Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_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: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 7 of 13
Found at i:1269120 original size:2 final size:2
Alignment explanation
Indices: 1269113--1269139 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1269103 ACATATGCGC
1269113 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1269140 GAGAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1269201 original size:21 final size:22
Alignment explanation
Indices: 1269161--1269202 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1269151 TTAAAACGAT
*
1269161 AAAAAAATGTAGGGATTAAATA
1 AAAAAAATGTAGGGAGTAAATA
*
1269183 AAAAAAATG-AGTGAGTAAAT
1 AAAAAAATGTAGGGAGTAAAT
1269203 TGATAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (22 bp):
AAAAAAATGTAGGGAGTAAATA
Found at i:1272384 original size:3 final size:3
Alignment explanation
Indices: 1272378--1272410 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1272368 TATTTTTTTT
1272378 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1272411 ATATACAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1273526 original size:16 final size:17
Alignment explanation
Indices: 1273495--1273527 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1273485 CTGTTTTCTG
1273495 GAGAAAGGAGGAGATGT
1 GAGAAAGGAGGAGATGT
*
1273512 GAGAAATGA-GAGATGT
1 GAGAAAGGAGGAGATGT
1273528 CACTGGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.15
Consensus pattern (17 bp):
GAGAAAGGAGGAGATGT
Found at i:1274074 original size:18 final size:18
Alignment explanation
Indices: 1274031--1274074 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1274021 TATGTATAAT
1274031 TTATTTTTACTTATGTTA
1 TTATTTTTACTTATGTTA
*
1274049 TTGTTTTTACTTAT-TTA
1 TTATTTTTACTTATGTTA
1274066 TTATATTTT
1 TTAT-TTTT
1274075 CTTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
TTATTTTTACTTATGTTA
Found at i:1285870 original size:14 final size:14
Alignment explanation
Indices: 1285851--1285913 Score: 78
Period size: 14 Copynumber: 4.6 Consensus size: 14
1285841 TATTACACTT
1285851 AAAAAAAATCATCA
1 AAAAAAAATCATCA
1285865 AAAAAAAATCA--A
1 AAAAAAAATCATCA
*
1285877 AAAAAAAATTAATC-
1 AAAAAAAA-TCATCA
1285891 AAAAAAAATCAATCA
1 AAAAAAAATC-ATCA
1285906 AAAAAAAA
1 AAAAAAAA
1285914 AAAAAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 9 0.21
13 3 0.07
14 22 0.52
15 8 0.19
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAAAATCATCA
Found at i:1285894 original size:26 final size:27
Alignment explanation
Indices: 1285851--1285912 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
1285841 TATTACACTT
*
1285851 AAAAAAAATCATCAAAAAAAAATCAA-
1 AAAAAAAATAATCAAAAAAAAATCAAC
1285877 AAAAAAAATTAATC-AAAAAAAATCAATC
1 AAAAAAAA-TAATCAAAAAAAAATCAA-C
1285905 AAAAAAAA
1 AAAAAAAA
1285913 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 20 0.62
27 4 0.12
28 8 0.25
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (27 bp):
AAAAAAAATAATCAAAAAAAAATCAAC
Found at i:1285928 original size:30 final size:30
Alignment explanation
Indices: 1285864--1285929 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
1285854 AAAAATCATC
* **
1285864 AAAAAAA--AATCAAAAAAAAAATTAATCA
1 AAAAAAATCAATCAAAAAAAAAATAAAAAA
1285892 AAAAAAATCAATCAAAAAAAAAA-AAAAAA
1 AAAAAAATCAATCAAAAAAAAAATAAAAAA
1285921 AAGAAAAAT
1 AA-AAAAAT
1285930 TAAATAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 20 0.62
ACGTcount: A:0.82, C:0.06, G:0.02, T:0.11
Consensus pattern (30 bp):
AAAAAAATCAATCAAAAAAAAAATAAAAAA
Found at i:1287023 original size:47 final size:46
Alignment explanation
Indices: 1286917--1287231 Score: 139
Period size: 43 Copynumber: 6.7 Consensus size: 46
1286907 TAACCAGCCG
* * * *
1286917 TCCTCATCACGTAGGAACCGA-GTTATCACCCTTCCTAAAGATGGCCAGAGT
1 TCCTCATCACGTAGGAACC-ATGTCATCACCC-T--T--AGACGACCAGACT
* * *
1286968 TCTTCATCATGTATGAACCATGTCATCTACCCTTAGACGACCAGACT
1 TCCTCATCACGTAGGAACCATGTCATC-ACCCTTAGACGACCAGACT
* * ** * *
1287015 TCCTCATCACGTAGGAGA--GTGTCA--A-CATTAGGATAACCAGCCG
1 TCCTCATCACGTAGGA-ACCATGTCATCACCCTTA-GACGACCAGACT
* * * *
1287058 TCCTCATCACGTAGGAACCGA-GTTATCACCCTTCCTAAAGATGGCCAGAGT
1 TCCTCATCACGTAGGAACC-ATGTCATCACCC-T--T--AGACGACCAGACT
* * *
1287109 TCTTCATCATGTATGAACCATGTCATCTACCCTTAGACGACCAGACT
1 TCCTCATCACGTAGGAACCATGTCATC-ACCCTTAGACGACCAGACT
** * ** * * *
1287156 TCCTCATCACGTAGGAGTCGTGTCA--A-CCTTAGATAATCAGCCG
1 TCCTCATCACGTAGGAACCATGTCATCACCCTTAGACGACCAGACT
*
1287199 TCCTCATCACGTAGGAACC-TAGTTATCACCCTT
1 TCCTCATCACGTAGGAACCAT-GTCATCACCCTT
1287232 CTTAAAGATG
Statistics
Matches: 198, Mismatches: 45, Indels: 47
0.68 0.16 0.16
Matches are distributed among these distances:
42 6 0.03
43 57 0.29
44 4 0.02
45 1 0.01
46 10 0.05
47 53 0.27
48 2 0.01
49 2 0.01
50 3 0.02
51 51 0.26
52 9 0.05
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (46 bp):
TCCTCATCACGTAGGAACCATGTCATCACCCTTAGACGACCAGACT
Found at i:1287083 original size:141 final size:141
Alignment explanation
Indices: 1286865--1287305 Score: 668
Period size: 141 Copynumber: 3.2 Consensus size: 141
1286855 AACATCAACT
1286865 GACCAGA-TCTCCTCGA-CACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
1 GACCAGACT-TCCTC-ATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
1286928 TAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCA
64 TAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCA
1286993 TCTACCCTTAGAC
129 TCTACCCTTAGAC
1287006 GACCAGACTTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
1 GACCAGACTTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
1287071 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
66 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
1287136 TACCCTTAGAC
131 TACCCTTAGAC
* * *
1287147 GACCAGACTTCCTCATCACGTAGGAGTCGTGTCAACCTTA-GATAATCAGCCGTCCTCATCACGT
1 GACCAGACTTCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
* * * ** ** * *
1287211 AGGAACCTAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCA-
65 AGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
1287275 -T-CCCTT----
130 CTACCCTTAGAC
*
1287281 GACCAGATTTCCTCATCACGTAGGA
1 GACCAGACTTCCTCATCACGTAGGA
1287306 ATCGTGTTTC
Statistics
Matches: 284, Mismatches: 13, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
134 24 0.08
138 5 0.02
139 1 0.00
140 1 0.00
141 241 0.85
142 12 0.04
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (141 bp):
GACCAGACTTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
TACCCTTAGAC
Found at i:1287531 original size:3 final size:3
Alignment explanation
Indices: 1287518--1287576 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
1287508 ATTTATTTAT
1287518 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1287565 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1287577 AAATACATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1288693 original size:16 final size:17
Alignment explanation
Indices: 1288662--1288694 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1288652 CTGTTTTCTG
1288662 GAGAAAGGAGGAGATGT
1 GAGAAAGGAGGAGATGT
*
1288679 GAGAAATGA-GAGATGT
1 GAGAAAGGAGGAGATGT
1288695 CACTGGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.15
Consensus pattern (17 bp):
GAGAAAGGAGGAGATGT
Found at i:1289238 original size:18 final size:19
Alignment explanation
Indices: 1289197--1289238 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1289187 ATGTATAATT
*
1289197 TATTTTACTTATGTTATTG
1 TATTTTACTTATGTTATTA
1289216 T-TTTTACTTAT-TTATTA
1 TATTTTACTTATGTTATTA
1289233 TATTTT
1 TATTTT
1289239 CTTTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 14 0.67
19 1 0.05
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTTTACTTATGTTATTA
Found at i:1292471 original size:42 final size:42
Alignment explanation
Indices: 1292401--1292492 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
1292391 AACAAAAATA
** * *
1292401 TTTTGTCATTAATCTTAATTTTTTATTTGTGAAGACAATTGT
1 TTTTGTCATTAATCTTAATTGGTGATTTGTGAAGACAATTAT
* **
1292443 TTTTGTCATTAATCTTAGTTGGTGATTTGTGGCGACAATTAT
1 TTTTGTCATTAATCTTAATTGGTGATTTGTGAAGACAATTAT
*
1292485 TGTTGTCA
1 TTTTGTCA
1292493 CTATTGAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (42 bp):
TTTTGTCATTAATCTTAATTGGTGATTTGTGAAGACAATTAT
Found at i:1298620 original size:75 final size:75
Alignment explanation
Indices: 1298533--1298715 Score: 237
Period size: 75 Copynumber: 2.4 Consensus size: 75
1298523 CTTAACCGAT
* * * *
1298533 TAAAATAAAATAGGCTCTACATTTTATGTTAAACTACATACC-GATTTGTTCGAA-GATTACTAA
1 TAAAATAAAATAGGCACTACATTTTATGTTAAAATACATACCAG-TTTGTTCAAATG-TTAATAA
1298596 TAATGTAAACGG
64 TAATGTAAACGG
* *
1298608 TAAAATAAAATAGGCACTA-TTTATTATGTTAAAATACATACCAGTTTGTTTAAATGTTAATAAT
1 TAAAATAAAATAGGCACTACATT-TTATGTTAAAATACATACCAGTTTGTTCAAATGTTAATAAT
1298672 AATGTAAACGG
65 AATGTAAACGG
* * *
1298683 TAAAATAAAATAGACGCTACATATTATGTTAAA
1 TAAAATAAAATAGGCACTACATTTTATGTTAAA
1298716 TAGGTGCTAC
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
74 2 0.02
75 89 0.95
76 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGCACTACATTTTATGTTAAAATACATACCAGTTTGTTCAAATGTTAATAATA
ATGTAAACGG
Found at i:1298716 original size:23 final size:23
Alignment explanation
Indices: 1298690--1298761 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
1298680 CGGTAAAATA
*
1298690 AAATAGACGCTACATATTATGTT
1 AAATAGACGCTACATATTACGTT
** *
1298713 AAATAGGTGCTACCTATTACGTT
1 AAATAGACGCTACATATTACGTT
1298736 AAATA-AGCGCTACATATTACGTT
1 AAATAGA-CGCTACATATTACGTT
1298759 AAA
1 AAA
1298762 CTAACTAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (23 bp):
AAATAGACGCTACATATTACGTT
Found at i:1298834 original size:75 final size:75
Alignment explanation
Indices: 1298750--1298890 Score: 228
Period size: 75 Copynumber: 1.9 Consensus size: 75
1298740 AAGCGCTACA
* *
1298750 TATTACGTTAAACTAACTAACGATTTGTTTAAAGGTTAATAATAATGTAAACAGTAAAATAAAAT
1 TATTACGTTAAAATAACTAACGATTTGTTTAAAGGTTAATAATAATATAAACAGTAAAATAAAAT
1298815 AGACGATACC
66 AGACGATACC
* * * *
1298825 TATTACGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAATAATATAAACAGTAAAATAAAAT
1 TATTACGTTAAAATAACTAACGATTTGTTTAAAGGTTAATAATAATATAAACAGTAAAATAAAAT
1298890 A
66 A
1298891 AACGTTATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (75 bp):
TATTACGTTAAAATAACTAACGATTTGTTTAAAGGTTAATAATAATATAAACAGTAAAATAAAAT
AGACGATACC
Found at i:1299005 original size:195 final size:195
Alignment explanation
Indices: 1298593--1299005 Score: 553
Period size: 196 Copynumber: 2.1 Consensus size: 195
1298583 CGAAGATTAC
* * ** *
1298593 TAATAATGTAAACGGTAAAATAAAATAGGCACTATTTATTATGTTAAAATACATACCAGTTTGTT
1 TAATAATGTAAAC-ATAAAATAAAATAGACACTACCTATTACGTTAAAATACATACCAGTTTGTT
* * * * *
1298658 TAAATGTTAATAATAATGTAAACGGTAAAATAAAATAGACGCTACATATTATGTTAAATAGGTGC
65 TAAAGGTTAATAATAATATAAACAGTAAAATAAAATAAACGCTACATATTATGTTAAATAGGCGC
* * * * *
1298723 TACCTATTACGTTAAATAAGCGCTACATATTACGTTAAACTAACTAACGATTTGTTTAAAGGTTA
130 TACCTATTACGTCAAATAAACGCTACATATTACGGTAAACTAACTAACGATTTATTTAAAAGTTA
1298788 A
195 A
*
1298789 TAATAATGTAAACAGTAAAATAAAATAGACGA-TACCTATTACGTTAAAATATC-TACCGGTTTG
1 TAATAATGTAAACA-TAAAATAAAATAGAC-ACTACCTATTACGTTAAAATA-CATACCAGTTTG
* * *
1298852 TTTAAAGGTTACTAATAATATAAACAGTAAAATAAAATAAACGTTA-TTATTATGTTAAATAGGC
63 TTTAAAGGTTAATAATAATATAAACAGTAAAATAAAATAAACGCTACATATTATGTTAAATAGGC
* * * *
1298916 GCTACCTATTACGTCAAATAAACGCTACCTATTACGGTAAACTAGCTACCGGTTTATTTAAAAGT
128 GCTACCTATTACGTCAAATAAACGCTACATATTACGGTAAACTAACTAACGATTTATTTAAAAGT
1298981 TAA
193 TAA
1298984 TAATAATGTAAAACATAAAATA
1 TAATAATGT-AAACATAAAATA
1299006 TATACAACTT
Statistics
Matches: 190, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
195 91 0.48
196 97 0.51
197 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (195 bp):
TAATAATGTAAACATAAAATAAAATAGACACTACCTATTACGTTAAAATACATACCAGTTTGTTT
AAAGGTTAATAATAATATAAACAGTAAAATAAAATAAACGCTACATATTATGTTAAATAGGCGCT
ACCTATTACGTCAAATAAACGCTACATATTACGGTAAACTAACTAACGATTTATTTAAAAGTTAA
Found at i:1299078 original size:25 final size:25
Alignment explanation
Indices: 1299049--1299101 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1299039 AATTCGAAAA
1299049 TATTAATACTTACTCTAAAAGTATG
1 TATTAATACTTACTCTAAAAGTATG
1299074 TATTAATACTTACTCTAAAAGTATG
1 TATTAATACTTACTCTAAAAGTATG
1299099 TAT
1 TAT
1299102 ATTGTTAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (25 bp):
TATTAATACTTACTCTAAAAGTATG
Found at i:1299541 original size:107 final size:106
Alignment explanation
Indices: 1299422--1299699 Score: 380
Period size: 107 Copynumber: 2.6 Consensus size: 106
1299412 TGCTAATATT
* * * * * *
1299422 TATTTATAACAAAATAAGAAATTAACATATTTTATTGTCGTGAGATTTCGAAGCCCCATCAATTT
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTGAGATTTCTAAG-CCCATCAATTT
*
1299487 AAACTTTGGTAACACTTTAGGCGCTATCTAATATGTTGATAA
65 AAACTTTGATAACACTTTAGGCGCTATCTAATATGTTGATAA
* *
1299529 TATTAATAACAAAATAACTAATTAACCTATTTTGTTATCGTTG-GATTTCTAAGGCCCATCAACT
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCG-TGAGATTTCTAA-GCCCATCAATT
* * *
1299593 TAAACTTTGATAATATTTTAGGCGTTATCTAATATGTTGATAA
64 TAAACTTTGATAACACTTTAGGCGCTATCTAATATGTTGATAA
* *
1299636 TATTAATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGA-ATTTCTAAGGCCATCAATTT
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGT-GAGATTTCTAAGCCCATCAATTT
1299700 TAAAAAGAAA
Statistics
Matches: 151, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
106 11 0.07
107 137 0.91
108 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (106 bp):
TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTGAGATTTCTAAGCCCATCAATTTA
AACTTTGATAACACTTTAGGCGCTATCTAATATGTTGATAA
Found at i:1299840 original size:213 final size:213
Alignment explanation
Indices: 1299547--1299946 Score: 606
Period size: 213 Copynumber: 1.9 Consensus size: 213
1299537 ACAAAATAAC
* * *
1299547 TAATTAACCTATTTTGTTATCGTTGGATTTCTAAGGCCCATCAACTTAAACTTTGATAATATTTT
1 TAATTAACCTATTTTATTATCGTTGGATTTCTAAGGCCCATCAACTTAAACCTTGATAACATTTT
* * *
1299612 AGGCGTTATCTAATATGTTGATAATATTAATAACAAATTAAGTAATTAACCTATTTTGTTATCGT
66 AGGCGTTACCTAATATGTTGATAATATTAATAACAAATCAAGTAATTAACATATTTTGTTATCGT
*
1299677 CGAATTTCTAAGG-CCATCAATTTTAAAAAGAAACTACCTATTACATTAAATAAGCGCTACTTAT
131 CGAATTTCTAAGGCCCAACAATTTTAAAAAGAAACTACCTATTACATTAAATAAGCGCTACTTAT
1299741 GGTTGATAATGTTTCATG
196 GGTTGATAATGTTTCATG
* *
1299759 TAATTAACCTATTTTATTATCGTTGGATTTCTATGGCTCCAT-AAGCTTAAACCTTGGTAACATT
1 TAATTAACCTATTTTATTATCGTTGGATTTCTAAGGC-CCATCAA-CTTAAACCTTGATAACATT
* *
1299823 TTAGGCGTTACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATT
64 TTAGGCGTTACCTAATATGTTGATAATATTAATAACAAATCAAGTAATTAACATATTTTGTTATC
* * *** *
1299888 GTCGGATTTCTAAGGCCCCAACAGTTTTAAAAAGGCGCTACCTATTACATTACATAAGC
129 GTCGAATTTCTAAGG-CCCAACAATTTTAAAAAGAAACTACCTATTACATTAAATAAGC
1299947 ATTACCTGTT
Statistics
Matches: 167, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
212 37 0.22
213 94 0.56
215 36 0.22
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (213 bp):
TAATTAACCTATTTTATTATCGTTGGATTTCTAAGGCCCATCAACTTAAACCTTGATAACATTTT
AGGCGTTACCTAATATGTTGATAATATTAATAACAAATCAAGTAATTAACATATTTTGTTATCGT
CGAATTTCTAAGGCCCAACAATTTTAAAAAGAAACTACCTATTACATTAAATAAGCGCTACTTAT
GGTTGATAATGTTTCATG
Found at i:1300209 original size:21 final size:21
Alignment explanation
Indices: 1300183--1300224 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1300173 CCTCCCTTGA
*
1300183 GCCCTG-TGTGATCTTATCTTT
1 GCCCTGTTGTAATCTT-TCTTT
1300204 GCCCTGTTGTAATCTTTCTTT
1 GCCCTGTTGTAATCTTTCTTT
1300225 CTTTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.10, C:0.24, G:0.17, T:0.50
Consensus pattern (21 bp):
GCCCTGTTGTAATCTTTCTTT
Found at i:1301652 original size:20 final size:20
Alignment explanation
Indices: 1301619--1301662 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1301609 GAAATTAGGT
* * * *
1301619 TTTTTTTTATAAATGTAATA
1 TTTTTTTAAAAAATATAAAA
1301639 TTTTTTTAAAAAATATAAAA
1 TTTTTTTAAAAAATATAAAA
1301659 TTTT
1 TTTT
1301663 CAAAATTACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTTTAAAAAATATAAAA
Found at i:1311265 original size:3 final size:3
Alignment explanation
Indices: 1311168--1311247 Score: 81
Period size: 3 Copynumber: 26.7 Consensus size: 3
1311158 AATTATTTAT
* * * *
1311168 TAA TAA TAA T-A TAA TAA TAT TTA TAA TAA TAA TAA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1311215 TAA TAA TAC TAA TATT TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA
1311248 GAATTTTAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.94
4 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1311538 original size:73 final size:73
Alignment explanation
Indices: 1311419--1311792 Score: 586
Period size: 73 Copynumber: 5.1 Consensus size: 73
1311409 TGGAAAATTT
* * * * * *
1311419 TGTTTCTAGTGAAACTGTCTTAAGTGAGACGAATCTTGTTTTAAGAAAAACAATCTCAAGTAAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
*
1311484 TAAACTTC
66 TAAAGTTC
* * *
1311492 TGTTTCAAGTGAATCTGTTTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1311557 TAAAGTTC
66 TAAAGTTC
* *
1311565 TGTTTCGAGTGAAACTGTCTCAAGTGAGACAAATTTTGTTATAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1311630 TAAAGTTC
66 TAAAGTTC
*
1311638 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACTATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1311703 TAAAGTTC
66 TAAAGTTC
* * *
1311711 TGTTTCGAGTGAAACTGTCTCAAGCGGGACAGATTTTGTTTTAAGAAAAGCAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
* *
1311776 TAAATTTA
66 TAAAGTTC
1311784 TGTTTCGAG
1 TGTTTCGAG
1311793 AACATCCGGC
Statistics
Matches: 278, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 278 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAAGTTC
Found at i:1312531 original size:20 final size:20
Alignment explanation
Indices: 1312495--1312550 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 20
1312485 AATAAAGCTT
1312495 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTG--AAGAGAATCTA
1312517 TCATCTTTGAAGAGAATCTA
1 TCATCTTTGAAGAGAATCTA
1312537 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1312551 TATACATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 25 0.74
22 9 0.26
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (20 bp):
TCATCTTTGAAGAGAATCTA
Found at i:1313985 original size:75 final size:75
Alignment explanation
Indices: 1313847--1314019 Score: 195
Period size: 75 Copynumber: 2.3 Consensus size: 75
1313837 TATATGAGCC
* * * * *
1313847 TTCAGCATGCCCCAACATTTGCTAATACAAGCGTTCAAAATGCGTCAACATTCTTGATTCTGA-T
1 TTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCCTGATTCTGATT
1313911 AAAAAAGGCT
66 AAAAAAGGCT
* * * * *
1313921 TTCAGCATGCCCCATCATTTTGTTGATATAAACATTCAGAATACATCAACATTCCTGATTCTGAT
1 TTCAGCATGCCCCAACA-TTTGCTAATACAAACATTCAAAATACATCAACATTCCTGATTCTGAT
* **
1313986 TGAAATGGGCT
65 TAAAAAAGGCT
* *
1313997 TTCAGCCTGCCCCAACATCTGCT
1 TTCAGCATGCCCCAACATTTGCT
1314020 TCTTGTTAAT
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
74 16 0.20
75 41 0.51
76 23 0.29
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTAATACAAACATTCAAAATACATCAACATTCCTGATTCTGATT
AAAAAAGGCT
Found at i:1316380 original size:72 final size:72
Alignment explanation
Indices: 1316261--1316395 Score: 234
Period size: 72 Copynumber: 1.9 Consensus size: 72
1316251 TATAATGGGT
* *
1316261 TAGCTGAATATTATCCATAAAGCCGGGGCGATTAACCAATTGCTTTAGAGGGATAACTCAAGCAA
1 TAGCTGAATATTATCCATAAAACCAGGGCGATTAACCAATTGCTTTAGAGGGATAACTCAAGCAA
1316326 AACAGAC
66 AACAGAC
* *
1316333 TAGCTGAATATTATCCATAAAACCAGGGCGATTAACCAATTGTTTTAGGGGGATAACTCAAGC
1 TAGCTGAATATTATCCATAAAACCAGGGCGATTAACCAATTGCTTTAGAGGGATAACTCAAGC
1316396 TTTATTGTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAACCAGGGCGATTAACCAATTGCTTTAGAGGGATAACTCAAGCAA
AACAGAC
Found at i:1318526 original size:14 final size:14
Alignment explanation
Indices: 1318500--1318540 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1318490 AAGTAAACAT
*
1318500 AAAAATACAAATGC
1 AAAAATGCAAATGC
*
1318514 AAAGATGCAAATGC
1 AAAAATGCAAATGC
*
1318528 AAAAATGTAAATG
1 AAAAATGCAAATG
1318541 TAAATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.17
Consensus pattern (14 bp):
AAAAATGCAAATGC
Found at i:1321539 original size:2 final size:2
Alignment explanation
Indices: 1321532--1321605 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
1321522 AGAATATTAA
1321532 AT AT AT 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 AT AT AT
1321574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1321606 AAAATAGACA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1323355 original size:3 final size:3
Alignment explanation
Indices: 1323347--1323436 Score: 69
Period size: 3 Copynumber: 30.3 Consensus size: 3
1323337 AATTATTTAT
* *
1323347 TAA TAA TAA T-A TAA TAA TAT TTA TAA TAA TAA TAA TTAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* * * * **
1323391 TAC TAA TATT TAG TAA TAA TAA TAA TAG TAA TTT TAA -AA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1323436 T
1 T
1323437 TTAAGTAAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
2 6 0.09
3 56 0.84
4 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1323373 original size:12 final size:12
Alignment explanation
Indices: 1323340--1323377 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1323330 TATTTGTAAT
1323340 TATTTATTAATAA
1 TATTTA-TAATAA
*
1323353 TA-ATATAATAA
1 TATTTATAATAA
1323364 TATTTATAATAA
1 TATTTATAATAA
1323376 TA
1 TA
1323378 ATAATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 8 0.36
12 12 0.55
13 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATTTATAATAA
Found at i:1323377 original size:15 final size:15
Alignment explanation
Indices: 1323357--1323414 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 15
1323347 TAATAATAAT
1323357 ATAATAATATTTATA
1 ATAATAATATTTATA
*
1323372 ATAATAATAATTAAAATA
1 ATAATAAT-ATT--TATA
*
1323390 ATACTAATATTTAGTA
1 ATAATAATATTTA-TA
1323406 ATAATAATA
1 ATAATAATA
1323415 ATAGTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 9 0.26
16 13 0.37
17 3 0.09
18 10 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAATAATATTTATA
Found at i:1323431 original size:23 final size:25
Alignment explanation
Indices: 1323386--1323436 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1323376 TAATAATTAA
*
1323386 AATAATACTAATATTTAGTAATAAT
1 AATAATACTAATATTTAGAAATAAT
*
1323411 AATAATAGTAAT-TTTA-AAATAAT
1 AATAATACTAATATTTAGAAATAAT
1323434 AAT
1 AAT
1323437 TTAAGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 4 0.17
25 11 0.46
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (25 bp):
AATAATACTAATATTTAGAAATAAT
Found at i:1323893 original size:13 final size:14
Alignment explanation
Indices: 1323861--1323893 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1323851 CTACAATCTT
1323861 AAGTAATTAAAAAC
1 AAGTAATTAAAAAC
1323875 AA-TAATT-AAAAC
1 AAGTAATTAAAAAC
1323887 AAGTAAT
1 AAGTAAT
1323894 ACACATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 9 0.50
14 2 0.11
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (14 bp):
AAGTAATTAAAAAC
Found at i:1328679 original size:3 final size:3
Alignment explanation
Indices: 1328671--1328735 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1328661 TATATTAGTA
1328671 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1328719 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
1328736 AAAGTGGAAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1339920 original size:19 final size:19
Alignment explanation
Indices: 1339896--1339946 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1339886 ACCAACAAAA
*
1339896 TCGCAATGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
1339915 TCGCAACGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
1339934 TCGCAACGCGATC
1 TCGCAACGCGATC
1339947 TCCATTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGATCGCTAAT
Found at i:1340102 original size:20 final size:20
Alignment explanation
Indices: 1340077--1340170 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
1340067 AATTGGGAAA
1340077 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1340097 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1340117 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1340138 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1340158 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1340171 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1340732 original size:19 final size:19
Alignment explanation
Indices: 1340710--1340892 Score: 206
Period size: 19 Copynumber: 10.1 Consensus size: 19
1340700 GAAACCAAAA
*
1340710 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1340729 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1340743 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1340762 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1340781 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1340800 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1340819 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1340833 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1340852 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
* * *
1340871 ATCTCGTTGTGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
1340891 TC
1 TC
1340893 AACCAAAAGA
Statistics
Matches: 141, Mismatches: 12, Indels: 22
0.81 0.07 0.13
Matches are distributed among these distances:
14 20 0.14
16 5 0.04
17 6 0.04
19 95 0.67
20 15 0.11
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1340851 original size:33 final size:33
Alignment explanation
Indices: 1340762--1340867 Score: 140
Period size: 33 Copynumber: 3.1 Consensus size: 33
1340752 GATTTTCATT
1340762 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGA--TTC
1340797 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
1 ---TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
* **
1340833 TCTCGTTGCGATAGTCATTTCGCGTTGCGATTC
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
1340866 TC
1 TC
1340868 ATTATCTCGT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
33 32 0.49
36 3 0.05
38 30 0.46
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTC
Found at i:1340870 original size:90 final size:91
Alignment explanation
Indices: 1340710--1340892 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 91
1340700 GAAACCAAAA
**
1340710 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATT
*
1340775 TTCATT-TCGCGTTGCGATTTTCATT
66 CTCATTATCGCGTTGCGATTTTCATT
*
1340800 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATT
* * *
1340865 CTCATTATCTCGTTGTGATTTTTATT
66 CTCATTATCGCGTTGCGATTTTCATT
1340891 TC
1 TC
1340893 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 67 0.79
91 18 0.21
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (91 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATT
CTCATTATCGCGTTGCGATTTTCATT
Found at i:1342452 original size:63 final size:63
Alignment explanation
Indices: 1342349--1342473 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
1342339 CGTGATGAGG
* *
1342349 TCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTGGAGA
1 TCAATGCCTTGCGTGAGGAGATCGGAACTCTACGCAATAACGATGGTGCATGGCGTGTGGAGA
1342412 TCAATGCCTTGCGTGAGGAGATCGGAACTCTACGCAATAACGATGGTGCATGGCGTGTGGAG
1 TCAATGCCTTGCGTGAGGAGATCGGAACTCTACGCAATAACGATGGTGCATGGCGTGTGGAG
1342474 GTGTCTACTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (63 bp):
TCAATGCCTTGCGTGAGGAGATCGGAACTCTACGCAATAACGATGGTGCATGGCGTGTGGAGA
Found at i:1343124 original size:42 final size:42
Alignment explanation
Indices: 1343078--1343211 Score: 162
Period size: 42 Copynumber: 3.2 Consensus size: 42
1343068 CCTATCGTTG
1343078 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
* * * * * * * *
1343120 AAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTA-TCATTG
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACT-GTTC
* *
1343162 AAGAGGCCCCTATAATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
1343204 AAGAGGCC
1 AAGAGGCC
1343212 ACTGTCATCG
Statistics
Matches: 72, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
41 1 0.01
42 71 0.99
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
Found at i:1343208 original size:21 final size:21
Alignment explanation
Indices: 1343184--1343250 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1343174 TAATTCCTCG
1343184 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1343205 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1343226 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1343247 AGAG
1 AGAG
1343251 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1343229 original size:84 final size:84
Alignment explanation
Indices: 1343045--1343220 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
1343035 CCCGACTCGC
* *
1343045 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
*
1343110 CCCACTGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1343129 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
1343194 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1343213 CTGTCATC
1 CTGTCATC
1343221 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1343236 original size:42 final size:41
Alignment explanation
Indices: 1343045--1343250 Score: 137
Period size: 42 Copynumber: 4.9 Consensus size: 41
1343035 CCCGACTCGC
* * * * * * *
1343045 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCC-CTCCCACCATTCAAGAGGCCA
* * **
1343087 CTATCATTCCTCG-AGAGTCCCCTCCCACTGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCATTCAAGAGGCCA
* * * * * *
1343129 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCC-CTCCCACCATTCAAGAGGCCA
* * * *
1343171 CTATAATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCATTCAAGAGGCCA
*
1343213 CTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CTGTCATCCTTGAAGA-GTCCCTCCCACCATTCAAGAG
1343251 CCCGATTCAC
Statistics
Matches: 122, Mismatches: 34, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
41 9 0.07
42 101 0.83
43 12 0.10
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (41 bp):
CTGTCATCCTTGAAGAGTCCCTCCCACCATTCAAGAGGCCA
Found at i:1343250 original size:84 final size:84
Alignment explanation
Indices: 1343045--1343250 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
1343035 CCCGACTCGC
* * * * *
1343045 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
*
1343110 CCCACTGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * *
1343129 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
1343194 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
1343213 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
1343251 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATAATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1344627 original size:14 final size:14
Alignment explanation
Indices: 1344608--1344643 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1344598 ATTGTTTAAT
1344608 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1344622 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1344636 TGATTTGT
1 TGATTTGT
1344644 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1344811 original size:19 final size:19
Alignment explanation
Indices: 1344750--1344802 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1344740 AAAAAGTACT
*
1344750 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1344769 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1344788 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1344803 TAAATTCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1344829 original size:19 final size:19
Alignment explanation
Indices: 1344807--1344957 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1344797 CGAAATTAAA
1344807 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1344826 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
1344841 -CCTCGTTGCGATTCTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1344859 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1344873 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1344892 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1344907 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1344925 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1344944 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1344958 AGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 28 0.30
16 5 0.05
17 6 0.06
19 45 0.48
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1344853 original size:33 final size:32
Alignment explanation
Indices: 1344811--1344937 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1344801 ATTAAATTCG
1344811 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
1344844 CGTTGCGATTCTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1344877 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1344910 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1344938 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1344900 original size:66 final size:66
Alignment explanation
Indices: 1344804--1344936 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1344794 ACGCGAAATT
*
1344804 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTCTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTCTCATTTCGCATTGC
1344869 G
66 G
* *
1344870 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTCTCATTTCGCATTGC
1344935 G
66 G
1344936 A
1 A
1344937 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTCTCATTTCGCATTGC
G
Found at i:1347245 original size:12 final size:12
Alignment explanation
Indices: 1347228--1347252 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1347218 TCTTCGGGGA
1347228 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1347240 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1347252 C
1 C
1347253 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1347454 original size:24 final size:24
Alignment explanation
Indices: 1347427--1347494 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1347417 CTGAAACACC
*
1347427 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1347451 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
1347475 ATCAAATTTCGAATATTGAC
1 ATCAAAATCCGAGTATTGAC
1347495 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1348252 original size:20 final size:20
Alignment explanation
Indices: 1348227--1348275 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1348217 TATTATCTCA
1348227 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCG
1348247 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCG
1348267 TTGCGAAAG
1 TTGCGAAAG
1348276 GCAATCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (20 bp):
TTGCGAAAGTCAGAATCGCG
Found at i:1348526 original size:19 final size:20
Alignment explanation
Indices: 1348488--1348537 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
1348478 ATTCATTTGA
1348488 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1348508 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
*
1348527 CTATCACAACG
1 CTATCGCAACG
1348538 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1348604 original size:19 final size:19
Alignment explanation
Indices: 1348563--1348627 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1348553 GAAATGAAAA
1348563 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1348579 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1348596 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1348615 TCGCATTGCGATT
1 TCGCATTGCGATT
1348628 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1348658 original size:20 final size:20
Alignment explanation
Indices: 1348633--1348671 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1348623 CGATTCTCTC
1348633 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
1348653 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
1348672 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:1348773 original size:14 final size:14
Alignment explanation
Indices: 1348754--1348790 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1348744 CATCAATTAA
1348754 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1348768 ACAAATCATCTTTT
1 ACAAATCAACATTT
1348782 ACAAATCAA
1 ACAAATCAA
1348791 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1350679 original size:21 final size:20
Alignment explanation
Indices: 1350634--1350700 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
1350624 TAGTTTACTT
* * **
1350634 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
1350654 TCGCAACACGAAAAATGACTA
1 TCGCAACACG-AAAATGACTA
* * *
1350675 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1350695 TCGCAA
1 TCGCAA
1350701 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1350709 original size:19 final size:20
Alignment explanation
Indices: 1350666--1350710 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1350656 GCAACACGAA
1350666 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1350686 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
1350705 AAATGA
1 AAATGA
1350711 AAATCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1350729 original size:14 final size:14
Alignment explanation
Indices: 1350710--1350767 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1350700 ATGCGAAATG
*
1350710 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
1350724 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1350740 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1350756 AAAATCGCAACG
1 AAAATCGCAACG
1350768 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1350753 original size:32 final size:33
Alignment explanation
Indices: 1350694--1350784 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1350684 GGAAATGGCT
*
1350694 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1350727 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1350759 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1350785 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1350778 original size:19 final size:19
Alignment explanation
Indices: 1350634--1350789 Score: 73
Period size: 19 Copynumber: 8.6 Consensus size: 19
1350624 TAGTTTACTT
* *
1350634 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
1350654 TCGCAACACGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
***
1350675 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1350695 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
1350714 TCACAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1350728 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1350746 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1350760 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1350779 TCGCAATGCGA
1 TCGCAACGCGA
1350790 TTTGTGTTTC
Statistics
Matches: 106, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
14 19 0.18
15 1 0.01
16 6 0.06
17 2 0.02
18 11 0.10
19 26 0.25
20 26 0.25
21 11 0.10
22 4 0.04
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1350820 original size:14 final size:14
Alignment explanation
Indices: 1350801--1350858 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1350791 TTGTGTTTCG
1350801 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1350815 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1350831 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1350847 CGTTGTGATTTT
1 CGTTGCGATTTT
1350859 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1350839 original size:32 final size:33
Alignment explanation
Indices: 1350796--1350874 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1350786 GCGATTTGTG
*
1350796 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1350828 TTTCGCATTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1350861 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1350875 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 25 0.57
33 19 0.43
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1350893 original size:20 final size:19
Alignment explanation
Indices: 1350859--1350913 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1350849 TTGTGATTTT
*
1350859 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1350878 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1350898 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1350914 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1351421 original size:18 final size:18
Alignment explanation
Indices: 1351395--1351439 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1351385 GTCGATTAGA
1351395 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
1351413 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
1351431 TGATGGCTC
1 TGATGGCTC
1351440 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:1353395 original size:20 final size:20
Alignment explanation
Indices: 1353289--1353423 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1353279 CGCTTTGAAA
*
1353289 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1353310 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1353330 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1353350 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1353371 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1353391 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1353411 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1353424 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1353395 original size:61 final size:61
Alignment explanation
Indices: 1353289--1353426 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
1353279 CGCTTTGAAA
* * * *
1353289 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
1353350 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1353411 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1353427 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1353442 original size:61 final size:61
Alignment explanation
Indices: 1353289--1353444 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
1353279 CGCTTTGAAA
* ** * * * *
1353289 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
1353350 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
1353411 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
1353445 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1356566 original size:20 final size:20
Alignment explanation
Indices: 1356541--1356588 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1356531 GGAGCGTGGG
1356541 GGGAATCGGTACCCCTCATA
1 GGGAATCGGTACCCCTCATA
1356561 GGGAATCGGTACCCCTCATA
1 GGGAATCGGTACCCCTCATA
1356581 GGGAATCG
1 GGGAATCG
1356589 ATTCCCTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (20 bp):
GGGAATCGGTACCCCTCATA
Found at i:1367540 original size:36 final size:36
Alignment explanation
Indices: 1367428--1367519 Score: 141
Period size: 35 Copynumber: 2.6 Consensus size: 36
1367418 AATTTTGAAA
*
1367428 AAAAATGATTTTTAAGGTTTGGTAAATGTTTATTTG
1 AAAAATGATTTTTAAAGTTTGGTAAATGTTTATTTG
* *
1367464 -AAAATGGTTTTTAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGATTTTTAAAGTTTGGTAAATGTTTATTTG
1367499 AAAAATGATTTTTCAAAGTTT
1 AAAAATGATTTTT-AAAGTTT
1367520 TGTAGATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
35 32 0.64
36 11 0.22
37 7 0.14
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (36 bp):
AAAAATGATTTTTAAAGTTTGGTAAATGTTTATTTG
Found at i:1372111 original size:37 final size:36
Alignment explanation
Indices: 1372012--1372118 Score: 153
Period size: 35 Copynumber: 2.9 Consensus size: 36
1372002 TGGCAACCAA
* *
1372012 CTTTGAAAAAATGATTTTCAAAATTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
1372049 TTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
1372084 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGT
1372119 ATGTTGAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
35 32 0.51
36 7 0.11
37 24 0.38
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1372126 original size:36 final size:35
Alignment explanation
Indices: 1372013--1372130 Score: 148
Period size: 35 Copynumber: 3.3 Consensus size: 35
1372003 GGCAACCAAC
* *
1372013 TTTGAAAAAATGATTTTCAAAATTTGGTAAATGTTTT
1 TTTG-AAAAATGGTTTTCAAAGTTTGGTAAATG-TTT
1372050 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
1372084 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTAT
1 -TTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
*
1372121 GTTGAAAAAT
1 TTTGAAAAAT
1372131 TATAATGGGA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.04
35 29 0.40
36 16 0.22
37 25 0.34
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (35 bp):
TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1382940 original size:26 final size:26
Alignment explanation
Indices: 1382909--1382974 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
1382899 AGTATGACAA
1382909 TGGAGGTGGAGGGGTGGTGGGAATGG
1 TGGAGGTGGAGGGGTGGTGGGAATGG
1382935 TGGAGGTGGAGGGGTGGTGGGAATGG
1 TGGAGGTGGAGGGGTGGTGGGAATGG
1382961 TGGAGGTGGAGGGG
1 TGGAGGTGGAGGGG
1382975 GTGGCGGAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.18
Consensus pattern (26 bp):
TGGAGGTGGAGGGGTGGTGGGAATGG
Found at i:1383201 original size:3 final size:3
Alignment explanation
Indices: 1383193--1383230 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1383183 TCAAGGAATG
*
1383193 GGT GGT GGT GGT GGT GAT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1383231 AGGAGGAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.66, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:1389416 original size:25 final size:25
Alignment explanation
Indices: 1389385--1389436 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1389375 TATATATATA
1389385 TCGAACAAACATATTATATATGTTT
1 TCGAACAAACATATTATATATGTTT
1389410 TCGAACAAACATATTATATATGTTT
1 TCGAACAAACATATTATATATGTTT
1389435 TC
1 TC
1389437 AAAGCAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (25 bp):
TCGAACAAACATATTATATATGTTT
Found at i:1391868 original size:34 final size:32
Alignment explanation
Indices: 1391815--1391884 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1391805 CCTTACAAAC
*
1391815 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1391847 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1391881 TCCC
1 TCCC
1391885 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1392337 original size:19 final size:19
Alignment explanation
Indices: 1392313--1392368 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1392303 GAGCCTCGGG
* *
1392313 TTACTGTTCAAACATTGAT
1 TTACTGTTCAAACAGTAAT
*
1392332 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
*
1392351 TTACTGTTCAAATAGTAA
1 TTACTGTTCAAACAGTAA
1392369 ATTATTATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:1392379 original size:19 final size:19
Alignment explanation
Indices: 1392332--1392379 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1392322 AAACATTGAT
* *
1392332 TTACTGTTCAAATAGTAAT
1 TTACTATTCAAATAGTAAA
*
1392351 TTACTGTTCAAATAGTAAA
1 TTACTATTCAAATAGTAAA
*
1392370 TTATTATTCA
1 TTACTATTCA
1392380 TAAAAACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (19 bp):
TTACTATTCAAATAGTAAA
Found at i:1392491 original size:30 final size:31
Alignment explanation
Indices: 1392444--1392533 Score: 166
Period size: 31 Copynumber: 3.0 Consensus size: 31
1392434 AAATTTTGAA
1392444 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1392473 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1392504 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
1392534 TCCTTAAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1392737 original size:22 final size:21
Alignment explanation
Indices: 1392694--1392739 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1392684 AAGCTCCCCC
1392694 TTTTTCATTAAGAAATTGATT
1 TTTTTCATTAAGAAATTGATT
* *
1392715 TTTTTTATTAAGAAATTGAAT
1 TTTTTCATTAAGAAATTGATT
1392736 TTTT
1 TTTT
1392740 CAAACTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.57
Consensus pattern (21 bp):
TTTTTCATTAAGAAATTGATT
Found at i:1394766 original size:34 final size:32
Alignment explanation
Indices: 1394713--1394782 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1394703 CCTTACAAAC
*
1394713 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1394745 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1394779 TCCC
1 TCCC
1394783 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1395092 original size:21 final size:21
Alignment explanation
Indices: 1395066--1395107 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1395056 CCAGAATGGG
*
1395066 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1395087 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1395108 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1395339 original size:29 final size:31
Alignment explanation
Indices: 1395307--1395366 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1395297 AAATTTTGAA
1395307 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1395336 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1395367 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1398909 original size:18 final size:19
Alignment explanation
Indices: 1398882--1398918 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1398872 ATATACATAA
*
1398882 AGTAAGTTAAT-TATAGTT
1 AGTAAATTAATATATAGTT
1398900 AGTAAATTAATATATAGTT
1 AGTAAATTAATATATAGTT
1398919 GATTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
AGTAAATTAATATATAGTT
Found at i:1398947 original size:37 final size:37
Alignment explanation
Indices: 1398841--1398998 Score: 113
Period size: 45 Copynumber: 4.1 Consensus size: 37
1398831 CAATCAAAAA
* *
1398841 AGTTATTTAAAATATATTAATAAATTATTTAATATAC
1 AGTTAATTAAAATATATTAATAAATTATTTAATATAT
* * ** * * * *
1398878 A-TAAAGTAAGTTA-ATTATAGTTAGTAAATTAATATAT
1 AGTTAATTAAAATATATTA-A-TAAATTATTTAATATAT
*
1398915 AGTTGATTAAAATATATTAATAAATTATTTAATATATAGAAAGT
1 AGTTAATTAAAATATATTAATAAATTATTT-A-ATAT----A-T
1398959 AAGTTAATTAAAATATATTAATAAATTATTTAATATAT
1 -AGTTAATTAAAATATATTAATAAATTATTTAATATAT
1398997 AG
1 AG
1398999 AAAGTAAGTT
Statistics
Matches: 89, Mismatches: 20, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
35 4 0.04
36 8 0.09
37 22 0.25
38 10 0.11
39 9 0.10
43 5 0.06
44 2 0.02
45 29 0.33
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (37 bp):
AGTTAATTAAAATATATTAATAAATTATTTAATATAT
Found at i:1398970 original size:45 final size:45
Alignment explanation
Indices: 1398915--1399009 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
1398905 ATTAATATAT
*
1398915 AGTTGATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
1 AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
1398960 AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
1 AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
1399005 AGTTA
1 AGTTA
1399010 GTAAATTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (45 bp):
AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
Found at i:1399067 original size:53 final size:53
Alignment explanation
Indices: 1398888--1399077 Score: 172
Period size: 53 Copynumber: 3.5 Consensus size: 53
1398878 ATAAAGTAAG
* * * * *
1398888 TTAAT-TATAGTTAGTAAATTAATATATAGT-TGATTAAAATATATTAATAAATTAT
1 TTAATATATAGTTAGTAAATTAAT-TAAAATAT-ATT--AATAAATTATTTAATTAT
** *
1398943 TTAATATATAGAAAGTAAGTTAATTAAAATATATTAATAAATTATTTAA-TAT
1 TTAATATATAGTTAGTAAATTAATTAAAATATATTAATAAATTATTTAATTAT
* * * *
1398995 ATAGAAAGTA-AGTTAGTAAATTATTTAAAATGTATTAATAAATTATTTAATTAT
1 TTA-ATA-TATAGTTAGTAAATTAATTAAAATATATTAATAAATTATTTAATTAT
*
1399049 TTAATATATAGTTGGTAAATTAATATAAA
1 TTAATATATAGTTAGTAAATTAAT-TAAA
1399078 TTATGATGTA
Statistics
Matches: 109, Mismatches: 19, Indels: 15
0.76 0.13 0.10
Matches are distributed among these distances:
52 7 0.06
53 63 0.58
54 11 0.10
55 12 0.11
56 16 0.15
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (53 bp):
TTAATATATAGTTAGTAAATTAATTAAAATATATTAATAAATTATTTAATTAT
Found at i:1399945 original size:53 final size:47
Alignment explanation
Indices: 1399880--1400001 Score: 167
Period size: 45 Copynumber: 2.5 Consensus size: 47
1399870 AAAAATCATA
*
1399880 AAATTATTTATTAATATATTTTAAAAATTTTACTAACTTACTTTCTATATATT
1 AAATAATTTATTAATATATTTT-AAAA---T--TAACTTACTTTCTATATATT
1399933 AAATAATTTATTAATATATTTT--AATTAACTTACTTTCTATATATT
1 AAATAATTTATTAATATATTTTAAAATTAACTTACTTTCTATATATT
1399978 AAATAATTTATTAATATATTTTAA
1 AAATAATTTATTAATATATTTTAA
1400002 TCAACTATAT
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
45 42 0.64
47 1 0.02
50 2 0.03
53 21 0.32
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (47 bp):
AAATAATTTATTAATATATTTTAAAATTAACTTACTTTCTATATATT
Found at i:1399956 original size:22 final size:22
Alignment explanation
Indices: 1399925--1400001 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
1399915 ACTTACTTTC
1399925 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
* * * **
1399947 TATATTTTAATTAACTTACTTTC
1 TATATATTAAATAATTTA-TTAA
1399970 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
*
1399992 TATATTTTAA
1 TATATATTAA
1400002 TCAACTATAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
22 26 0.60
23 17 0.40
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATATTAAATAATTTATTAA
Found at i:1399963 original size:45 final size:45
Alignment explanation
Indices: 1399913--1400007 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
1399903 AAAATTTTAC
1399913 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1399958 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
*
1400003 CAACT
1 TAACT
1400008 ATATATTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (45 bp):
TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
Found at i:1400039 original size:18 final size:19
Alignment explanation
Indices: 1400004--1400053 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
1399994 TATTTTAATC
*
1400004 AACTATATATTAATTTACT
1 AACTATATATTAACTTACT
1400023 AACTATA-ATTAACTTACT
1 AACTATATATTAACTTACT
**
1400041 TTCTATATATTAA
1 AACTATATATTAA
1400054 ATACTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (19 bp):
AACTATATATTAACTTACT
Found at i:1401916 original size:18 final size:19
Alignment explanation
Indices: 1401893--1401935 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1401883 ACTTTTGATA
* *
1401893 TTTATTATAAA-TTTTATT
1 TTTATTATAAAGTATAATT
*
1401911 TTTATTTTAAAGTATAATT
1 TTTATTATAAAGTATAATT
1401930 TTTATT
1 TTTATT
1401936 TTTGAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTATTATAAAGTATAATT
Found at i:1407209 original size:3 final size:3
Alignment explanation
Indices: 1407197--1407242 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
1407187 CATTTGCTTA
1407197 TAT TATT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TA- TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1407240 TAT
1 TAT
1407243 ATTTATTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.15
3 30 0.77
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1407228 original size:30 final size:30
Alignment explanation
Indices: 1407194--1407250 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1407184 TCTCATTTGC
1407194 TTATATTAT-TTATTATTAT-TATTATTATTA
1 TTATATTATATTA-TATTATAT-TTATTATTA
1407224 TTATATTATATTATATTATATTTATTA
1 TTATATTATATTATATTATATTTATTA
1407251 AATAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TTATATTATATTATATTATATTTATTATTA
Found at i:1408656 original size:26 final size:26
Alignment explanation
Indices: 1408600--1408658 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
1408590 TTATTTGCAA
* * *
1408600 TATTATTTTTTTATTATTATTGCTTT
1 TATTATTATTTCATTATTATTACTTT
* * *
1408626 AATTATTATTTCATTATTTTTATTTT
1 TATTATTATTTCATTATTATTACTTT
1408652 TATTATT
1 TATTATT
1408659 TATATAAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (26 bp):
TATTATTATTTCATTATTATTACTTT
Found at i:1409486 original size:21 final size:21
Alignment explanation
Indices: 1409456--1409496 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1409446 AATTCATTTA
* *
1409456 TTTAATTTTTAATTATTTTCT
1 TTTAAATTTTAATGATTTTCT
*
1409477 TTTAAATTTTTATGATTTTC
1 TTTAAATTTTAATGATTTTC
1409497 ATAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTAAATTTTAATGATTTTCT
Found at i:1411163 original size:14 final size:14
Alignment explanation
Indices: 1411125--1411163 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1411115 ATTTTAAATA
*
1411125 ATTTATATTTACAT
1 ATTTATATTTGCAT
* *
1411139 TTTTACATTTGCAT
1 ATTTATATTTGCAT
1411153 ATTTATATTTG
1 ATTTATATTTG
1411164 GCATCTTTGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (14 bp):
ATTTATATTTGCAT
Found at i:1411186 original size:29 final size:29
Alignment explanation
Indices: 1411125--1411192 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
1411115 ATTTTAAATA
*
1411125 ATTTATATTT-ACATTTTTACATTTGCAT
1 ATTTATATTTGACATCTTTACATTTGCAT
* * *
1411153 ATTTATATTTGGCATCTTTGCATTTGTAT
1 ATTTATATTTGACATCTTTACATTTGCAT
* *
1411182 TTTTATGTTTG
1 ATTTATATTTG
1411193 CTTTTGTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.30
29 23 0.70
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (29 bp):
ATTTATATTTGACATCTTTACATTTGCAT
Found at i:1415177 original size:23 final size:22
Alignment explanation
Indices: 1415133--1415177 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1415123 AATGTCATGG
*
1415133 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1415155 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1415178 AAACTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1416610 original size:103 final size:103
Alignment explanation
Indices: 1416385--1416602 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1416375 GTCGAGGGTC
1416385 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1416450 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATAATTCTTAAGGAATGA
*
1416488 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1416553 TTGATCCCTAGTATATGTATATAATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATAATTCTTAAGGAATGA
1416591 TATGTGGTCCTT
1 TATGTGGTCCTT
1416603 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATAATTCTTAAGGAATGA
Found at i:1416649 original size:23 final size:23
Alignment explanation
Indices: 1416619--1416678 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1416609 ATTATTATAT
1416619 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
1416642 GGCACTACGGTGCAATTTTATGT
1 GGCACTACGGTGCAATTCTACGC
*
1416665 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
1416679 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1416686 original size:23 final size:22
Alignment explanation
Indices: 1416608--1416686 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
1416598 TCCTTATGGA
*
1416608 CATTATTATATGGCACTACGGTG
1 CATT-TTATGTGGCACTACGGTG
* * *
1416631 CAATTCTACGCGGCACTACGGTG
1 C-ATTTTATGTGGCACTACGGTG
*
1416654 CAATTTTATGTGGCACTTCGGTG
1 C-ATTTTATGTGGCACTACGGTG
1416677 CATTTATATG
1 CATTT-TATG
1416687 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 4 0.09
23 39 0.85
24 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (22 bp):
CATTTTATGTGGCACTACGGTG
Found at i:1420542 original size:23 final size:22
Alignment explanation
Indices: 1420498--1420542 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1420488 AATGTCATGG
*
1420498 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1420520 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1420543 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1421878 original size:18 final size:18
Alignment explanation
Indices: 1421855--1421890 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1421845 AGGAATGATA
*
1421855 TGTGGTCTTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1421873 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1421891 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1421910 original size:121 final size:121
Alignment explanation
Indices: 1421752--1421982 Score: 435
Period size: 121 Copynumber: 1.9 Consensus size: 121
1421742 CGAGGGTCTA
1421752 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1421817 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACAT
**
1421873 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
1421938 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
1421983 CTTATGGACA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 107 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACAT
Found at i:1422068 original size:23 final size:23
Alignment explanation
Indices: 1421992--1422069 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
1421982 CCTTATGGAC
*
1421992 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
1422016 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
1422039 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
1422062 TTTATATG
1 ATTATATG
1422070 ATCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1422901 original size:13 final size:12
Alignment explanation
Indices: 1422873--1422900 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1422863 AGAAAAATTG
1422873 AAAAGCAAAAAA
1 AAAAGCAAAAAA
1422885 AAAAGCAAAAAA
1 AAAAGCAAAAAA
1422897 AAAA
1 AAAA
1422901 AAGAAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAGCAAAAAA
Found at i:1425370 original size:114 final size:114
Alignment explanation
Indices: 1425165--1425381 Score: 362
Period size: 114 Copynumber: 1.9 Consensus size: 114
1425155 CACGTTCTCG
*
1425165 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
1425230 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATAAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATAAATTTGCTCA
* * *
1425279 TAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
1425344 GGTAGGAACCCCAGAACCAATTATTGGAATTGAAAGAT
66 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGAT
1425382 GACCTGCATG
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 95 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATAAATTTGCTCA
Found at i:1427529 original size:50 final size:50
Alignment explanation
Indices: 1427454--1427596 Score: 259
Period size: 50 Copynumber: 2.9 Consensus size: 50
1427444 TAATTCGAGC
* *
1427454 AGAAACCACAGGAAAGGATAAATGTGTTGCCAAATGTTTTACATCTGAGT
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTGAGT
1427504 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTGAGT
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTGAGT
*
1427554 AGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACA
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACA
1427597 AACCAGTTAT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (50 bp):
AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTGAGT
Found at i:1427989 original size:22 final size:22
Alignment explanation
Indices: 1427964--1428040 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1427954 ATCTACACTC
1427964 TTAAAAGATGATAGATTATCTT
1 TTAAAAGATGATAGATTATCTT
*
1427986 TTAAAAGATGATAGATTCTCTT
1 TTAAAAGATGATAGATTATCTT
*
1428008 TTTAAAGATGATAGATTATCTT
1 TTAAAAGATGATAGATTATCTT
*
1428030 TTCAAAGATGA
1 TTAAAAGATGA
1428041 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.40
Consensus pattern (22 bp):
TTAAAAGATGATAGATTATCTT
Found at i:1428866 original size:76 final size:77
Alignment explanation
Indices: 1428718--1429027 Score: 507
Period size: 76 Copynumber: 4.1 Consensus size: 77
1428708 CTATTTCCCA
*
1428718 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1428783 AAGCCTTAGGGT
66 AAACCTTAGGGT
* * **
1428795 CATCTATAAGTCCTACAGTGCATGATGTTTCC-AAAAATCCTTCAAGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1428859 AAACCTTAGGGT
66 AAACCTTAGGGT
* *
1428871 TATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1428936 AAGCCTTAGGGT
66 AAACCTTAGGGT
*
1428948 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTTGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
1429012 AAACCTTCGGGT
66 AAACCTTAGGGT
1429024 CATC
1 CATC
1429028 AGCATTTCCA
Statistics
Matches: 214, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
76 114 0.53
77 100 0.47
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (77 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAACCTTAGGGT
Found at i:1428997 original size:153 final size:153
Alignment explanation
Indices: 1428719--1429023 Score: 556
Period size: 153 Copynumber: 2.0 Consensus size: 153
1428709 TATTTCCCAC
1428719 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1428784 AGCCTTAGGGTCATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCAAGAGCTTTTT
66 AGCCTTAGGGTCATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAAGAGCTTTTT
1428849 GATGTTTTCAAAACCTTAGGGTT
131 GATGTTTTCAAAACCTTAGGGTT
1428872 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* ***
1428937 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
66 AGCCTTAGGGTCATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAAGAGCTTTTT
*
1429002 GATGTTTTCAAAACCTTCGGGT
131 GATGTTTTCAAAACCTTAGGGT
1429024 CATCAGCATT
Statistics
Matches: 146, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
153 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (153 bp):
ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAAGAGCTTTTT
GATGTTTTCAAAACCTTAGGGTT
Found at i:1429424 original size:113 final size:111
Alignment explanation
Indices: 1429025--1429577 Score: 746
Period size: 113 Copynumber: 4.9 Consensus size: 111
1429015 CCTTCGGGTC
* * * *
1429025 ATCAGCATTTCCAGAAGAATTCATAATGAGAAGAACTCATCTGAAGAATGAAAAAGAAGTTCATA
1 ATCAACATTTCCAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
**
1429090 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGG
65 ATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGG
** * * *
1429137 ATCAGTATTACCAGAAAGCTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * * *
1429202 TGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATTACTCGATGG
66 TGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGG
*
1429248 ATCAACTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * * * * * * *
1429313 ATAAGAAGAACTTGTTTAACCTTTCGTTTGAATTCATCATTCGGTGA
65 ATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGG
* * * * *
1429360 ATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACATTTCCAG--AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
1429425 AATGAGAAGAACTTGTTTAACCTTTTGTTTAAATTCATCACTTGATGG
64 AATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGG
*
1429473 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCC--AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
1429538 AATGAGAAGAACTTGTTCAACGTTTTGCTTAAATTCATCA
64 AATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA
1429578 GCATTTCCAG
Statistics
Matches: 385, Mismatches: 51, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
111 98 0.25
112 105 0.27
113 179 0.46
114 1 0.00
115 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (111 bp):
ATCAACATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGG
Found at i:1429590 original size:61 final size:62
Alignment explanation
Indices: 1429525--1429672 Score: 237
Period size: 61 Copynumber: 2.4 Consensus size: 62
1429515 TGAAGAAGGA
1429525 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACGTTTTGCTTAAATTCATCAGCATTTCC-
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACGTTTTGCTTAAATTCATCAGCATTTCCG
* *
1429586 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCAGCATTTCCG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACGTTTTGCTTAAATTCATCAGCATTTCCG
* **
1429648 GGTCG-AGTTCATAATGAGAAGAACT
1 AGAAGAAGTTCATAATGAGAAGAACT
1429673 CATCTGAAGA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
61 79 0.98
62 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (62 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACGTTTTGCTTAAATTCATCAGCATTTCCG
Found at i:1430178 original size:3 final size:3
Alignment explanation
Indices: 1430166--1430196 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
1430156 CATTTGCTTA
1430166 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
1430197 GTTATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1431503 original size:14 final size:14
Alignment explanation
Indices: 1431465--1431538 Score: 53
Period size: 14 Copynumber: 5.1 Consensus size: 14
1431455 ATTTTAATCA
1431465 TTAA-ATTTTCATTT
1 TTAATATTTT-ATTT
*
1431479 TTGACTA-TTTATTT
1 TT-AATATTTTATTT
*
1431493 TTAATATTTTACATT
1 TTAATATTTTA-TTT
* *
1431508 TTAATACTATATTT
1 TTAATATTTTATTT
1431522 TTAATTCATTTTATTT
1 TTAA-T-ATTTTATTT
1431538 T
1 T
1431539 AATCATTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
13 3 0.07
14 18 0.39
15 16 0.35
16 9 0.20
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (14 bp):
TTAATATTTTATTT
Found at i:1431567 original size:3 final size:3
Alignment explanation
Indices: 1431554--1431612 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
1431544 TTATTTGCAA
* * *
1431554 TAT TAT T-T TAT TAT TAT TAT TGCT T-T AAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
1431597 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
1431613 TATATAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Done.