTC-AAAATGTTTAAAAA
1992630 AAAACTATATATTATATAAGTTTTCAAAATGTTTAAAAA
1 AAAACTATATATTATATAAGTTTTCAAAATGTTTAAAAA
*
1992669 AAAACCATATATTATAT-A-TTTTCAAAATG
1 AAAACTATATATTATATAAGTTTTCAAAATG
1992698 ACTTCAAACT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
37 11 0.17
38 1 0.02
39 26 0.41
40 5 0.08
41 20 0.32
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (39 bp):
AAAACTATATATTATATAAGTTTTCAAAATGTTTAAAAA
Found at i:1993352 original size:58 final size:59
Alignment explanation
Indices: 1993256--1993374 Score: 186
Period size: 58 Copynumber: 2.0 Consensus size: 59
1993246 TCTTTTCGCC
* *
1993256 TTGAGTTATGCTACAAATGATGGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGCCT
1 TTGAGCTATGCTACAAATGATGGTGCCTTTAAGATGAGTGTAATCGAACTCGAAGGCCT
* * *
1993315 TTGAGCTATGCTGCAAATGAT-GTGCCTTTGAGATGAGTGTAATCGAACTCGAAGGTCT
1 TTGAGCTATGCTACAAATGATGGTGCCTTTAAGATGAGTGTAATCGAACTCGAAGGCCT
1993373 TT
1 TT
1993375 TGTTGGCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 36 0.65
59 19 0.35
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (59 bp):
TTGAGCTATGCTACAAATGATGGTGCCTTTAAGATGAGTGTAATCGAACTCGAAGGCCT
Found at i:1993419 original size:84 final size:84
Alignment explanation
Indices: 1993315--1993664 Score: 502
Period size: 84 Copynumber: 4.2 Consensus size: 84
1993305 TCGAAGGCCT
* *
1993315 TTGAGCTATGCTGCAAATGATGTGCCTTTGAGATGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
1 TTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
* *
1993380 GCAAATAACCTTTCTAGCC
66 GCAGATAACCCTTCTAGCC
* * * * *
1993399 TTGAGTTATACTGCAAATGATGTGGCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTG
1 TTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
* * *
1993464 GCATATAGCCCTTCTTGCC
66 GCAGATAACCCTTCTAGCC
* * * * * *
1993483 TTGAGCTATGCTACAAATGTTGTACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTATTG
1 TTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
1993548 GCAGATAACCCTTCTAGCC
66 GCAGATAACCCTTCTAGCC
* * *
1993567 TTTAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTG
1 TTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
*
1993632 GCAGATAACCCTTCTAGGC
66 GCAGATAACCCTTCTAGCC
1993651 TTGAGTTATGCTGC
1 TTGAGTTATGCTGC
1993665 CAATAGTTTC
Statistics
Matches: 230, Mismatches: 36, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 230 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (84 bp):
TTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
GCAGATAACCCTTCTAGCC
Found at i:1995004 original size:95 final size:95
Alignment explanation
Indices: 1994800--1995060 Score: 389
Period size: 95 Copynumber: 2.7 Consensus size: 95
1994790 GGCTAGCTGA
* * * *
1994800 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATATCATTCTATAG-AT
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
*
1994864 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTACCAGGCTAGCTGAATATT
1994898 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
1994963 TAATCACCTTTACCAGGCTAGTTGAATCTT
66 TAATCACCTTTACCAGGCTAGCTGAATATT
* *
1994993 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGATAGCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
1995058 ATA
65 ATA
1995061 TAATTATAAT
Statistics
Matches: 152, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
94 4 0.03
95 96 0.63
96 6 0.04
97 2 0.01
98 44 0.29
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTACCAGGCTAGCTGAATATT
Found at i:1997701 original size:23 final size:21
Alignment explanation
Indices: 1997641--1997956 Score: 106
Period size: 23 Copynumber: 14.3 Consensus size: 21
1997631 TGAAAATGTT
*
1997641 AAATAAAAATAAATAAATAAATAA
1 AAATAAATA-AAAT-AATAAAT-A
1997665 AAATTACAATAATAATAAATAAATA
1 AAA-TA-AATAA-AAT-AATAAATA
1997690 TGAAATAAAATAAAA-AATAAAATGA
1 --AAAT-AAATAAAATAAT-AAAT-A
*
1997715 AAATGAAA-AAAATACTAAA-A
1 AAAT-AAATAAAATAATAAATA
* * *
1997735 TAATAAATCAAATGAAGAAA-A
1 AAATAAATAAAAT-AATAAATA
* *
1997756 AATATAAATATAAACAAACAAAT-
1 AA-ATAAATA-AAA-TAATAAATA
1997779 AAATAAAT-AAATAA-ATAATA
1 AAATAAATAAAATAATA-AATA
*
1997799 AAATAAAATAAAATATTAACATA
1 AAAT-AAATAAAATAATAA-ATA
1997822 ACACA-AAATAAAATAATAAATCA
1 A-A-ATAAATAAAATAATAAAT-A
*
1997845 AAGGAAAAAT-AAATAAATAAATA
1 AA--ATAAATAAAAT-AATAAATA
**
1997868 AAAGGAA-AAAATAATAAA-A
1 AAATAAATAAAATAATAAATA
*
1997887 AATATCAAAT-AAATGATAAATA
1 AA-AT-AAATAAAATAATAAATA
* * *
1997909 AAA-AAACAATATAA-AAGAGA
1 AAATAAATAAAATAATAA-ATA
1997929 CAAA-AAAT-AAATAAATAAATA
1 -AAATAAATAAAAT-AATAAATA
1997950 AAATAAA
1 AAATAAA
1997957 AAACTTTGAG
Statistics
Matches: 227, Mismatches: 27, Indels: 79
0.68 0.08 0.24
Matches are distributed among these distances:
18 1 0.00
19 16 0.07
20 34 0.15
21 42 0.19
22 33 0.15
23 50 0.22
24 19 0.08
25 8 0.04
26 20 0.09
27 4 0.02
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (21 bp):
AAATAAATAAAATAATAAATA
Found at i:1997778 original size:31 final size:30
Alignment explanation
Indices: 1997721--1997810 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
1997711 ATGAAAATGA
* *
1997721 AAAAAATACTAAA-ATAATAAATCAAATGAAG
1 AAAAAATA-TAAATATAA-AAAACAAATAAAG
*
1997752 AAAAAATATAAATATAAACAAACAAATAAAT
1 AAAAAATATAAATATAAA-AAACAAATAAAG
* *
1997783 AAATAA-ATAAATAATAAAATA-AAATAAA
1 AAAAAATATAAAT-ATAAAAAACAAATAAA
1997811 ATATTAACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 7 0.14
30 13 0.25
31 31 0.61
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (30 bp):
AAAAAATATAAATATAAAAAACAAATAAAG
Found at i:1997957 original size:5 final size:4
Alignment explanation
Indices: 1997647--1997956 Score: 91
Period size: 4 Copynumber: 75.8 Consensus size: 4
1997637 TGTTAAATAA
*
1997647 AAAT AAAT AAAT AAAT AAA- AATT ACAAT -AAT -AAT AAAT AAAT --AT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT
* *
1997691 GAAAT AAAAT AAA- AAAT AAAAT GAAAAT GAAAA AAAT -ACT AAA- ATAAT
1 -AAAT -AAAT AAAT AAAT -AAAT --AAAT -AAAT AAAT AAAT AAAT A-AAT
* * * * *
1997739 AAAT CAAAT GAAG AAA- AAAT ATAA- ATAT AAAC AAAC AAAT AAAT AAAT
1 AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
1997787 AAAT AAAT -AAT AAAAT AAAAT AAA- ATATT AACAT AACACA AAAT AAA-
1 AAAT AAAT AAAT -AAAT -AAAT AAAT A-AAT AA-AT AA-A-T AAAT AAAT
* * *
1997834 ATAAT AAAT CAAAG GAA- AAAT AAAT AAAT AAAT AAA- AGGAAA AAAT
1 A-AAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT A--AAT AAAT
* * * * *
1997880 -AAT AAAA AATAT CAAAT AAAT -GAT AAAT AAAA AAAC AATAT AAA- AGAGAC
1 AAAT AAAT AA-AT -AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT A-A-AT
1997930 AAA- AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAA
1997957 AAACTTTGAG
Statistics
Matches: 237, Mismatches: 30, Indels: 78
0.69 0.09 0.23
Matches are distributed among these distances:
2 2 0.01
3 35 0.15
4 134 0.57
5 55 0.23
6 11 0.05
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:1998997 original size:14 final size:13
Alignment explanation
Indices: 1998971--1999012 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1998961 CTAGGTTTTA
1998971 AAAAAATAA-AAT
1 AAAAAATAATAAT
1998983 AAAAAATAATTAAT
1 AAAAAATAA-TAAT
*
1998997 AACAAATAAATAAT
1 AAAAAAT-AATAAT
1999011 AA
1 AA
1999013 TTATAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 9 0.35
14 15 0.58
15 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:1999037 original size:27 final size:26
Alignment explanation
Indices: 1999002--1999059 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1998992 TTAATAACAA
* *
1999002 ATAAATAATAATTATAATA-ATACTAT
1 ATAATTAATAA-TATAATATAAACTAT
1999028 ACTAATTAATAATATAATATAAACTAT
1 A-TAATTAATAATATAATATAAACTAT
1999055 ATAAT
1 ATAAT
1999060 ATATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (26 bp):
ATAATTAATAATATAATATAAACTAT
Found at i:1999048 original size:20 final size:20
Alignment explanation
Indices: 1999001--1999048 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1998991 ATTAATAACA
*
1999001 AATAA-ATAATAATTATAAT
1 AATAATATACTAATTATAAT
*
1999020 AATACTATACTAATTAATAAT
1 AATAATATACTAATT-ATAAT
1999041 -ATAATATA
1 AATAATATA
1999049 AACTATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 15 0.62
21 5 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATATACTAATTATAAT
Found at i:1999235 original size:38 final size:38
Alignment explanation
Indices: 1999100--1999401 Score: 329
Period size: 38 Copynumber: 8.3 Consensus size: 38
1999090 ATATATTATA
* *
1999100 TTTTT-AAAAAAGTTTTTAAAACTATATATTAT-T---
1 TTTTTCAAAAATGTATTTAAAACTATATATTATATAAG
*
1999133 TTGTTTCAAAAATG-ATTTTAAA--A-ATATTATATAAG
1 TT-TTTCAAAAATGTATTTAAAACTATATATTATATAAG
*
1999168 -TTTTCAAAAATTGTTTTTTAAAACTATATATTATATAAG
1 TTTTTCAAAAA-TG-TATTTAAAACTATATATTATATAAG
1999207 TTTTTCAAAAATGTATTTAAAACTATATATTATATAAG
1 TTTTTCAAAAATGTATTTAAAACTATATATTATATAAG
1999245 TTTTTCAAAAATGTATTTAAAACTATATATTATATAAG
1 TTTTTCAAAAATGTATTTAAAACTATATATTATATAAG
1999283 TTTTTCAAAAATGT-TTTAAAAACTATATATTATATAAG
1 TTTTTCAAAAATGTATTT-AAAACTATATATTATATAAG
*
1999321 -TTTTC-AAAATGT-TTTAAAAAAGTCATATATTATAT-A-
1 TTTTTCAAAAATGTATTT--AAAACT-ATATATTATATAAG
* *
1999357 -TTTTC-AAAAGGTATTTTGAAACTATATATTATATAA-
1 TTTTTCAAAAATGTA-TTTAAAACTATATATTATATAAG
1999393 TTTTT-AAAA
1 TTTTTCAAAA
1999402 TGACTTCAAA
Statistics
Matches: 238, Mismatches: 10, Indels: 38
0.83 0.03 0.13
Matches are distributed among these distances:
31 7 0.03
32 2 0.01
33 11 0.05
34 12 0.05
35 17 0.07
36 32 0.13
37 22 0.09
38 111 0.47
39 14 0.06
40 10 0.04
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (38 bp):
TTTTTCAAAAATGTATTTAAAACTATATATTATATAAG
Found at i:1999330 original size:36 final size:36
Alignment explanation
Indices: 1999048--1999401 Score: 326
Period size: 38 Copynumber: 9.8 Consensus size: 36
1999038 AATATAATAT
* * *
1999048 AAACTATATAATATAT-A-TATTTCAAAAAAATATTTTT
1 AAACTATATATTATATAAGT-TTTC--AAAAATGTTTTA
* *
1999085 AACCTATATATTATAT---TTTT-AAAAAAGTTTTTA
1 AAACTATATATTATATAAGTTTTCAAAAATG-TTTTA
**
1999118 AAACTATATATTAT-TTTG-TTTCAAAAATGATTTT-
1 AAACTATATATTATATAAGTTTTCAAAAATG-TTTTA
1999152 AAA--A-ATATTATATAAGTTTTCAAAAATTGTTTTTTA
1 AAACTATATATTATATAAGTTTTCAAAAA-TG--TTTTA
1999188 AAACTATATATTATATAAGTTTTTCAAAAATGTATTTA
1 AAACTATATATTATATAAG-TTTTCAAAAATGT-TTTA
1999226 AAACTATATATTATATAAGTTTTTCAAAAATGTATTTA
1 AAACTATATATTATATAAG-TTTTCAAAAATGT-TTTA
1999264 AAACTATATATTATATAAGTTTTTCAAAAATGTTTTAA
1 AAACTATATATTATATAAG-TTTTCAAAAATGTTTT-A
1999302 AAACTATATATTATATAAGTTTTC-AAAATGTTTTAAA
1 AAACTATATATTATATAAGTTTTCAAAAATGTTTT--A
* * * *
1999339 AAAGTCATATATTATAT-A-TTTTCAAAAGGTATTTTG
1 AAACT-ATATATTATATAAGTTTTCAAAA-ATGTTTTA
*
1999375 AAACTATATATTATATAA-TTTTTAAAA
1 AAACTATATATTATATAAGTTTTCAAAA
1999402 TGACTTCAAA
Statistics
Matches: 279, Mismatches: 17, Indels: 43
0.82 0.05 0.13
Matches are distributed among these distances:
31 7 0.03
32 9 0.03
33 26 0.09
34 8 0.03
35 28 0.10
36 32 0.11
37 33 0.12
38 112 0.40
39 14 0.05
40 10 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (36 bp):
AAACTATATATTATATAAGTTTTCAAAAATGTTTTA
Found at i:2009567 original size:29 final size:29
Alignment explanation
Indices: 2009530--2009595 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
2009520 TTACAATTTC
* **
2009530 AGTCCCTAAACTTTCAAATTTTATACTTT
1 AGTCACTAAACTTTCAAAACTTATACTTT
2009559 AGTCACTAAACTTTCAAAACTTATACTTT
1 AGTCACTAAACTTTCAAAACTTATACTTT
2009588 AGTCACTA
1 AGTCACTA
2009596 GATAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (29 bp):
AGTCACTAAACTTTCAAAACTTATACTTT
Found at i:2017257 original size:29 final size:30
Alignment explanation
Indices: 2017209--2017270 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
2017199 ATTTCGGTCT
**
2017209 CTAAACTTTTCAAAGTTTATACTTTAGCCA
1 CTAAACTTTTCAAAACTTATACTTTAGCCA
*
2017239 CTAAAC-TTTCAAAACTTATACTTTAGTCA
1 CTAAACTTTTCAAAACTTATACTTTAGCCA
2017268 CTA
1 CTA
2017271 GACAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
CTAAACTTTTCAAAACTTATACTTTAGCCA
Found at i:2020396 original size:13 final size:13
Alignment explanation
Indices: 2020380--2020422 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2020370 CTATGACGTC
*
2020380 CATTTATGGCACG
1 CATTTATGACACG
*
2020393 CATTTATGACACA
1 CATTTATGACACG
2020406 CATTTATGACACG
1 CATTTATGACACG
2020419 CATT
1 CATT
2020423 GAACGTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (13 bp):
CATTTATGACACG
Found at i:2020506 original size:83 final size:83
Alignment explanation
Indices: 2020394--2020605 Score: 266
Period size: 85 Copynumber: 2.5 Consensus size: 83
2020384 TATGGCACGC
* * *** * *
2020394 ATTTATGACACACATTTATGACACGCATTGAACGTCATTGAAGCCCCCGTTATAAATGAAGATG-
1 ATTTATGACACGCATGTATGACTTACATTG-ACGTCATTGAAGCCCCCATCATAAATGAAGATGA
*
2020458 ACACATTTATGTGTCATAA
65 ACACAATTATGTGTCATAA
*
2020477 ATTTATGACATGCATGTATGACTTACATTG-CGTATCATTGAAGCCCCCATCATAAATGAAGATG
1 ATTTATGACACGCATGTATGACTTACATTGACG--TCATTGAAGCCCCCATCATAAATGAAGATG
2020541 ACACACAATTATGTGTCATAA
64 A-ACACAATTATGTGTCATAA
**
2020562 ATTTATGACACGCATGTATGACTTACATTGCATATCATTGAAGC
1 ATTTATGACACGCATGTATGACTTACATTG-ACGTCATTGAAGC
2020606 ACACGTCATC
Statistics
Matches: 111, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
81 2 0.02
83 52 0.47
85 57 0.51
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (83 bp):
ATTTATGACACGCATGTATGACTTACATTGACGTCATTGAAGCCCCCATCATAAATGAAGATGAA
CACAATTATGTGTCATAA
Found at i:2020581 original size:85 final size:83
Alignment explanation
Indices: 2020428--2020605 Score: 293
Period size: 85 Copynumber: 2.1 Consensus size: 83
2020418 GCATTGAACG
* * * *
2020428 TCATTGAAGCCCCCGTTATAAATGAAGATGACACATTTATGTGTCATAAATTTATGACATGCATG
1 TCATTGAAGCCCCCATCATAAATGAAGATGACACAATTATGTGTCATAAATTTATGACACGCATG
*
2020493 TATGACTTACATTGCGTA
66 TATGACTTACATTGCATA
2020511 TCATTGAAGCCCCCATCATAAATGAAGATGACACACAATTATGTGTCATAAATTTATGACACGCA
1 TCATTGAAGCCCCCATCATAAATGAAGATG--ACACAATTATGTGTCATAAATTTATGACACGCA
2020576 TGTATGACTTACATTGCATA
64 TGTATGACTTACATTGCATA
2020596 TCATTGAAGC
1 TCATTGAAGC
2020606 ACACGTCATC
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 28 0.32
85 60 0.68
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (83 bp):
TCATTGAAGCCCCCATCATAAATGAAGATGACACAATTATGTGTCATAAATTTATGACACGCATG
TATGACTTACATTGCATA
Found at i:2020670 original size:2 final size:2
Alignment explanation
Indices: 2020663--2020697 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2020653 TTTCGTAAAT
2020663 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 T
2020698 GTATTGTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2020762 original size:2 final size:2
Alignment explanation
Indices: 2020755--2020799 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
2020745 ATAATACTAA
2020755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
2020797 AT A
1 AT A
2020800 ACCAATCCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2035792 original size:109 final size:108
Alignment explanation
Indices: 2035538--2035798 Score: 289
Period size: 109 Copynumber: 2.4 Consensus size: 108
2035528 TCACTACAAA
* *
2035538 TGACCAAAATGCAAAAAGACGCTTAAA-TAAGAGGGACTAAATAAAAAATATTCCAATAAATATA
1 TGACCAAAATGCAAAAACACGC-TAAACT-AGAGGGACTAAACAAAAAATATTCCAATAAATATA
2035602 TAACATACAAGAAAAGGGGTAAATAACAATTTTGGTCCTCGCAAG
64 TAACATACAAGAAAAGGGGTAAATAACAATTTTGGTCCTCGCAAG
* ** * * * *
2035647 TGACCAAAGTTAAAAAACGCGCTAAACTTAGAGGGACTAAACAAAAATTAATT-CAATCACTATA
1 TGACCAAAATGCAAAAACACGCTAAAC-TAGAGGGACTAAACAAAAAAT-ATTCCAATAAATATA
* * *
2035711 TAACACGTA-TA-AAAAGGGGTAAAT-ACTAATTTTGGTCCTTGCAGG
64 TAACA--TACAAGAAAAGGGGTAAATAAC-AATTTTGGTCCTCGCAAG
*
2035756 TGACCAAAATGCAAAAACACGCTAAACCTAGGGGGACTTAAAC
1 TGACCAAAATGCAAAAACACGCTAAA-CTAGAGGGAC-TAAAC
2035799 GTGATTTTAC
Statistics
Matches: 127, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
108 6 0.05
109 108 0.85
110 11 0.09
111 2 0.02
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (108 bp):
TGACCAAAATGCAAAAACACGCTAAACTAGAGGGACTAAACAAAAAATATTCCAATAAATATATA
ACATACAAGAAAAGGGGTAAATAACAATTTTGGTCCTCGCAAG
Found at i:2038035 original size:19 final size:18
Alignment explanation
Indices: 2038007--2038048 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
2037997 TTATTCGTAA
*
2038007 TTTTATTTTTTTTTTCAT
1 TTTTATTTTTTTTATCAT
2038025 TTTTCATTTTTTTTATCAT
1 TTTT-ATTTTTTTTATCAT
2038044 TTTTA
1 TTTTA
2038049 GGAACATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTTTTATCAT
Found at i:2040157 original size:5 final size:5
Alignment explanation
Indices: 2040147--2040171 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2040137 ATAATTGAAT
2040147 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
2040172 CATTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:2059406 original size:29 final size:29
Alignment explanation
Indices: 2059318--2059407 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 29
2059308 CCAAATTCAT
* *
2059318 AACTTTTAAAAATTATACTTTGGTCCCTA
1 AACTTTCAAAAATTATACTTTGGTCACTA
* * *
2059347 AACTTTTCCAAAAAATTTTACTTTAGCCACTA
1 AAC-TTT-C-AAAAATTATACTTTGGTCACTA
* *
2059379 AACTTTCAAAAATTACATTTTGGTCACTA
1 AACTTTCAAAAATTATACTTTGGTCACTA
2059408 GTCAAAATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 20 0.42
30 4 0.08
31 3 0.06
32 21 0.44
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.39
Consensus pattern (29 bp):
AACTTTCAAAAATTATACTTTGGTCACTA
Found at i:2060047 original size:2 final size:2
Alignment explanation
Indices: 2060040--2060075 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2060030 GTTTAGTGGC
2060040 AT 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 AT
2060076 CATAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2062165 original size:11 final size:12
Alignment explanation
Indices: 2062135--2062173 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
2062125 AATTACATGT
*
2062135 ATATACTTAAAA
1 ATATATTTAAAA
2062147 ATATATTTAAAA
1 ATATATTTAAAA
2062159 ATA-ATTTAAAA
1 ATATATTTAAAA
2062170 ATAT
1 ATAT
2062174 TTTTTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATTTAAAA
Found at i:2062617 original size:30 final size:30
Alignment explanation
Indices: 2062581--2062651 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
2062571 TGGATTTTTG
*
2062581 AAAAAATGACCGGAAACATTATTACGCGCT
1 AAAAAATGACCGGAAACATTACTACGCGCT
* *
2062611 AAAAAATGACCGGAAACATTACTAGGTGCT
1 AAAAAATGACCGGAAACATTACTACGCGCT
2062641 -AAAAATGACCG
1 AAAAAATGACCG
2062652 AAAAATGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 11 0.29
30 27 0.71
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (30 bp):
AAAAAATGACCGGAAACATTACTACGCGCT
Found at i:2063808 original size:128 final size:128
Alignment explanation
Indices: 2063574--2063859 Score: 457
Period size: 128 Copynumber: 2.2 Consensus size: 128
2063564 TTTGATGCCT
* * * *
2063574 TAAGTAGAGGATACC-ACTAGAAGATGATGCCTTTTTAGAAACATCTTGGGTTTGATGGAGAGTG
1 TAAGTTGAGGATGCCAAC-AGAAGATGATGCATTTTTAGAAACATCGTGGGTTTGATGGAGAGTG
* *
2063638 AATCGAGCATAAAAATGGAATTCGGAAGTCATACCCATCACTGTCACATCCACGTCACTAGCGA
65 AATCGAGCATAAAAATGGAATTCGAAAGTCATACCCACCACTGTCACATCCACGTCACTAGCGA
2063702 TAAGTTGAGGATGCCAACAGAAGATGATGCATTTTTAGAAACATCGTGGGTTTGATGGAGAGTGA
1 TAAGTTGAGGATGCCAACAGAAGATGATGCATTTTTAGAAACATCGTGGGTTTGATGGAGAGTGA
* ** * *
2063767 ATCGGGCATAAAAATGGAATTCGAAAGTCATGTCCACCACTGTTACATCCACGTCACTAGGGA
66 ATCGAGCATAAAAATGGAATTCGAAAGTCATACCCACCACTGTCACATCCACGTCACTAGCGA
2063830 TAAGTTGAGGATGCCAACAGAAGATGATGC
1 TAAGTTGAGGATGCCAACAGAAGATGATGC
2063860 CTTCTAGAAA
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 144 0.99
129 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (128 bp):
TAAGTTGAGGATGCCAACAGAAGATGATGCATTTTTAGAAACATCGTGGGTTTGATGGAGAGTGA
ATCGAGCATAAAAATGGAATTCGAAAGTCATACCCACCACTGTCACATCCACGTCACTAGCGA
Found at i:2065236 original size:27 final size:27
Alignment explanation
Indices: 2065187--2065239 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2065177 TATTTTTTAA
**
2065187 AAAATGGAGTTTTATTAACTAAAAAAG
1 AAAATGGAGTTCGATTAACTAAAAAAG
2065214 AAAATGGAGTTCGATTTAA-TAAAAAA
1 AAAATGGAGTTCGA-TTAACTAAAAAA
2065240 ATTACAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (27 bp):
AAAATGGAGTTCGATTAACTAAAAAAG
Found at i:2067310 original size:20 final size:19
Alignment explanation
Indices: 2067285--2067324 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
2067275 ATTTGAAATG
2067285 AATAAAAAAATTATTACAAA
1 AATAAAAAAATTATT-CAAA
*
2067305 AATAAATAAATTATTCAAA
1 AATAAAAAAATTATTCAAA
2067324 A
1 A
2067325 TAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAAAAAAATTATTCAAA
Found at i:2067329 original size:17 final size:18
Alignment explanation
Indices: 2067285--2067350 Score: 80
Period size: 17 Copynumber: 3.6 Consensus size: 18
2067275 ATTTGAAATG
*
2067285 AATAAAAAAATTATTACAAA
1 AATAAATAAATTATT-C-AA
2067305 AATAAATAAATTATTCAA
1 AATAAATAAATTATTCAA
*
2067323 AAT-AATAAATAATTCAA
1 AATAAATAAATTATTCAA
*
2067340 AGTAAATAAAT
1 AATAAATAAAT
2067351 AAATAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 15 0.36
18 12 0.29
19 1 0.02
20 14 0.33
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (18 bp):
AATAAATAAATTATTCAA
Found at i:2067336 original size:20 final size:20
Alignment explanation
Indices: 2067285--2067336 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
2067275 ATTTGAAATG
2067285 AATAA-AAA-AATTATTACA
1 AATAATAAATAATTATTACA
2067303 AA-AATAAATAAATTATT-CAA
1 AATAATAAAT-AATTATTAC-A
2067323 AATAATAAATAATT
1 AATAATAAATAATT
2067337 CAAAGTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 1 0.03
20 14 0.48
21 7 0.24
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAATAAATAATTATTACA
Found at i:2068918 original size:6 final size:7
Alignment explanation
Indices: 2068902--2068928 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2068892 TATATAAATC
2068902 TTTTAAT
1 TTTTAAT
2068909 TTTTAAT
1 TTTTAAT
2068916 TTTTAAT
1 TTTTAAT
2068923 TTTTAA
1 TTTTAA
2068929 AATGAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTAAT
Found at i:2069533 original size:21 final size:21
Alignment explanation
Indices: 2069509--2069729 Score: 152
Period size: 21 Copynumber: 10.3 Consensus size: 21
2069499 CATATTCGCA
*
2069509 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTATTCCAAGTT-GCG
*
2069530 TTGCGATTTATTCCAAGTT-CT
1 TTGCGA-TTATTCCAAGTTGCG
* *
2069551 TTGCGA-TAGTCGAAGTTTGCG
1 TTGCGATTATTCCAAG-TTGCG
*
2069572 TTGCGATTTATTCCAAATT-CG
1 TTGCGA-TTATTCCAAGTTGCG
*
2069593 TTGCGATTTATTCCAAATT-CG
1 TTGCGA-TTATTCCAAGTTGCG
*
2069614 TTGCGATTTATTCCAAGTTCGTG
1 TTGCGA-TTATTCCAAGTT-GCG
*
2069637 TTGCGATTTATTCCAAATT-CG
1 TTGCGA-TTATTCCAAGTTGCG
* *
2069658 TTGCGATT-GTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT-GCG
* * * *
2069679 TTGCAATTTATTACAAATTCGCC
1 TTGCGA-TTATTCCAAGTT-GCG
2069702 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA-TTATTCCAAGTTGCG
2069723 TTGCGAT
1 TTGCGAT
2069730 AGTCCAAAAT
Statistics
Matches: 163, Mismatches: 25, Indels: 25
0.77 0.12 0.12
Matches are distributed among these distances:
19 13 0.08
20 5 0.03
21 82 0.50
22 4 0.02
23 59 0.36
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (21 bp):
TTGCGATTATTCCAAGTTGCG
Found at i:2069560 original size:42 final size:42
Alignment explanation
Indices: 2069509--2069737 Score: 202
Period size: 42 Copynumber: 5.4 Consensus size: 42
2069499 CATATTCGCA
* *
2069509 TTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCT
1 TTGCGATTAGTCCAAATT-GCGTTGCGATTTATTCCAAGTTCG
* * *
2069551 TTGCGA-TAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATTAGTCCAA-ATTGCGTTGCGATTTATTCCAAGTTCG
*
2069593 TTGCGATTTATTCCAAATT-CGTTGCGATTTATTCCAAGTTCGTG
1 TTGCGA-TTAGTCCAAATTGCGTTGCGATTTATTCCAAGTTC--G
* * *
2069637 TTGCGATTTATTCCAAATT-CGTTGCGA-TT-GTCGAAGTTCGCG
1 TTGCGA-TTAGTCCAAATTGCGTTGCGATTTATTCCAAGTT--CG
* * * *
2069679 TTGCAATTTATTACAAATTCGCCTTGCGATTTATTCCAAGTTCG
1 TTGCGA-TTAGTCCAAATT-GCGTTGCGATTTATTCCAAGTTCG
2069723 TTGCGA-TAGTCCAAA
1 TTGCGATTAGTCCAAA
2069738 ATCGCAACGA
Statistics
Matches: 158, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
42 94 0.59
43 6 0.04
44 49 0.31
45 2 0.01
46 7 0.04
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (42 bp):
TTGCGATTAGTCCAAATTGCGTTGCGATTTATTCCAAGTTCG
Found at i:2069647 original size:65 final size:65
Alignment explanation
Indices: 2069528--2069729 Score: 241
Period size: 65 Copynumber: 3.1 Consensus size: 65
2069518 TCCAAGTTCG
* * * *
2069528 CGTTGCGATTTATTCCAAGTTCTTTGCGA--TAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
2069591 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCGTGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * * * * * *
2069656 CGTTGCGA-TT-GTCGAAGTTCGCGTTGCAATTTATTACAAATTCGCCTTGCGATTTATTCCAAG
1 CGTTGCGATTTATTCCAAGTT--CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAA
2069719 TT
64 TT
2069721 CGTTGCGAT
1 CGTTGCGAT
2069730 AGTCCAAAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
63 33 0.28
64 2 0.02
65 84 0.71
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (65 bp):
CGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:2069833 original size:6 final size:6
Alignment explanation
Indices: 2069822--2069853 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2069812 GACACGTATT
2069822 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2069854 TGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2070434 original size:21 final size:21
Alignment explanation
Indices: 2070410--2070457 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2070400 ACATGTCCGC
2070410 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
*
2070431 TTGCGATAGTCGAATTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
2070452 TTGCGA
1 TTGCGA
2070458 ATTTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:2070926 original size:17 final size:17
Alignment explanation
Indices: 2070900--2070932 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2070890 ATTTTATTAT
*
2070900 TTCTTTATAACATTTTC
1 TTCTTCATAACATTTTC
2070917 TTCTTCATAACATTTT
1 TTCTTCATAACATTTT
2070933 TTGTTGACAA
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:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTTCATAACATTTTC
Found at i:2071375 original size:20 final size:20
Alignment explanation
Indices: 2071350--2071482 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
2071340 GACCAACAAA
* *
2071350 ATCGCAATGCGATCTCCAGT
1 ATCGCAACGCGATTTCCAGT
**
2071370 ATCGCAAATC-AGTTTCCAG-
1 ATCGCAACGCGA-TTTCCAGT
* *
2071389 ATTCGCAACGCGA-TTCTGACT
1 A-TCGCAACGCGATTTC-CAGT
2071410 ATCGCAACGCGATTTCCAGT
1 ATCGCAACGCGATTTCCAGT
**
2071430 ATCGCAAATC-AGTTTCCAG-
1 ATCGCAACGCGA-TTTCCAGT
** *
2071449 ATTCGCAACGCGATTTTGACT
1 A-TCGCAACGCGATTTCCAGT
2071470 ATCGCAACGCGAT
1 ATCGCAACGCGAT
2071483 AATACAAAAT
Statistics
Matches: 87, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
19 7 0.08
20 73 0.84
21 7 0.08
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTTCCAGT
Done.