Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008208.1 Hibiscus syriacus cultivar Beakdansim tig00110830_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: 2533913
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:933319 original size:23 final size:22
Alignment explanation
Indices: 933291--933347 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 22
933281 TTGTCAAACT
933291 AGAAAACTATTAATAATAAAGCA
1 AGAAAA-TATTAATAATAAAGCA
933314 AGAAAATTATTAATAATAAAGCA
1 AGAAAA-TATTAATAATAAAGCA
933337 AGAAAATATTA
1 AGAAAATATTA
933348 TAAAGTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 5 0.15
23 28 0.85
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (22 bp):
AGAAAATATTAATAATAAAGCA
Found at i:940679 original size:106 final size:108
Alignment explanation
Indices: 940494--940707 Score: 414
Period size: 106 Copynumber: 2.0 Consensus size: 108
940484 TCATGATAAA
940494 TGTAAAAACATCCTAGGTTTTGAAATGGAGTTTCAGGGTGGGCTCTAATTCCCTGTAGTCTCCCG
1 TGTAAAAACATCCTAGGTTTTGAAATGGAGTTTCAGGGTGGGCTCTAATTCCCTGTAGTCTCCCG
940559 GTTTAGGTTCTAAAAAAGGTACCCGAG-TTT-CTTGCTAGTGC
66 GTTTAGGTTCTAAAAAAGGTACCCGAGTTTTCCTTGCTAGTGC
940600 TGTAAAAACATCCTAGGTTTTGAAATGGAGTTTCAGGGTGGGCTCTAATTCCCTGTAGTCTCCCG
1 TGTAAAAACATCCTAGGTTTTGAAATGGAGTTTCAGGGTGGGCTCTAATTCCCTGTAGTCTCCCG
940665 GTTTAGGTTCTAAAAAAGGTACCCGAGTTTTCCTTGCTAGTGC
66 GTTTAGGTTCTAAAAAAGGTACCCGAGTTTTCCTTGCTAGTGC
940708 CCCGTTGGGC
Statistics
Matches: 106, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
106 92 0.87
107 3 0.03
108 11 0.10
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (108 bp):
TGTAAAAACATCCTAGGTTTTGAAATGGAGTTTCAGGGTGGGCTCTAATTCCCTGTAGTCTCCCG
GTTTAGGTTCTAAAAAAGGTACCCGAGTTTTCCTTGCTAGTGC
Found at i:941476 original size:2 final size:2
Alignment explanation
Indices: 941469--941503 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
941459 ATGATGCCAG
*
941469 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
941504 GATTTTGTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:944793 original size:54 final size:54
Alignment explanation
Indices: 944728--945202 Score: 443
Period size: 54 Copynumber: 8.8 Consensus size: 54
944718 TACCAAATAG
* * *
944728 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTCA
1 GCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCA
* * *
944782 GCACTATGTGTGTAACTCACGAAATTCATCATTTGTTGATGAACAACCATTTC-
1 GCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCA
*
944835 GACACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCG
1 G-CACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCA
* * * * * * * * **
944890 GCACTATGTATGCCACCCATGCAACTCATCATATGTTAATGAAAAACCGTTTTG
1 GCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCA
*** *
944944 GCACTATGTGTGCAACTCGTAAAATTCATCATATGTTGATGAACAACTGTTTC-
1 GCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCA
* *
944997 GACACTATGTGTGCAACTCACTG-AATTCATCATGA-GTTGATGAACAACTG-TACAA
1 G-CACTATGTGTGCAACTCAC-GAAATTCATCAT-ATGTTGATGAACAACCGTTTC-A
* *
945052 GCACTATGTGTGCAA-TCCAC-ATAATTCATCGTGA-GTTGATGAACAACCG-TACA
1 GCACTATGTGTGCAACT-CACGA-AATTCATCAT-ATGTTGATGAACAACCGTTTCA
* * * * *
945105 TGCACTATGTGTGCAACCCATGGAATTCATCATGA-GATGATGAACAACCG-TACA
1 -GCACTATGTGTGCAACTCACGAAATTCATCAT-ATGTTGATGAACAACCGTTTCA
* * * * *
945159 GGCTCTCTGTGTGCAA-TCCACAAAATTCATGATGTGTTGATGAA
1 -GCACTATGTGTGCAACT-CACGAAATTCATCATATGTTGATGAA
945203 TGACCGTATA
Statistics
Matches: 356, Mismatches: 50, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
53 6 0.02
54 347 0.97
55 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
GCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCA
Found at i:946780 original size:170 final size:170
Alignment explanation
Indices: 946498--946838 Score: 682
Period size: 170 Copynumber: 2.0 Consensus size: 170
946488 AAATCATTGA
946498 TAGAGTTGGAAAAATTACTTACAAACTTGACTTACCAGATGATAGAGAAGCGGCAACGAATGATG
1 TAGAGTTGGAAAAATTACTTACAAACTTGACTTACCAGATGATAGAGAAGCGGCAACGAATGATG
946563 TGAACGTTACTCTCATTGAGGAAACAAACCTAGGAAGGCTTTAGACTCGAGGATGAAACGAATGG
66 TGAACGTTACTCTCATTGAGGAAACAAACCTAGGAAGGCTTTAGACTCGAGGATGAAACGAATGG
946628 ATTTGAATGGAGGCTATAGAAGTGGTGGAAATGTTAGGGT
131 ATTTGAATGGAGGCTATAGAAGTGGTGGAAATGTTAGGGT
946668 TAGAGTTGGAAAAATTACTTACAAACTTGACTTACCAGATGATAGAGAAGCGGCAACGAATGATG
1 TAGAGTTGGAAAAATTACTTACAAACTTGACTTACCAGATGATAGAGAAGCGGCAACGAATGATG
946733 TGAACGTTACTCTCATTGAGGAAACAAACCTAGGAAGGCTTTAGACTCGAGGATGAAACGAATGG
66 TGAACGTTACTCTCATTGAGGAAACAAACCTAGGAAGGCTTTAGACTCGAGGATGAAACGAATGG
946798 ATTTGAATGGAGGCTATAGAAGTGGTGGAAATGTTAGGGT
131 ATTTGAATGGAGGCTATAGAAGTGGTGGAAATGTTAGGGT
946838 T
1 T
946839 CTTGGGAGGA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (170 bp):
TAGAGTTGGAAAAATTACTTACAAACTTGACTTACCAGATGATAGAGAAGCGGCAACGAATGATG
TGAACGTTACTCTCATTGAGGAAACAAACCTAGGAAGGCTTTAGACTCGAGGATGAAACGAATGG
ATTTGAATGGAGGCTATAGAAGTGGTGGAAATGTTAGGGT
Found at i:960366 original size:24 final size:25
Alignment explanation
Indices: 960339--960385 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
960329 ATAAATAAAA
960339 TATGACAAAAA-TATAAAAATTCGC
1 TATGACAAAAATTATAAAAATTCGC
** *
960363 TATGGTAAAAATTATCAAAATTC
1 TATGACAAAAATTATAAAAATTC
960386 TGTCAATTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (25 bp):
TATGACAAAAATTATAAAAATTCGC
Found at i:973946 original size:20 final size:20
Alignment explanation
Indices: 973910--973959 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
973900 TAAAATGATC
*
973910 CAATTTC-ACATTTTAACAT
1 CAATTTCAACACTTTAACAT
*
973929 CAATTTGAACACTTTAACAT
1 CAATTTCAACACTTTAACAT
*
973949 TAATTTCAACA
1 CAATTTCAACA
973960 TAGTACAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (20 bp):
CAATTTCAACACTTTAACAT
Found at i:979880 original size:33 final size:33
Alignment explanation
Indices: 979842--979907 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
979832 CAACCTGCTG
*
979842 TTGGACTCTATGGCATAGTAACTATTCAACTGT
1 TTGGACTCTATGGCATAGCAACTATTCAACTGT
979875 TTGGACTCTATGGCATAGCAACTATTCAACTGT
1 TTGGACTCTATGGCATAGCAACTATTCAACTGT
979908 CCCTCAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (33 bp):
TTGGACTCTATGGCATAGCAACTATTCAACTGT
Found at i:993426 original size:348 final size:345
Alignment explanation
Indices: 992779--993476 Score: 1130
Period size: 348 Copynumber: 2.0 Consensus size: 345
992769 CTAACTCTTT
* *
992779 TAATGTATTATATCCTTTTGTCCTTTATATATATAATAGACTCAAGTCTTGGAATAGTCACAGTT
1 TAATGTATTATATCATTTTGTCCTTTATATATAGAATAGACTCAAGTCTTGGAATAGTCACAGTT
992844 GTGTAAAACATCTATTATTTCTTGATATCTATAGTAGACTAAAATAAGTGAATAATTTGTGATAT
66 GTGTAAAACATCTATTATTTCTTGATATCTATAGTAGACTAAAATAAGTGAATAATTTGTGATAT
* *
992909 CTCATACAAACTTATTCGAGCATGGCCATGCATTTCTACTCTCACTAAATCAAGTGGCCTATGAT
131 CTCATACAAACTTATTCCAGCATGGCCATGCATTTCTACTCTCACTAAATCAAGTGGCATATGAT
*
992974 ATATTTCTTATTATGTAGGAATGACAAATCATATCTAATCATTCACACCCCACTACATCTATCGT
196 ATATTTCTTATTATGTAGGAATAACAAATCATATCTAATCATTCACACCCCACTACATCTATCGT
*
993039 GATATGTTCAATGTCAGTCTTTATAGTGTATCAAGTTACGGAGCATGTTTAACTGTACCAAAACA
261 GATATGTTCAATGTCAGTCTTTATAGTGCATCAAGTTACGGAGCATGTTTAACTGTACCAAAACA
993104 TAAAACAATATATGTTGAGATTG
326 T---ACAATATATGTTGAGATTG
* * * *
993127 TAATGTATTATATCATTTTGTCCTTTATATCTAGGATA-AGTCCAAGTCTTGGAATAGTCATAGT
1 TAATGTATTATATCATTTTGTCCTTTATATATAGAATAGACT-CAAGTCTTGGAATAGTCACAGT
* * *
993191 TGTGTAGAACATCTATTATTTCTTGATATCTATAGTAGATTATAATAAGTGAATAATTTGTGATA
65 TGTGTAAAACATCTATTATTTCTTGATATCTATAGTAGACTAAAATAAGTGAATAATTTGTGATA
* * * * * * *
993256 TCTCATGCCAACTTATTCCAGCATGGCTATGCATTTTTATTCTCACTCAATCAAGTGGCATGTGA
130 TCTCATACAAACTTATTCCAGCATGGCCATGCATTTCTACTCTCACTAAATCAAGTGGCATATGA
993321 TATATTT-TCTATTATGTAGGAATAACAAATCATATCTAATCATTCACACCCCACTACATCTATC
195 TATATTTCT-TATTATGTAGGAATAACAAATCATATCTAATCATTCACACCCCACTACATCTATC
* * *
993385 GTGATATGTTCAATGTCAGTCTTTATAGTGCATCCAGTTACGGAGCATGTTTAATTGTATCAAAA
259 GTGATATGTTCAATGTCAGTCTTTATAGTGCATCAAGTTACGGAGCATGTTTAACTGTACCAAAA
993450 CATACAATATATGTTGAGATTG
324 CATACAATATATGTTGAGATTG
993472 TAATG
1 TAATG
993477 ATATCAAGTC
Statistics
Matches: 325, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
345 24 0.07
347 3 0.01
348 298 0.92
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (345 bp):
TAATGTATTATATCATTTTGTCCTTTATATATAGAATAGACTCAAGTCTTGGAATAGTCACAGTT
GTGTAAAACATCTATTATTTCTTGATATCTATAGTAGACTAAAATAAGTGAATAATTTGTGATAT
CTCATACAAACTTATTCCAGCATGGCCATGCATTTCTACTCTCACTAAATCAAGTGGCATATGAT
ATATTTCTTATTATGTAGGAATAACAAATCATATCTAATCATTCACACCCCACTACATCTATCGT
GATATGTTCAATGTCAGTCTTTATAGTGCATCAAGTTACGGAGCATGTTTAACTGTACCAAAACA
TACAATATATGTTGAGATTG
Found at i:1013196 original size:2 final size:2
Alignment explanation
Indices: 1013191--1013224 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
1013181 CTTGTGTGTG
1013191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1013225 GTCTATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1034012 original size:270 final size:261
Alignment explanation
Indices: 1033489--1034019 Score: 956
Period size: 270 Copynumber: 2.0 Consensus size: 261
1033479 TCCCCCAAAC
1033489 TTAAAGGAAACATTGCCTCAATTCATAAAAAGAAACTAAATAAATAAACTAAATGCCATGCAATG
1 TTAAAGGAAACATTGCCTCAATTCATAAAAAGAAACTAAATAAATAAACTAAATGCCATGCAATG
1033554 AAATGCAACTAATGAAAATGAATGCAAAGAGGTACCTCAATGATTGTGTGGTGGCGGGCCTTGGA
66 AAATGCAACTAATGAAAATGAATGCAAAGAGGTACCTCAATGATTGTGTGGTGGCGGGCCTTGGA
1033619 GGTGCTAGCAGCTCCTCGCCTAGTGCGCTTTGAAGGGGTGATGGGTGGACTCGGAAGAATAAGAG
131 GGTGCTAGCAGCTCCTCGCCTAGTGCGCTTTGAAGGGGTGATGGGTGGACTCGGAAGAATAAGAG
1033684 TAATGATGCGCAATCTTCTACATCCAGCCGTGGTCTTGGTGTGCCGACCACTACGGGGTGCAGGC
196 TAATGATGCGCAATCTTCTACATCCAGCCGTGGTCTTGGTGTGCCGACCACTACGGGGTGCAGGC
1033749 G
261 G
*
1033750 TTAAAGGAAACATTGTCCTCAATTCATAAAGAG-AACTAAACTAAATATAAACTAAATGCCATGC
1 TTAAAGGAAACATTG-CCTCAATTCATAAAAAGAAACTAAA-T-AA-ATAAACTAAATGCCATGC
1033814 AATGAAATGCAACTAAATGAAAATGAATGCAAAAGAGGTACCTCAATGATTGTGTGGTGGCGTGG
62 AATGAAATGCAACT-AATGAAAATGAATGC-AAAGAGGTACCTCAATGATTGTGTGGTGGCG-GG
1033879 CCTTGGAGGTGCTAGCAGCTCCTCGCCTAGTGCGCTTTTGAAGGGGTGATGGGCTGGACTCGGAA
124 CCTTGGAGGTGCTAGCAGCTCCTCGCCTAGTGCGC-TTTGAAGGGGTGATGGG-TGGACTCGGAA
1033944 GAATAAGAGTAATGATGCGCAATCTTCTTACATCCAGCCGTGGTCTTGGTGTGCCGACCACTACG
187 GAATAAGAGTAATGATGCGCAATCTTC-TACATCCAGCCGTGGTCTTGGTGTGCCGACCACTACG
1034009 GGGTGCAGGCG
251 GGGTGCAGGCG
1034020 AAGGATTGGG
Statistics
Matches: 259, Mismatches: 1, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
261 22 0.08
262 17 0.07
263 2 0.01
264 32 0.12
265 15 0.06
266 31 0.12
267 37 0.14
268 17 0.07
269 38 0.15
270 48 0.19
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (261 bp):
TTAAAGGAAACATTGCCTCAATTCATAAAAAGAAACTAAATAAATAAACTAAATGCCATGCAATG
AAATGCAACTAATGAAAATGAATGCAAAGAGGTACCTCAATGATTGTGTGGTGGCGGGCCTTGGA
GGTGCTAGCAGCTCCTCGCCTAGTGCGCTTTGAAGGGGTGATGGGTGGACTCGGAAGAATAAGAG
TAATGATGCGCAATCTTCTACATCCAGCCGTGGTCTTGGTGTGCCGACCACTACGGGGTGCAGGC
G
Found at i:1038861 original size:23 final size:23
Alignment explanation
Indices: 1038817--1038861 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1038807 ATAAAGATAA
*
1038817 AAAATAAACTCAAATATATCATC
1 AAAATAAACTCAAACATATCATC
*
1038840 AAAATAAAGTCTAAACAT-TCAT
1 AAAATAAACTC-AAACATATCAT
1038862 TAAACCAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCAAACATATCATC
Found at i:1045084 original size:17 final size:17
Alignment explanation
Indices: 1045074--1045133 Score: 95
Period size: 17 Copynumber: 3.5 Consensus size: 17
1045064 TAGTTAGATT
1045074 AATGAACTAGT-TAAATG
1 AATGAACTAGTCT-AATG
1045091 AATGAACTAGTCTAATG
1 AATGAACTAGTCTAATG
*
1045108 AATGAACTAGTCTAATA
1 AATGAACTAGTCTAATG
1045125 AATGAACTA
1 AATGAACTA
1045134 ACTTTATTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 40 0.98
18 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (17 bp):
AATGAACTAGTCTAATG
Found at i:1045114 original size:34 final size:35
Alignment explanation
Indices: 1045074--1045151 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 35
1045064 TAGTTAGATT
* *
1045074 AATGAACTAGT-TAAATGAATGAACT-AGTCTAATG
1 AATGAACTAGTCT-AATAAATGAACTAACTCTAATG
* *
1045108 AATGAACTAGTCTAATAAATGAACTAACTTTATTG
1 AATGAACTAGTCTAATAAATGAACTAACTCTAATG
1045143 AATGAACTA
1 AATGAACTA
1045152 AGGTTCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 22 0.58
35 16 0.42
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (35 bp):
AATGAACTAGTCTAATAAATGAACTAACTCTAATG
Found at i:1045164 original size:18 final size:18
Alignment explanation
Indices: 1045125--1045193 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
1045115 TAGTCTAATA
*
1045125 AATGAACTAACTTTATTG
1 AATGAACTAACTTCATTG
*
1045143 AATGAACTAAGGTTCATT-
1 AATGAACTAA-CTTCATTG
* * * *
1045161 AATGAAGTAGCTT-ACTA
1 AATGAACTAACTTCATTG
*
1045178 AATGAACTAAATTCAT
1 AATGAACTAACTTCAT
1045194 AAATAAACTA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
16 2 0.05
17 12 0.32
18 19 0.50
19 5 0.13
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (18 bp):
AATGAACTAACTTCATTG
Found at i:1045196 original size:17 final size:17
Alignment explanation
Indices: 1045122--1045216 Score: 59
Period size: 17 Copynumber: 5.5 Consensus size: 17
1045112 AACTAGTCTA
*
1045122 ATAAATGAACTAACTTT
1 ATAAATGAACTAACTTC
* *
1045139 ATTGAATGAACTAAGGTTC
1 A-TAAATGAACTAA-CTTC
* * *
1045158 ATTAATGAAGTAGCTT-
1 ATAAATGAACTAACTTC
*
1045174 ACTAAATGAACTAAATTC
1 A-TAAATGAACTAACTTC
* *
1045192 ATAAATAAACTACTCTTC
1 ATAAATGAACTA-ACTTC
1045210 -TAAATGA
1 ATAAATGA
1045217 TCTGGAAGCT
Statistics
Matches: 58, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
16 1 0.02
17 30 0.52
18 24 0.41
19 3 0.05
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (17 bp):
ATAAATGAACTAACTTC
Found at i:1049145 original size:17 final size:16
Alignment explanation
Indices: 1049125--1049187 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 16
1049115 GTTAGTTCAT
1049125 TGAATGAACTAGTTAA
1 TGAATGAACTAGTTAA
1049141 CTGAATGAACTAGTTTAA
1 -TGAATGAACTAG-TTAA
* *
1049159 TTAATGAACTAACTTTAA
1 TGAATGAACT-A-GTTAA
1049177 TGAATGAACTA
1 TGAATGAACTA
1049188 AGGCGCATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 22 0.55
18 18 0.45
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (16 bp):
TGAATGAACTAGTTAA
Found at i:1049175 original size:18 final size:18
Alignment explanation
Indices: 1049125--1049188 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1049115 GTTAGTTCAT
*
1049125 TGAATGAACT-A-GTTAA
1 TGAATGAACTAACTTTAA
*
1049141 CTGAATGAACT-AGTTTAA
1 -TGAATGAACTAACTTTAA
*
1049159 TTAATGAACTAACTTTAA
1 TGAATGAACTAACTTTAA
1049177 TGAATGAACTAA
1 TGAATGAACTAA
1049189 GGCGCATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
17 20 0.49
18 21 0.51
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (18 bp):
TGAATGAACTAACTTTAA
Found at i:1054137 original size:64 final size:62
Alignment explanation
Indices: 1053928--1054137 Score: 201
Period size: 65 Copynumber: 3.3 Consensus size: 62
1053918 ATTTTCAAAG
* * * *
1053928 TGATGCACCGATGCACCAATCCATGTATCGATGCACCAT-GAATTAAATTAAACATCGAATGCAT
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTATAGTATT---TTAAACATCGAATGCAT
1053992 T
62 T
* * * * *
1053993 TCATGCATCGATGCA-AATACCATGCACCGATGCACT-GAGGATTTTATAAAAGCATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTATAGTA-TTT-T-AAA-CATCGAATGCA
1054056 TT
61 TT
* *
1054058 TGATGCATCGATGCACCAGCCATGCATCGATGCACTATAGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTATAG-TATTTT-AAACATCGAATGCATT
1054122 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1054138 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 48 0.40
65 63 0.52
66 6 0.05
67 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (62 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTATAGTATTTTAAACATCGAATGCATT
Found at i:1054153 original size:64 final size:62
Alignment explanation
Indices: 1053977--1054163 Score: 166
Period size: 64 Copynumber: 2.9 Consensus size: 62
1053967 GAATTAAATT
* *
1053977 AAACATCGAATGCATTTCATGCATCGATGCAAATACCA-TGCACCGATGCACTGAGGATTTTATA
1 AAACATCGAATGCATTTGATGCATCGATGC-ACT--CAGTGCACCGATGCACTGAGGATTTTATA
* * *
1054041 AAAGCATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACT-ATAGCTATTT
1 AAA-CATCGAATGCATTTGATGCATCGATGCACTCAG---TGCACCGATGCACTGA-GGAT-TTT
*
1054104 -TG
60 ATA
* * *
1054106 AAACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCCCTAAGGAT
1 AAACATCGAATGCATTTGATGCATCGATGCACTC--AGTGCACCGATGCACTGAGGAT
1054164 ACAACGGTCA
Statistics
Matches: 101, Mismatches: 11, Indels: 22
0.75 0.08 0.16
Matches are distributed among these distances:
61 2 0.02
64 47 0.47
65 47 0.47
66 3 0.03
67 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (62 bp):
AAACATCGAATGCATTTGATGCATCGATGCACTCAGTGCACCGATGCACTGAGGATTTTATA
Found at i:1062460 original size:65 final size:64
Alignment explanation
Indices: 1062391--1062516 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 64
1062381 TATTCACATA
* *
1062391 CCATGCA-CAGATGCACTGA-GGAT-TTTATGAAAACATCGAATGCATTTTATGCATCGATGCAC
1 CCATGCATC-GATGCACT-ATGGATATTT-TG-AAACATCGAATGCACTTGATGCATCGATGCAC
1062453 CAG
62 CAG
*
1062456 CCATGCATCGATGCACTATGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 CCATGCATCGATGCACTATGGATATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1062517 TCTTAGTGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
64 31 0.56
65 20 0.36
66 4 0.07
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (64 bp):
CCATGCATCGATGCACTATGGATATTTTGAAACATCGAATGCACTTGATGCATCGATGCACCAG
Found at i:1076687 original size:16 final size:16
Alignment explanation
Indices: 1076666--1076722 Score: 114
Period size: 16 Copynumber: 3.6 Consensus size: 16
1076656 TTTATTCAAA
1076666 TTAAATCCTCAAAATT
1 TTAAATCCTCAAAATT
1076682 TTAAATCCTCAAAATT
1 TTAAATCCTCAAAATT
1076698 TTAAATCCTCAAAATT
1 TTAAATCCTCAAAATT
1076714 TTAAATCCT
1 TTAAATCCT
1076723 TTCGTTATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAATCCTCAAAATT
Found at i:1080037 original size:75 final size:76
Alignment explanation
Indices: 1079909--1080059 Score: 295
Period size: 75 Copynumber: 2.0 Consensus size: 76
1079899 TAGGATTGGT
1079909 CCTTCCTACATGATAGAAAATATATCACATGCCATTTGATTGAGTGAGACTAGAAACACATGGCC
1 CCTTCCTACATGATAGAAAATATATCACATGCCATTTGATTGAGTGAGACTAGAAACACATGGCC
1079974 ATGCTCGAATA
66 ATGCTCGAATA
1079985 CCTT-CTACATGATAGAAAATATATCACATGCCATTTGATTGAGTGAGACTAGAAACACATGGCC
1 CCTTCCTACATGATAGAAAATATATCACATGCCATTTGATTGAGTGAGACTAGAAACACATGGCC
1080049 ATGCTCGAATA
66 ATGCTCGAATA
1080060 AGTTGACATG
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 71 0.95
76 4 0.05
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (76 bp):
CCTTCCTACATGATAGAAAATATATCACATGCCATTTGATTGAGTGAGACTAGAAACACATGGCC
ATGCTCGAATA
Found at i:1082816 original size:12 final size:12
Alignment explanation
Indices: 1082799--1082827 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1082789 TAGCAAAGTC
1082799 TAAGGGCAATGG
1 TAAGGGCAATGG
1082811 TAAGGGCAATGG
1 TAAGGGCAATGG
1082823 TAAGG
1 TAAGG
1082828 CCAAACTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.41, T:0.17
Consensus pattern (12 bp):
TAAGGGCAATGG
Found at i:1084781 original size:54 final size:54
Alignment explanation
Indices: 1084717--1084824 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1084707 AGTAGCTAAA
1084717 GGTTTTCGATAAGTTCATGGTGTAGGCTATGATGAAACAATTTCCCCTGTAGCT
1 GGTTTTCGATAAGTTCATGGTGTAGGCTATGATGAAACAATTTCCCCTGTAGCT
1084771 GGTTTTCGATAAGTTCATGGTGTAGGCTATGATGAAACAATTTCCCCTGTAGCT
1 GGTTTTCGATAAGTTCATGGTGTAGGCTATGATGAAACAATTTCCCCTGTAGCT
1084825 ATGTTTACGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (54 bp):
GGTTTTCGATAAGTTCATGGTGTAGGCTATGATGAAACAATTTCCCCTGTAGCT
Found at i:1089129 original size:46 final size:46
Alignment explanation
Indices: 1089068--1089158 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
1089058 TTCAAATACC
1089068 TCAATGAAAAGGGGATAGAGTGACCATGGACTTCGTTATTGGTTTA
1 TCAATGAAAAGGGGATAGAGTGACCATGGACTTCGTTATTGGTTTA
* *
1089114 TCAATGGAAATGGGATAGAGTGACCATGGACTTCGTTATTGGTTT
1 TCAATGAAAAGGGGATAGAGTGACCATGGACTTCGTTATTGGTTT
1089159 TACCGAGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (46 bp):
TCAATGAAAAGGGGATAGAGTGACCATGGACTTCGTTATTGGTTTA
Found at i:1094266 original size:54 final size:54
Alignment explanation
Indices: 1094180--1094728 Score: 539
Period size: 54 Copynumber: 10.2 Consensus size: 54
1094170 TATTACCAAA
* * * * *
1094180 TAGGCACTAAGTGTGCAACTAACAGAAATCATCATATGTTAATGAACAATCGTT
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTT
** * * *
1094234 TATTCACTATGTGTGCAACTCACAGAATTCATCTTATGTTGATGAACAATCATT
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTT
* * * * * * *
1094288 TCGGTAGTATGTGTGCAACTCATAGAACTCATCATATGTTGATGAACAATCGTA
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTT
* **
1094342 CAGGCACTATGTGTGCAACTCAC-GAAATTCATCATATGTTGATGAACAACTATT
1 TAGGCACTATGTGTGCAACTCACAG-AATTCATCATATGTTGATGAACAACCGTT
* * *
1094396 TTGGCACTATGTGTGCAACTCATAGAATTCATCATATGTTGATCAACAACCGTT
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTT
* * *
1094450 TCGGCACTATGTGTACAACTCAC-GAAATTCATCACATGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACTCACAG-AATTCATCATATGTTGATGAACAACCGTT
* * * * * ** *
1094504 TAGACACTATGTGTGTAACCCACGGAATTCATCATTTACTGATGAACAACCATT
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTT
* * * * * *
1094558 TCGGCACTATGTGTACAACTCACGGAATTTATTATGA-GTTGATGAACAACCGTA
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCAT-ATGTTGATGAACAACCGTT
* * * * *
1094612 CAGGCACTATGTGTGCAACCCACAGAATTCATCATGA-GATGATGAACAATCGTA
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCAT-ATGTTGATGAACAACCGTT
* ** * * * * ** *
1094666 CAAACACTATGTGTGCAACTCACGGAATTTATCATGTGTTGATAAATGACCGTA
1 TAGGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTT
1094720 TAGGCACTA
1 TAGGCACTA
1094729 CGCGTGCATC
Statistics
Matches: 405, Mismatches: 84, Indels: 12
0.81 0.17 0.02
Matches are distributed among these distances:
53 2 0.00
54 401 0.99
55 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (54 bp):
TAGGCACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCGTT
Found at i:1100054 original size:54 final size:54
Alignment explanation
Indices: 1099970--1100522 Score: 573
Period size: 54 Copynumber: 10.2 Consensus size: 54
1099960 ACCAAATAGA
* * * * *
1099970 CACTAAGTGTGCAACTCACAGAATTAATCATTTGTTAATGAACAACCGTTTCGG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
* ** ** *
1100024 CACTATGTGTGCAACTAACAAAATTCATCATATGTTGATGAACAACTATTTTGG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
* *
1100078 CACTATGTGTGCAACTCAC-GACATTCATCATATGTTGATGAACAACCG-TGCAAG
1 CACTATGTGTGCAACTCACGGA-ATTCATCATATGTTGATGAACAACCGTTTC-GG
* * * * *
1100132 CACTATGTGTGAAACTCACGAAATTCTTTATATGTTGATGAACAACCCTTTCGG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
* * * * *
1100186 TACTATGTGTGCAATTCACGGAATTCATCAAATGTGGATGAGCAACCGTTTCGG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
* * * * *
1100240 CACTATGTGTACAACTCATGGAATTCATCATACGTTAATGAACAACTGTTTCGG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
* *
1100294 CACTATGTGTGCAACTCAC-GAAGTTCATCATATGTTTATGAACAATCGTTTCGG
1 CACTATGTGTGCAACTCACGGAA-TTCATCATATGTTGATGAACAACCGTTTCGG
* ** *
1100348 CACTATGTGTGCAACTCACGGAGTTCATCATGA-GTTGATGAACAA-C-TAAACAGT
1 CACTATGTGTGCAACTCACGGAATTCATCAT-ATGTTGATGAACAACCGT-TTC-GG
* * * *
1100402 CACTATGTGTGCAACCCACGGAATTCATCATGA-GATGATGAACAACCG-TACAGA
1 CACTATGTGTGCAACTCACGGAATTCATCAT-ATGTTGATGAACAACCGTTTC-GG
* * ** * * *
1100456 CACTATGTGTACAACCCACATAATTCATCATATGTTGATGAACGACCGTATAGG
1 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
1100510 CACTATGTGTGCA
1 CACTATGTGTGCA
1100523 TGTTAATAAA
Statistics
Matches: 417, Mismatches: 69, Indels: 26
0.81 0.13 0.05
Matches are distributed among these distances:
52 1 0.00
53 8 0.02
54 401 0.96
55 7 0.02
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
Found at i:1104268 original size:21 final size:21
Alignment explanation
Indices: 1104242--1104297 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1104232 TAGTACTCAT
1104242 GAGAGTATCGATACGAATGGG
1 GAGAGTATCGATACGAATGGG
1104263 GAGAGTATCGATACGAATGGG
1 GAGAGTATCGATACGAATGGG
1104284 GAGAGTATCGATAC
1 GAGAGTATCGATAC
1104298 TCTCCATCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.36, T:0.20
Consensus pattern (21 bp):
GAGAGTATCGATACGAATGGG
Found at i:1117405 original size:7 final size:7
Alignment explanation
Indices: 1117393--1117419 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1117383 AACCAATTTA
1117393 TGAATAG
1 TGAATAG
1117400 TGAATAG
1 TGAATAG
1117407 TGAATAG
1 TGAATAG
1117414 TGAATA
1 TGAATA
1117420 CTAAAAAGAG
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:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (7 bp):
TGAATAG
Found at i:1118038 original size:44 final size:45
Alignment explanation
Indices: 1117918--1118043 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
1117908 TATAAAATCC
*
1117918 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1117963 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1118010 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1118044 GTATGCTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 38 0.51
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1118244 original size:59 final size:59
Alignment explanation
Indices: 1118152--1118280 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
1118142 AGTAGTGCTA
* * **
1118152 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
1118211 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
1118270 TCCCGAATATG
1 TCCCGAATATG
1118281 CAGCCTGCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1119787 original size:18 final size:18
Alignment explanation
Indices: 1119760--1119829 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
1119750 ACCGGTCACA
*
1119760 ACCCGGCCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1119778 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
1119795 ----GACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1119809 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1119827 ACC
1 ACC
1119830 GTTGACCCGT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
13 13 0.28
18 33 0.72
ACGTcount: A:0.16, C:0.50, G:0.23, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1119798 original size:8 final size:8
Alignment explanation
Indices: 1119787--1119851 Score: 59
Period size: 8 Copynumber: 8.5 Consensus size: 8
1119777 GACCCGACCC
1119787 GACCCGTT
1 GACCCGTT
1119795 GACCC---
1 GACCCGTT
1119800 GACCCGTT
1 GACCCGTT
**
1119808 GACCCGACCC
1 GACCCG--TT
1119818 GACCCGTT
1 GACCCGTT
1119826 GA-CCGTT
1 GACCCGTT
1119833 GACCCGTT
1 GACCCGTT
1119841 GA-CCGTT
1 GACCCGTT
1119848 GACC
1 GACC
1119852 GTCGTTGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
5 5 0.11
7 14 0.30
8 21 0.46
10 6 0.13
ACGTcount: A:0.15, C:0.42, G:0.25, T:0.18
Consensus pattern (8 bp):
GACCCGTT
Found at i:1119804 original size:31 final size:31
Alignment explanation
Indices: 1119766--1119844 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
1119756 CACAACCCGG
1119766 CCCGACCCGTTGACCCGACCCGACCCGTTGA
1 CCCGACCCGTTGACCCGACCCGACCCGTTGA
1119797 CCCGACCCGTTGACCCGACCCGACCCGTTGA
1 CCCGACCCGTTGACCCGACCCGACCCGTTGA
*
1119828 CCGTTGACCCGTTGACC
1 CC--CGACCCGTTGACC
1119845 GTTGACCGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 33 0.73
33 12 0.27
ACGTcount: A:0.15, C:0.47, G:0.23, T:0.15
Consensus pattern (31 bp):
CCCGACCCGTTGACCCGACCCGACCCGTTGA
Found at i:1119829 original size:13 final size:13
Alignment explanation
Indices: 1119782--1119818 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1119772 CCGTTGACCC
1119782 GACCCGACCCGTT
1 GACCCGACCCGTT
1119795 GACCCGACCCGTT
1 GACCCGACCCGTT
1119808 GACCCGACCCG
1 GACCCGACCCG
1119819 ACCCGTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1119833 original size:7 final size:7
Alignment explanation
Indices: 1119821--1119853 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
1119811 CCGACCCGAC
1119821 CCGTTGA
1 CCGTTGA
1119828 CCGTTGA
1 CCGTTGA
1119835 CCCGTTGA
1 -CCGTTGA
1119843 CCGTTGA
1 CCGTTGA
1119850 CCGT
1 CCGT
1119854 CGTTGACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.12, C:0.33, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:1119838 original size:15 final size:15
Alignment explanation
Indices: 1119818--1119851 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1119808 GACCCGACCC
1119818 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1119833 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1119848 GACC
1 GACC
1119852 GTCGTTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1122408 original size:12 final size:12
Alignment explanation
Indices: 1122393--1122462 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1122383 GATAAATGAC
1122393 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1122405 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
1122417 CTGGATTCTATT
1 CTGAATTCTGTT
1122429 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
*
1122441 TTGAATTCTGTT
1 CTGAATTCTGTT
* *
1122453 TTGATTTCTG
1 CTGAATTCTG
1122463 ATATCTTCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1122412 original size:48 final size:48
Alignment explanation
Indices: 1122356--1122464 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
1122346 AAATATTTTA
*
1122356 TCTGATTTCTGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTATTCTGATAAATGACCTGAATTCTGT
* ** ***
1122404 TCTGATTTCTGATCTGGATTCTATTCTGATATCTGTTTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTATTCTGATAAATGACCTGAATTCTGT
*
1122452 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1122465 ATCTTCGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 51 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTATTCTGATAAATGACCTGAATTCTGT
Found at i:1122424 original size:24 final size:24
Alignment explanation
Indices: 1122356--1122464 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
1122346 AAATATTTTA
1122356 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** *
1122380 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
1122404 TCTGATTTCTGATCTGGATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
1122428 TCTGATATCTGTTTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
1122452 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1122465 ATCTTCGTTT
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
24 66 0.99
25 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1128849 original size:44 final size:45
Alignment explanation
Indices: 1128737--1128854 Score: 157
Period size: 47 Copynumber: 2.6 Consensus size: 45
1128727 CCCTTATCAT
* *
1128737 TTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAT
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAA
* * *
1128782 TTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATACTT-GCAA
1 TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAA
*
1128828 TTATTCCAAAAGCTCGTAAGCTTATTT
1 TTATTCCATAAGCTCGTAAGCTTATTT
1128855 GTATGATTAC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
44 24 0.37
45 2 0.03
46 4 0.06
47 35 0.54
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.37
Consensus pattern (45 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAA
Found at i:1129088 original size:59 final size:58
Alignment explanation
Indices: 1128955--1129091 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 58
1128945 ATAAGCACCG
* * **
1128955 TAGTGCTATCCCGAATATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTT
* ** * *
1129014 AAGTACAGTCTCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTT
1129073 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
1129092 CAACCTGTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
58 1 0.02
59 62 0.98
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTT
Found at i:1133243 original size:44 final size:45
Alignment explanation
Indices: 1133123--1133248 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
1133113 TATAAAATCC
* *
1133123 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1133168 CTTACCATTTAAATTCCAGAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT--ATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATA
*
1133215 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCAAAAGCTCGTAAGCTTATTT
1133249 GTATGCTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 38 0.51
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1133484 original size:59 final size:58
Alignment explanation
Indices: 1133349--1133485 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 58
1133339 ATAAGAACCA
* * **
1133349 TAGTGCTATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
* ** *
1133408 AAGTACAGTCCTGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
*
1133467 TAGTGTATTCCCAAATATG
1 TAGTGTA-TCCCGAATATG
1133486 CAGCTTGCTG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
58 1 0.02
59 62 0.98
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
Found at i:1139768 original size:47 final size:45
Alignment explanation
Indices: 1139695--1139820 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
1139685 TATAAAATCC
* *
1139695 CTTACCATTTATCCCGTAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1139740 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1139787 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1139821 GTATGCTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 24 0.33
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1140021 original size:59 final size:59
Alignment explanation
Indices: 1139929--1140057 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
1139919 CGTAGTGTTA
* * **
1139929 TCCCGAATATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * ** *
1139988 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
1140047 TCCCGAATATG
1 TCCCGAATATG
1140058 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1145177 original size:6 final size:6
Alignment explanation
Indices: 1145160--1145190 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1145150 ACACTTGTAT
*
1145160 CATGAC CGTGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
1145191 TATGGGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:1146183 original size:21 final size:22
Alignment explanation
Indices: 1146159--1146200 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1146149 CATGCTACAG
* *
1146159 TAAATTC-TGAAAATTTACATA
1 TAAATTCATAAAAATTCACATA
1146180 TAAATTCATAAAAATTCACAT
1 TAAATTCATAAAAATTCACAT
1146201 TTCATCACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAATTCATAAAAATTCACATA
Found at i:1146646 original size:44 final size:45
Alignment explanation
Indices: 1146526--1146651 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
1146516 TATAAAATCC
* *
1146526 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1146571 CTTACCATTTAAATTCCAGAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATA
*
1146618 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCAAAAGCTCGTAAGCTTATTT
1146652 GTATGCTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 24 0.33
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCAAAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1146887 original size:59 final size:58
Alignment explanation
Indices: 1146752--1146888 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 58
1146742 ATAAGCACCG
* * * **
1146752 TAGTGCTATCCCGAATATGACACATAAGGTTGTGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
* **
1146811 AAGTACAGTCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
*
1146870 TAGTGTATTCCCAAATATG
1 TAGTGTA-TCCCGAATATG
1146889 CAGCCTGCTG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
Found at i:1151559 original size:6 final size:6
Alignment explanation
Indices: 1151542--1151572 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1151532 ACACTTGTAT
*
1151542 CATGAC CGTGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
1151573 TATGGGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:1153201 original size:47 final size:45
Alignment explanation
Indices: 1153128--1153253 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
1153118 TATAAAATCC
* *
1153128 CTTACCATTTATCCCGTAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1153173 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1153220 GTTGCCA-TTATTCCAAAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1153254 GTATGCTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1153488 original size:59 final size:58
Alignment explanation
Indices: 1153354--1153490 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 58
1153344 ATAAGCACCG
* * **
1153354 TAGTGCTATCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
* ** *
1153413 AAGTACAGTCCTGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1153472 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
1153491 CAGCCTGCTG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
Found at i:1158609 original size:6 final size:6
Alignment explanation
Indices: 1158592--1158622 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1158582 ACACTTGTAT
*
1158592 CATGAC CGTGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
1158623 TATGGGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:1160295 original size:44 final size:45
Alignment explanation
Indices: 1160183--1160300 Score: 157
Period size: 47 Copynumber: 2.6 Consensus size: 45
1160173 CCCTTATCAT
* *
1160183 TTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAT
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAA
* * *
1160228 TTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATACTT-GCAA
1 TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAA
*
1160274 TTATTCCAAAAGCTCGTAAGCTTATTT
1 TTATTCCATAAGCTCGTAAGCTTATTT
1160301 GTATGATTAC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
44 24 0.37
45 2 0.03
46 4 0.06
47 35 0.54
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.37
Consensus pattern (45 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAA
Found at i:1160534 original size:59 final size:58
Alignment explanation
Indices: 1160401--1160537 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 58
1160391 ATAAGCACCG
* * **
1160401 TAGTGCTATCCCGAATATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTT
* ** * *
1160460 AAGTACAGTCTCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTT
1160519 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
1160538 CAACCTGTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
58 1 0.02
59 62 0.98
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTT
Found at i:1161800 original size:44 final size:45
Alignment explanation
Indices: 1161680--1161805 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
1161670 TATAAAATCC
*
1161680 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAGATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAGATA
* *
1161725 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAGATA
* *
1161772 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1161806 GTATGCTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 38 0.51
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAGATA
Found at i:1162006 original size:59 final size:58
Alignment explanation
Indices: 1161914--1162042 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 58
1161904 CATAGTGCTA
*
1161914 TCCCGAATATGACACATAAGGTCGTGTCCACCATCAGT-ACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCAT-A-TAACTAGGTATCCTTAAGTACAG
* ** *
1161973 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATA-ACTAGGTATCCTTAAGTACAG
1162032 TCCCGAATATG
1 TCCCGAATATG
1162043 CAGCCTGCTG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
57 1 0.02
58 1 0.02
59 61 0.97
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (58 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATAACTAGGTATCCTTAAGTACAG
Found at i:1165357 original size:22 final size:22
Alignment explanation
Indices: 1165329--1165371 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1165319 ATAATTAAAT
*
1165329 TATAATATTATAATT-TGAAAAA
1 TATAATACTAT-ATTATGAAAAA
1165351 TATAATACTATATTATGAAAA
1 TATAATACTATATTATGAAAA
1165372 TTTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
TATAATACTATATTATGAAAAA
Found at i:1165883 original size:27 final size:27
Alignment explanation
Indices: 1165853--1165930 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 27
1165843 ATGATTTTTT
*
1165853 TAATAGTCTAAGATTATTATATTAAAA
1 TAATATTCTAAGATTATTATATTAAAA
*
1165880 TAATATTATGAGATGATTATTATATTAAAA
1 TAATATTCT-A-A-GATTATTATATTAAAA
* *
1165910 TAATATTCTGAGATGATTATA
1 TAATATTCTAAGATTATTATA
1165931 ATATAATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 16 0.37
28 2 0.05
29 1 0.02
30 24 0.56
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (27 bp):
TAATATTCTAAGATTATTATATTAAAA
Found at i:1165900 original size:30 final size:30
Alignment explanation
Indices: 1165864--1165934 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1165854 AATAGTCTAA
1165864 GATTATTATATTAAAATAATATTATGAGAT
1 GATTATTATATTAAAATAATATTATGAGAT
*
1165894 GATTATTATATTAAAATAATATTCTGAGAT
1 GATTATTATATTAAAATAATATTATGAGAT
*
1165924 GATTATAATAT
1 GATTATTATAT
1165935 AATATTTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (30 bp):
GATTATTATATTAAAATAATATTATGAGAT
Found at i:1166887 original size:23 final size:27
Alignment explanation
Indices: 1166857--1166912 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 27
1166847 AGACCGATGC
1166857 TTTATTTAT-TTT-TG-TTTATTCAT-
1 TTTATTTATATTTGTGTTTTATTCATA
1166880 TTTATTTATATTTGTGTTTTATTCATA
1 TTTATTTATATTTGTGTTTTATTCATA
1166907 TTTATT
1 TTTATT
1166913 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.31
24 3 0.10
25 2 0.07
26 9 0.31
27 6 0.21
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (27 bp):
TTTATTTATATTTGTGTTTTATTCATA
Found at i:1169932 original size:3 final size:3
Alignment explanation
Indices: 1169915--1169953 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1169905 TTTCCTATAC
*
1169915 ATT ATT -TT AATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1169954 GCTAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1170728 original size:164 final size:164
Alignment explanation
Indices: 1170457--1170784 Score: 656
Period size: 164 Copynumber: 2.0 Consensus size: 164
1170447 TTAGCCAATT
1170457 CTAGGCCAAAACCGAATATGTTTTGAGTAGAAAAGTGTACATATGCCACTGGGATGTCATTATTA
1 CTAGGCCAAAACCGAATATGTTTTGAGTAGAAAAGTGTACATATGCCACTGGGATGTCATTATTA
1170522 TAGATATGATGATTTAGATTTAATTGATGTTGTTCTTTACTAATATCGATTGAATATGTGTTTAT
66 TAGATATGATGATTTAGATTTAATTGATGTTGTTCTTTACTAATATCGATTGAATATGTGTTTAT
1170587 ATAGATTTTTTAGGCTGAGGGATCTCGTAGAGCG
131 ATAGATTTTTTAGGCTGAGGGATCTCGTAGAGCG
1170621 CTAGGCCAAAACCGAATATGTTTTGAGTAGAAAAGTGTACATATGCCACTGGGATGTCATTATTA
1 CTAGGCCAAAACCGAATATGTTTTGAGTAGAAAAGTGTACATATGCCACTGGGATGTCATTATTA
1170686 TAGATATGATGATTTAGATTTAATTGATGTTGTTCTTTACTAATATCGATTGAATATGTGTTTAT
66 TAGATATGATGATTTAGATTTAATTGATGTTGTTCTTTACTAATATCGATTGAATATGTGTTTAT
1170751 ATAGATTTTTTAGGCTGAGGGATCTCGTAGAGCG
131 ATAGATTTTTTAGGCTGAGGGATCTCGTAGAGCG
1170785 ACTGATCAGG
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (164 bp):
CTAGGCCAAAACCGAATATGTTTTGAGTAGAAAAGTGTACATATGCCACTGGGATGTCATTATTA
TAGATATGATGATTTAGATTTAATTGATGTTGTTCTTTACTAATATCGATTGAATATGTGTTTAT
ATAGATTTTTTAGGCTGAGGGATCTCGTAGAGCG
Found at i:1172440 original size:53 final size:53
Alignment explanation
Indices: 1172380--1172486 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
1172370 TGTCTGCTAA
1172380 AAATTGTTATTACAAGGTTGTCAAACTTTCTTAGTCAATGTAGTAGACAATCG
1 AAATTGTTATTACAAGGTTGTCAAACTTTCTTAGTCAATGTAGTAGACAATCG
1172433 AAATTGTTATTACAAGGTTGTCAAACTTTCTTAGTCAATGTAGTAGACAATCG
1 AAATTGTTATTACAAGGTTGTCAAACTTTCTTAGTCAATGTAGTAGACAATCG
1172486 A
1 A
1172487 GTTTCAGGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (53 bp):
AAATTGTTATTACAAGGTTGTCAAACTTTCTTAGTCAATGTAGTAGACAATCG
Found at i:1177775 original size:24 final size:24
Alignment explanation
Indices: 1177748--1177810 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
1177738 CACGACACTT
* *
1177748 TATGTGCAATTCTATCTGGCAATA
1 TATGTGCAATTCTATATAGCAATA
* *
1177772 TATGTGTAATTCTATATAGCACTA
1 TATGTGCAATTCTATATAGCAATA
*
1177796 TATGCGCAATTCTAT
1 TATGTGCAATTCTAT
1177811 GCGGCACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (24 bp):
TATGTGCAATTCTATATAGCAATA
Found at i:1177817 original size:24 final size:23
Alignment explanation
Indices: 1177743--1177820 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
1177733 TTCTACACGA
*
1177743 CACTTTATGTGCAATTCTATCTGG
1 CACTATATGTGCAATTCTATC-GG
* * **
1177767 CAATATATGTGTAATTCTATATAG
1 CACTATATGTGCAATTCTAT-CGG
*
1177791 CACTATATGCGCAATTCTATGCGG
1 CACTATATGTGCAATTCTAT-CGG
1177815 CACTAT
1 CACTAT
1177821 TTACGCATTC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (23 bp):
CACTATATGTGCAATTCTATCGG
Found at i:1178747 original size:2 final size:2
Alignment explanation
Indices: 1178740--1178769 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1178730 TTCCTAAAAT
1178740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1178770 AGCATGCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1179952 original size:17 final size:19
Alignment explanation
Indices: 1179916--1179952 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1179906 TACATGATGG
*
1179916 ATGAAATATTAAATATAAT
1 ATGAAATATAAAATATAAT
1179935 ATGAAA-ATAAAATA-AAT
1 ATGAAATATAAAATATAAT
1179952 A
1 A
1179953 AATGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
ATGAAATATAAAATATAAT
Found at i:1180727 original size:24 final size:22
Alignment explanation
Indices: 1180690--1180734 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1180680 TGACTAAAAT
1180690 AAACCAAATAAAATTAGAAGCTCA
1 AAACCAAATAAAA-TA-AAGCTCA
1180714 AAACCAAA-ACAAATAAAGCTC
1 AAACCAAATA-AAATAAAGCTC
1180735 TATTCAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.60, C:0.20, G:0.07, T:0.13
Consensus pattern (22 bp):
AAACCAAATAAAATAAAGCTCA
Found at i:1181732 original size:14 final size:13
Alignment explanation
Indices: 1181711--1181772 Score: 58
Period size: 14 Copynumber: 4.7 Consensus size: 13
1181701 AATATAAATA
*
1181711 AATAAATAATACT
1 AATAAATAATAAT
1181724 AATATAATAATAAT
1 AATA-AATAATAAT
1181738 AA-AAA-AATAAT
1 AATAAATAATAAT
1181749 AATAGAAATAA-AAT
1 AAT--AAATAATAAT
1181763 ATATAAATAA
1 A-ATAAATAA
1181773 ACTCAGATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
11 8 0.19
12 2 0.05
13 11 0.26
14 17 0.40
15 4 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:1181761 original size:17 final size:16
Alignment explanation
Indices: 1181701--1181773 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 16
1181691 AGGAAAGAAA
1181701 AATATAAAT-AAATAAAT
1 AATA-AAATAAAAT-AAT
* *
1181718 AATACTAATATAATAAT
1 AATA-AAATAAAATAAT
1181735 AAT-AAA-AAAATAAT
1 AATAAAATAAAATAAT
1181749 AATAGAAATAAAATATAT
1 AATA-AAATAAAATA-AT
1181767 AAATAAA
1 -AATAAA
1181774 CTCAGATGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.22
15 2 0.04
16 3 0.07
17 19 0.42
18 7 0.16
19 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (16 bp):
AATAAAATAAAATAAT
Found at i:1181763 original size:25 final size:26
Alignment explanation
Indices: 1181700--1181772 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
1181690 AAGGAAAGAA
* *
1181700 AAATATAAATAAATAAATAATACTAAT
1 AAATA-AAATAAATAAATAATAATAAG
*
1181727 ATAATAATAATAAAAAAATAATAAT-AG
1 A-AATAA-AATAAATAAATAATAATAAG
*
1181754 AAATAAAATATATAAATAA
1 AAATAAAATAAATAAATAA
1181773 ACTCAGATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 11 0.28
26 5 0.13
27 4 0.10
28 19 0.49
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (26 bp):
AAATAAAATAAATAAATAATAATAAG
Found at i:1183967 original size:26 final size:26
Alignment explanation
Indices: 1183933--1183998 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
1183923 AGATCAATGC
1183933 AGAAGTTTTAAAAAAATGGTTGATAAA
1 AGAA-TTTTAAAAAAATGGTTGATAAA
** *
1183960 AGAATTTTTGAAAAATGGTTGATGAA
1 AGAATTTTAAAAAAATGGTTGATAAA
1183986 AGAA-TTTAAAAAA
1 AGAATTTTAAAAAA
1183999 TGTTTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 7 0.21
26 23 0.68
27 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (26 bp):
AGAATTTTAAAAAAATGGTTGATAAA
Found at i:1185221 original size:20 final size:22
Alignment explanation
Indices: 1185193--1185249 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
1185183 GATTACTCAT
*
1185193 GCAGATTTGGT-TC-TAAAACG
1 GCAGCTTTGGTATCATAAAACG
* *
1185213 GCAGCTTT-GTATCATGAAGCG
1 GCAGCTTTGGTATCATAAAACG
1185234 GCAGCTTTGG-ATCATA
1 GCAGCTTTGGTATCATA
1185250 TTTAATGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.07
20 9 0.30
21 18 0.60
22 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (22 bp):
GCAGCTTTGGTATCATAAAACG
Found at i:1189779 original size:674 final size:675
Alignment explanation
Indices: 1188493--1189839 Score: 2371
Period size: 674 Copynumber: 2.0 Consensus size: 675
1188483 TTCGAGATCA
*
1188493 AAATGGACATATTTAAAATAAAGAAATCAAATTAAAATAATCATAAAGATAAAGTAATAAACATA
1 AAATGGACATATTTAAAATAAAGAAATCAAATTAAAATAATCATAAAGATAAAATAATAAACATA
1188558 AAGGGACTAAAATAATAAAACTGGAAAATTAATATCTCAAAAAATTAAATAAATAACACAACACA
66 AAGGGACTAAAATAATAAAACTGGAAAATTAATATCTCAAAAAATTAAATAAATAACACAACACA
*
1188623 AACTATAAAAACAACATATTACAAACACTAAAAATGTAATAAATCCATATATTTCGGACCGAAAT
131 AACTATAAAAACAACATATTACAAACACTAAAAATGTAATAAATCCATATATTTCGAACCGAAAT
*
1188688 ACAACTATTTAAAATTACATGTTGGAAATCAAAATAATGAAAAATACATAGCTTACAGTGACCAA
196 ACAACTATTCAAAATTACATGTTGGAAATCAAAATAATGAAAAATACATAGCTTACAGTGACCAA
*
1188753 AATGAACACGTATAACTAAAAGAGGCCAAAATCATAAACTTATGAAAAGTTGCAATCTGGGGCTA
261 AATGAACACGCATAACTAAAAGAGGCCAAAATCATAAACTTATGAAAAGTTGCAATCTGGGGCTA
*
1188818 AAATGCAAACTCTAGAAACATGAGACCCATCTCTCGCAAATATCTCATAATATTAAGATAATAAC
326 AAATACAAACTCTAGAAACATGAGACCCATCTCTCGCAAATATCTCATAATATTAAGATAATAAC
*
1188883 AGTGACTAAAATATAACATGTACAAAATAAAAAGGATCGAACACAATAGTACCCCATTTTCATTT
391 AGTGACTAAAATATAACATGTACAAAATAAAAAGGATCGAACACAATAGTAACCCATTTTCATTT
* *
1188948 CATGACCGATATAAAGAAATTACAATAGTGAGGGACCTAGCGTGCTATTAACCCATGCGCTAAAC
456 CATGACCGAAATAAAGAAATTACAATAGTGAGGGACCTAGAGTGCTATTAACCCATGCGCTAAAC
*
1189013 ACATGGAACCCTAATGCCAAAATGACTTCGTTTCCTTGTGTGGTTATAAACCACCTTAAGGGCTT
521 ACATGGAACCCTAATGCCAAAACGACTTCGTTTCCTTGTGTGGTTATAAACCACCTTAAGGGCTT
*
1189078 TTAGAACCCTAAATCATTTTAACTCCCCTCAGTCGTTTCTCTCATTCTCCCCC-ACCATTCCT-T
586 TTAGAACCCTAAACCATTTTAACTCCCCTCAGTCGTTTCTCTCATTCTCCCCCTACCATTCCTCT
1189141 TTTTTT-GTTTTCTTCTTAAACCTT
651 TTTTTTCGTTTTCTTCTTAAACCTT
* * **
1189165 AAATGGACATATTTAAACTAAAGAATTCAAATTAAAATAATCATAAAGATAAAATAATAAATGTA
1 AAATGGACATATTTAAAATAAAGAAATCAAATTAAAATAATCATAAAGATAAAATAATAAACATA
* *
1189230 AAGGGACTAAAATAATAAAATTGGAAAATTAATGTCTCAAAAACAAATTAAATAAATAACACAAC
66 AAGGGACTAAAATAATAAAACTGGAAAATTAATATCTC--AAA-AAATTAAATAAATAACACAAC
*
1189295 ACATAA-TGTAAAAACAACATATTACAAACACTAAAAATGTAATAAATCCATATATTTCGAACCG
128 ACA-AACTATAAAAACAACATATTACAAACACTAAAAATGTAATAAATCCATATATTTCGAACCG
*
1189359 AAATACAACTATTCAAAATTACATGTTGGAAATCGAAATAATGAAAAATACATAGCTTACAGTGA
192 AAATACAACTATTCAAAATTACATGTTGGAAATCAAAATAATGAAAAATACATAGCTTACAGTGA
* * *
1189424 CCAAAATGAACACGCGTGACTAAAAGAGGCCAAAATCATAAACTTATGAAAAGTT-TAATCTGGG
257 CCAAAATGAACACGCATAACTAAAAGAGGCCAAAATCATAAACTTATGAAAAGTTGCAATCTGGG
1189488 GCTAAAATACAAACTCTAGAAACATGAGACCCATCTCTCGCAAATATCTCATAATATTAAGATAA
322 GCTAAAATACAAACTCTAGAAACATGAGACCCATCTCTCGCAAATATCTCATAATATTAAGATAA
*
1189553 TAAGAGTGACTAAAATATAACATGTACAAAATAAAAAGGATCGAACACAATAGTAACCCATTTTC
387 TAACAGTGACTAAAATATAACATGTACAAAATAAAAAGGATCGAACACAATAGTAACCCATTTTC
* * *
1189618 ATTTCATGACCGAAATAACGAAATTACAATAGTGAGGGGCCTATAGTGCTATTAACCCATGCGCT
452 ATTTCATGACCGAAATAAAGAAATTACAATAGTGAGGGACCTAGAGTGCTATTAACCCATGCGCT
* *
1189683 AAACGCATGGAACCCTAATGCCAAAACGACTTCGTTTCCTTGTGTGGTTATAAACCATCTTAAGG
517 AAACACATGGAACCCTAATGCCAAAACGACTTCGTTTCCTTGTGTGGTTATAAACCACCTTAAGG
*
1189748 GTTTTTAGAACCCTAAACCATTTTAACTCCCCTCAGTCGTTTCTCTCATTCTCCCCCTACCATTC
582 GCTTTTAGAACCCTAAACCATTTTAACTCCCCTCAGTCGTTTCTCTCATTCTCCCCCTACCATTC
1189813 CTCTTTTTTTCGTTTTCTTCTTAAACC
647 CTCTTTTTTTCGTTTTCTTCTTAAACC
1189840 CTCTAGCCAC
Statistics
Matches: 640, Mismatches: 28, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
672 96 0.15
674 315 0.49
675 204 0.32
676 9 0.01
677 16 0.03
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (675 bp):
AAATGGACATATTTAAAATAAAGAAATCAAATTAAAATAATCATAAAGATAAAATAATAAACATA
AAGGGACTAAAATAATAAAACTGGAAAATTAATATCTCAAAAAATTAAATAAATAACACAACACA
AACTATAAAAACAACATATTACAAACACTAAAAATGTAATAAATCCATATATTTCGAACCGAAAT
ACAACTATTCAAAATTACATGTTGGAAATCAAAATAATGAAAAATACATAGCTTACAGTGACCAA
AATGAACACGCATAACTAAAAGAGGCCAAAATCATAAACTTATGAAAAGTTGCAATCTGGGGCTA
AAATACAAACTCTAGAAACATGAGACCCATCTCTCGCAAATATCTCATAATATTAAGATAATAAC
AGTGACTAAAATATAACATGTACAAAATAAAAAGGATCGAACACAATAGTAACCCATTTTCATTT
CATGACCGAAATAAAGAAATTACAATAGTGAGGGACCTAGAGTGCTATTAACCCATGCGCTAAAC
ACATGGAACCCTAATGCCAAAACGACTTCGTTTCCTTGTGTGGTTATAAACCACCTTAAGGGCTT
TTAGAACCCTAAACCATTTTAACTCCCCTCAGTCGTTTCTCTCATTCTCCCCCTACCATTCCTCT
TTTTTTCGTTTTCTTCTTAAACCTT
Found at i:1195412 original size:54 final size:54
Alignment explanation
Indices: 1195346--1195878 Score: 474
Period size: 54 Copynumber: 9.9 Consensus size: 54
1195336 TAATTCACGA
*
1195346 AATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTGCAACTCAAGG
1 AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACTCAAGG
* * * *
1195400 AATTCATCATATGTTGATGAACAACCGTTTCGGTACTATGTGCGCAACTCACGA
1 AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACTCAAGG
* * * * * *
1195454 AATTCATCATATGTTGATGAACAACCGTTTTGGATACTATCTGTTCAATTCATGG
1 AATTCATCATATGTTGATGAACAACCGTTTCGG-CACTATGTGTGCAACTCAAGG
* * *
1195509 AATTCATCATATGTTGATGAACAACCATTTCGGCACTACGTGTGCAACCCATA-G
1 AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACTCA-AGG
* * * * * *
1195563 AATTTATCTTATGTTGATAAACAACCATTTCGGCATTATGTGTGCAACTCACGG
1 AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACTCAAGG
* *
1195617 AATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACA-A
1 AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACTCA-AGG
*** * *
1195671 AATTCATCATGA-GTTGATGAACAACCGTAAAGGCACTATGTGTGCAA-TCCATGT
1 AATTCATCAT-ATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACT-CAAGG
* * * * *
1195725 AATTCATCATGA-GTTGATGAACATCC-ATACATGCACTATGTGTGCAAC-CTACGG
1 AATTCATCAT-ATGTTGATGAACAACCGTTTC-GGCACTATGTGTGCAACTC-AAGG
* * * * * * * *
1195779 AAATCATCATGA-GATGAAGAAGAACC-ATACAAGCACTATGTGTGCAACCCACA-G
1 AATTCATCAT-ATGTTGATGAACAACCGTTTC-GGCACTATGTGTGCAACTCA-AGG
* * * * * * *
1195833 AATTTATTATGTGTTGATGAACGACCGTATAGGCACTACGTGTGCA
1 AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCA
1195879 TCTTAATAAA
Statistics
Matches: 397, Mismatches: 68, Indels: 28
0.81 0.14 0.06
Matches are distributed among these distances:
53 3 0.01
54 346 0.87
55 48 0.12
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (54 bp):
AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAACTCAAGG
Found at i:1195623 original size:163 final size:162
Alignment explanation
Indices: 1195332--1195696 Score: 491
Period size: 163 Copynumber: 2.2 Consensus size: 162
1195322 AGGCACCAAG
* * * *
1195332 TGTGTAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTGCAACTCA
1 TGTGCAATTCACGAAATTCATCATATGTTGATGAACAACCATTTCGACACTACGTGTGCAACCCA
* * *
1195397 AGGAATTCATCATATGTTGATGAACAACCGTTTCGGTACTATGTGCGCAACTCACGAAATTCATC
66 AGGAATTCATCATATGTTGATAAACAACCATTTCGGCACTATGTGCGCAACTCACGAAATTCATC
* * *
1195462 ATATGTTGATGAACAACCGTTTTGGATACTATC
131 ATATGTTGATGAACAACCATTTCGG-CACTATC
* * * *
1195495 TGTTCAATTCATGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTACGTGTGCAACCCA
1 TGTGCAATTCACGAAATTCATCATATGTTGATGAACAACCATTTCGACACTACGTGTGCAACCCA
* * * * *
1195560 TA-GAATTTATCTTATGTTGATAAACAACCATTTCGGCATTATGTGTGCAACTCACGGAATTCAT
66 -AGGAATTCATCATATGTTGATAAACAACCATTTCGGCACTATGTGCGCAACTCACGAAATTCAT
*
1195624 CATATGTTGATGAACAACCATTTCGGCACTATG
130 CATATGTTGATGAACAACCATTTCGGCACTATC
* *
1195657 TGTGCAACTCACAAAATTCATCATGA-GTTGATGAACAACC
1 TGTGCAATTCACGAAATTCATCAT-ATGTTGATGAACAACC
1195697 GTAAAGGCAC
Statistics
Matches: 175, Mismatches: 25, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
162 38 0.22
163 136 0.78
164 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (162 bp):
TGTGCAATTCACGAAATTCATCATATGTTGATGAACAACCATTTCGACACTACGTGTGCAACCCA
AGGAATTCATCATATGTTGATAAACAACCATTTCGGCACTATGTGCGCAACTCACGAAATTCATC
ATATGTTGATGAACAACCATTTCGGCACTATC
Found at i:1195786 original size:108 final size:108
Alignment explanation
Indices: 1195331--1195878 Score: 527
Period size: 108 Copynumber: 5.1 Consensus size: 108
1195321 TAGGCACCAA
* * * *
1195331 GTGTGTAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTGCAACTC
1 GTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTAGGCACTATGTGTGCAACTC
* * *
1195396 AAGGAATTCATCATATGTTGATGAACAACCGTTTCGGTACTAT
66 ATGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAT
* * * * * *
1195439 GTGCGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTTGGATACTATCTGTTCAATT
1 GTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTAGG-CACTATGTGTGCAACT
*
1195504 CATGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAC
65 CATGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAT
* * * * * * * *
1195548 GTGTGCAACCCA-TAGAATTTATCTTATGTTGATAAACAACCATTTCGGCATTATGTGTGCAACT
1 GTGTGCAACTCACGA-AATTCATCATATGTTGATGAACAACCGTTTAGGCACTATGTGTGCAACT
*
1195612 CACGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAT
65 CATGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAT
* **
1195656 GTGTGCAACTCACAAAATTCATCATGA-GTTGATGAACAACCGTAAAGGCACTATGTGTGCAA-T
1 GTGTGCAACTCACGAAATTCATCAT-ATGTTGATGAACAACCGTTTAGGCACTATGTGTGCAACT
* * * *
1195719 CCATGTAATTCATCATGA-GTTGATGAACATCCA-TACATGCACTAT
65 -CATGGAATTCATCAT-ATGTTGATGAACAACCATTTC-GGCACTAT
* * * * ** *
1195764 GTGTGCAAC-CTACGGAAA-TCATCATGA-GATGAAGAAGAACCATACAAGCACTATGTGTGCAA
1 GTGTGCAACTC-AC-GAAATTCATCAT-ATGTTGATGAACAACCGTTTAGGCACTATGTGTGCAA
* ** * * * * * * * *
1195826 CCCACAGAATTTATTATGTGTTGATGAACGACCGTATAGGCACTAC
63 CTCATGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAT
1195872 GTGTGCA
1 GTGTGCA
1195879 TCTTAATAAA
Statistics
Matches: 363, Mismatches: 65, Indels: 24
0.80 0.14 0.05
Matches are distributed among these distances:
107 4 0.01
108 263 0.72
109 96 0.26
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (108 bp):
GTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTAGGCACTATGTGTGCAACTC
ATGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAT
Found at i:1199487 original size:13 final size:14
Alignment explanation
Indices: 1199462--1199491 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1199452 AAGAAAAACG
1199462 AAAATAAATAAATA
1 AAAATAAATAAATA
1199476 AAAATAAA-AAATA
1 AAAATAAATAAATA
1199489 AAA
1 AAA
1199492 TGAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:1199577 original size:26 final size:24
Alignment explanation
Indices: 1199533--1199585 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 24
1199523 TATACTATAT
1199533 AAAATATAAATATATATATTTTAA
1 AAAATATAAATATATATATTTTAA
*
1199557 AAAACTATATAATATATATATTTTCA
1 AAAA-TATA-AATATATATATTTTAA
1199583 AAA
1 AAA
1199586 TATTTTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 4 0.15
25 4 0.15
26 18 0.69
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATATAAATATATATATTTTAA
Found at i:1199605 original size:73 final size:73
Alignment explanation
Indices: 1199526--1199679 Score: 197
Period size: 73 Copynumber: 2.1 Consensus size: 73
1199516 ATAGTATTAT
*
1199526 ACTATATA-AAATATAA-ATATATATATTTTAAAAAACTATATAATATATATATTTTCAAAATA-
1 ACTATATATAAATATAATATA-AAATATTTTAAAAAACTATATAATATATATATTTTCAAAATAT
1199588 TTTTCAAAA
65 TTTTCAAAA
** * * * *
1199597 ACTATATATTTATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATTTTCAAAATAT
1 ACTATATATAAATATAATAT-AAAATATTTTAAAAAACTATATAATATATATATTTTCAAAATAT
*
1199662 TTTTTAAAA
65 TTTTCAAAA
1199671 ACTATATAT
1 ACTATATAT
1199680 TATATATATG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
71 8 0.11
72 5 0.07
73 40 0.56
74 18 0.25
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (73 bp):
ACTATATATAAATATAATATAAAATATTTTAAAAAACTATATAATATATATATTTTCAAAATATT
TTTCAAAA
Found at i:1199611 original size:38 final size:37
Alignment explanation
Indices: 1199548--1199722 Score: 264
Period size: 37 Copynumber: 4.7 Consensus size: 37
1199538 ATAAATATAT
*
1199548 ATATTTTAAAAAACTATATAATATATATATTTTCAAA
1 ATATTTTAAAAAACTATATATTATATATATTTTCAAA
*
1199585 ATATTTTCAAAAACTATATATT-TATATATTTTCAAA
1 ATATTTTAAAAAACTATATATTATATATATTTTCAAA
*
1199621 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
1 ATATTTTAAAAAACTATATATTATATATATTTTCAAA
*
1199658 ATATTTTTTAAAAACTATATATTATATATATGTTTTCAAA
1 ATA-TTTTAAAAAACTATATATTATATATA--TTTTCAAA
1199698 AT-TTTATAAAAAACTATATATTATA
1 ATATTT-TAAAAAACTATATATTATA
1199723 CACTATATAT
Statistics
Matches: 129, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
36 36 0.28
37 37 0.29
38 28 0.22
39 18 0.14
40 10 0.08
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (37 bp):
ATATTTTAAAAAACTATATATTATATATATTTTCAAA
Found at i:1199671 original size:13 final size:13
Alignment explanation
Indices: 1199546--1199677 Score: 50
Period size: 13 Copynumber: 10.5 Consensus size: 13
1199536 ATATAAATAT
1199546 ATATATTTTAAAA
1 ATATATTTTAAAA
* *
1199559 A-ACTA-TATAATAT
1 ATA-TATTTTAA-AA
*
1199572 ATATATTTTCAAA
1 ATATATTTTAAAA
*
1199585 ATAT-TTTCAAAA
1 ATATATTTTAAAA
1199597 ACTATATATTT----
1 A-TATAT-TTTAAAA
*
1199608 ATATATTTTCAAA
1 ATATATTTTAAAA
*
1199621 ATAT-TTTCAAAA
1 ATATATTTTAAAA
* *
1199633 ACTATATATT--AT
1 A-TATATTTTAAAA
*
1199645 ATATATTTTCAAA
1 ATATATTTTAAAA
*
1199658 ATATTTTTTAAAA
1 ATATATTTTAAAA
1199671 ACTATAT
1 A-TATAT
1199678 ATTATATATA
Statistics
Matches: 85, Mismatches: 18, Indels: 31
0.63 0.13 0.23
Matches are distributed among these distances:
9 3 0.04
10 5 0.06
11 8 0.09
12 21 0.25
13 35 0.41
14 11 0.13
15 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATTTTAAAA
Found at i:1199683 original size:73 final size:75
Alignment explanation
Indices: 1199548--1199722 Score: 275
Period size: 73 Copynumber: 2.3 Consensus size: 75
1199538 ATAAATATAT
*
1199548 ATATTTTAAAAAACTATATAATATATATATTTTCAAAATATTTTCAAAAACTATATATT-TATAT
1 ATATTTTAAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATAT
1199612 A-TTTTCAAA
66 AGTTTTCAAA
* *
1199621 ATATTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTTTAAAAACTATATATTATATA
1 ATATTTTAAAAAACTATATATTATATATATTTTCAAAATA-TTTTCAAAAACTATATATTATATA
1199686 TATGTTTTCAAA
65 TA-GTTTTCAAA
1199698 AT-TTTATAAAAAACTATATATTATA
1 ATATTT-TAAAAAACTATATATTATA
1199723 CACTATATAT
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
73 38 0.41
74 18 0.19
75 6 0.06
76 3 0.03
77 28 0.30
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (75 bp):
ATATTTTAAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATAT
AGTTTTCAAA
Found at i:1199729 original size:14 final size:13
Alignment explanation
Indices: 1199710--1199750 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
1199700 TTTATAAAAA
1199710 ACTATATATTATAC
1 ACTATATA-TATAC
*
1199724 ACTATATATATAT
1 ACTATATATATAC
1199737 A-TATATATATAC
1 ACTATATATATAC
1199749 AC
1 AC
1199751 ACACACACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.46
13 5 0.21
14 8 0.33
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
ACTATATATATAC
Found at i:1201221 original size:45 final size:45
Alignment explanation
Indices: 1201170--1201269 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 45
1201160 ATCTTGGACC
*
1201170 CATTTTTTTAAAATTTAAGGCACACTTTCAGATTTTCACCCTAAA
1 CATTTTTTTAAAACTTAAGGCACACTTTCAGATTTTCACCCTAAA
* * * ** *
1201215 CATTTTTTT-TAACTTAGGGCACCCTTTTGGGTTTTCACCCTAAA
1 CATTTTTTTAAAACTTAAGGCACACTTTCAGATTTTCACCCTAAA
1201259 CATTTTTTTAA
1 CATTTTTTTAA
1201270 CAAAAGATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 37 0.80
45 9 0.20
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (45 bp):
CATTTTTTTAAAACTTAAGGCACACTTTCAGATTTTCACCCTAAA
Found at i:1204341 original size:45 final size:45
Alignment explanation
Indices: 1204271--1204535 Score: 354
Period size: 45 Copynumber: 5.9 Consensus size: 45
1204261 TTATATCATA
* * * * * * *
1204271 CTTTTATGTTGATAATGCACACATATGCATT-TCAACTATGGTATC
1 CTTTCATGTCGATAATGCACCCATATGCATTAT-TATTTTGGCATC
*
1204316 CTTTCATGTCGATAGTGCACCCATATGCATTATTATTTTGGCATC
1 CTTTCATGTCGATAATGCACCCATATGCATTATTATTTTGGCATC
*
1204361 ATTTCATGTCGATAATGCACCCATATGCATTATTATTTTGGCATC
1 CTTTCATGTCGATAATGCACCCATATGCATTATTATTTTGGCATC
* * *
1204406 ATTTCATGCCGATAATGCACCCATATTCATTATTATTTTGGCATC
1 CTTTCATGTCGATAATGCACCCATATGCATTATTATTTTGGCATC
*
1204451 CTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGGCATC
1 CTTTCATGTCGATAATGCACCCATATGCATTATTATTTTGGCATC
** *
1204496 CTTTCATACCGATAATG-AGCCCATATGAATTATTATTTTG
1 CTTTCATGTCGATAATGCA-CCCATATGCATTATTATTTTG
1204536 TTCATTTGTT
Statistics
Matches: 202, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
44 1 0.00
45 200 0.99
46 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (45 bp):
CTTTCATGTCGATAATGCACCCATATGCATTATTATTTTGGCATC
Found at i:1205006 original size:19 final size:19
Alignment explanation
Indices: 1204982--1205034 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1204972 TACCATTCTC
1204982 TGGTATCGATA-TTATTTT
1 TGGTATCGATACTTATTTT
* *
1205000 ATGGTATCGTTACCTTCTTTT
1 -TGGTATCGATA-CTTATTTT
1205021 TGGTATCGATACTT
1 TGGTATCGATACTT
1205035 CACCTTCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 13 0.45
20 10 0.34
21 6 0.21
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (19 bp):
TGGTATCGATACTTATTTT
Found at i:1211217 original size:45 final size:45
Alignment explanation
Indices: 1211166--1211432 Score: 428
Period size: 45 Copynumber: 6.0 Consensus size: 45
1211156 TCAACTATGA
* * *
1211166 CATCCTTTCATGCCGATAGTACACCTATATGCATTATTATTTTGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGG
*
1211211 CATCCTTTCATGCTGATAATGCACCCATATGCATTATTATTTTGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGG
*
1211256 CATCCTTTAATG-CGATAATGCACCCATATGCATTATTATTTTGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGG
*
1211300 CATCCTTTCATGCCGATAATGAACCCATATGCATTATTATTTTGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGG
* * *
1211345 CATCTTTTCATGCCAATAATGCACTCATATGCATTATTATTTTGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGG
* *
1211390 TATCCTTTCATGACGATAATGCACCCATATGCATTATTATTTT
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTT
1211433 TTTCAGTCAT
Statistics
Matches: 204, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
44 42 0.21
45 162 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (45 bp):
CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGG
Found at i:1211260 original size:90 final size:89
Alignment explanation
Indices: 1211166--1211432 Score: 412
Period size: 89 Copynumber: 3.0 Consensus size: 89
1211156 TCAACTATGA
* *
1211166 CATCCTTTCATGCCGATAGTACACCTATATGCATTATTATTTTGGCATCCTTTCATGCTGATAAT
1 CATCCTTTCATGCCGATAATGCACCTATATGCATTATTATTTTGGCATCCTTTCATGC-GATAAT
1211231 GCACCCATATGCATTATTATTTTGG
65 GCACCCATATGCATTATTATTTTGG
* *
1211256 CATCCTTTAATG-CGATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCGATAAT
1 CATCCTTTCATGCCGATAATGCACCTATATGCATTATTATTTTGGCATCCTTTCATG-CGATAAT
*
1211320 GAACCCATATGCATTATTATTTTGG
65 GCACCCATATGCATTATTATTTTGG
* * *
1211345 CATCTTTTCATGCCAATAATGCA-CTCATATGCATTATTATTTTGGTATCCTTTCATGACGATAA
1 CATCCTTTCATGCCGATAATGCACCT-ATATGCATTATTATTTTGGCATCCTTTCATG-CGATAA
1211409 TGCACCCATATGCATTATTATTTT
64 TGCACCCATATGCATTATTATTTT
1211433 TTTCAGTCAT
Statistics
Matches: 162, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
89 82 0.51
90 80 0.49
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (89 bp):
CATCCTTTCATGCCGATAATGCACCTATATGCATTATTATTTTGGCATCCTTTCATGCGATAATG
CACCCATATGCATTATTATTTTGG
Found at i:1211317 original size:134 final size:135
Alignment explanation
Indices: 1211166--1211432 Score: 439
Period size: 134 Copynumber: 2.0 Consensus size: 135
1211156 TCAACTATGA
* * **
1211166 CATCCTTTCATGCCGATAGT-ACACCTATATGCATTATTATTTTGGCATCCTTTCATGCTGATAA
1 CATCCTTTCATGCCGATAATGA-ACCCATATGCATTATTATTTTGGCATCCTTTCATGCCAATAA
1211230 TGCACCCATATGCATTATTATTTTGGCATCCTTTAATG-CGATAATGCACCCATATGCATTATTA
65 TGCACCCATATGCATTATTATTTTGGCATCCTTTAATGACGATAATGCACCCATATGCATTATTA
1211294 TTTTGG
130 TTTTGG
*
1211300 CATCCTTTCATGCCGATAATGAACCCATATGCATTATTATTTTGGCATCTTTTCATGCCAATAAT
1 CATCCTTTCATGCCGATAATGAACCCATATGCATTATTATTTTGGCATCCTTTCATGCCAATAAT
* * *
1211365 GCACTCATATGCATTATTATTTTGGTATCCTTTCATGACGATAATGCACCCATATGCATTATTAT
66 GCACCCATATGCATTATTATTTTGGCATCCTTTAATGACGATAATGCACCCATATGCATTATTAT
1211430 TTT
131 TTT
1211433 TTTCAGTCAT
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
134 92 0.75
135 31 0.25
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (135 bp):
CATCCTTTCATGCCGATAATGAACCCATATGCATTATTATTTTGGCATCCTTTCATGCCAATAAT
GCACCCATATGCATTATTATTTTGGCATCCTTTAATGACGATAATGCACCCATATGCATTATTAT
TTTGG
Found at i:1211903 original size:20 final size:20
Alignment explanation
Indices: 1211878--1211929 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1211868 TAGTATGCTA
1211878 TGGTATCGATACATTC-CCTT
1 TGGTATCGATAC-TTCACCTT
1211898 TGGTATCGATACTTCACCTT
1 TGGTATCGATACTTCACCTT
* *
1211918 CGATATCGATAC
1 TGGTATCGATAC
1211930 CGATTAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (20 bp):
TGGTATCGATACTTCACCTT
Found at i:1216694 original size:3 final size:3
Alignment explanation
Indices: 1216666--1216776 Score: 132
Period size: 3 Copynumber: 37.0 Consensus size: 3
1216656 GATTTATTTT
* * * * * * *
1216666 TTA TTA TAA TTA TAA TTA TAA TTA TTA TTA TTA TAA TTA CTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1216714 TTA TTA TTA TTA TTA TTA TTA TAA ATA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1216762 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1216777 AATACATATA
Statistics
Matches: 90, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1217309 original size:11 final size:11
Alignment explanation
Indices: 1217293--1217329 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1217283 ACGATCTCAG
1217293 CAGAAAAGAAA
1 CAGAAAAGAAA
1217304 CAGAAAAG-AA
1 CAGAAAAGAAA
1217314 -AGAAAAGAAA
1 CAGAAAAGAAA
*
1217324 AAGAAA
1 CAGAAA
1217330 GAAGAGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.29
10 4 0.17
11 13 0.54
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (11 bp):
CAGAAAAGAAA
Found at i:1217317 original size:15 final size:15
Alignment explanation
Indices: 1217297--1217338 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1217287 TCTCAGCAGA
1217297 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1217312 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1217327 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1217339 CTTACCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1217319 original size:20 final size:20
Alignment explanation
Indices: 1217294--1217338 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1217284 CGATCTCAGC
*
1217294 AGAAAAGAAACAGAAAAGAA-
1 AGAAAAGAAAAAG-AAAGAAG
1217314 AGAAAAGAAAAAGAAAGAAG
1 AGAAAAGAAAAAGAAAGAAG
1217334 AGAAA
1 AGAAA
1217339 CTTACCGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAAAGAAAGAAG
Found at i:1229498 original size:12 final size:11
Alignment explanation
Indices: 1229483--1229530 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
1229473 ATGCTTGAAG
1229483 AAAAAAGTGAAA
1 AAAAAAG-GAAA
1229495 AAAAAA-GAAGA
1 AAAAAAGGAA-A
1229506 GAAAAAAGGAAA
1 -AAAAAAGGAAA
1229518 AAAAAA-GAAA
1 AAAAAAGGAAA
1229528 AAA
1 AAA
1229531 GGGGGGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.30
11 7 0.21
12 13 0.39
13 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAGGAAA
Found at i:1229517 original size:23 final size:24
Alignment explanation
Indices: 1229481--1229526 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
1229471 TTATGCTTGA
1229481 AGAAAAAAGTGAAAAAAAAAGAAG
1 AGAAAAAAGTGAAAAAAAAAGAAG
1229505 AGAAAAAAG-GAAAAAAAAAGAA
1 AGAAAAAAGTGAAAAAAAAAGAA
1229527 AAAAGGGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (24 bp):
AGAAAAAAGTGAAAAAAAAAGAAG
Found at i:1229526 original size:18 final size:20
Alignment explanation
Indices: 1229495--1229532 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
1229485 AAAAGTGAAA
1229495 AAAAAAGAAGAGAAAAAAGG
1 AAAAAAGAAGAGAAAAAAGG
1229515 AAAAAA-AA-AGAAAAAAGG
1 AAAAAAGAAGAGAAAAAAGG
1229533 GGGGTCAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAGAGAAAAAAGG
Found at i:1230805 original size:83 final size:83
Alignment explanation
Indices: 1230666--1231101 Score: 700
Period size: 83 Copynumber: 5.3 Consensus size: 83
1230656 AAACATTAAC
1230666 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAC
1 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAC
1230731 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
1230749 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG-G
1 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGAA
* *
1230813 TA-AACAAATCATTGAATT
65 CAGAACCAATCATTGAATT
* *
1230831 TAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
1 TGGAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
*
1230895 TAGAACCAATCATTGAATT
65 CAGAACCAATCATTGAATT
* *
1230914 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTGTTTGAGTTATCTGATCTGGTTGGAC
1 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAC
1230979 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* * *
1230997 TAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
1 TGGAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAA
1231061 CAGAACCAATCATTGAATT
65 CAGAACCAATCATTGAATT
* *
1231080 TGGAAGATGATTTTGCTCATAG
1 TGGAAGATGAATGTGCTCATAG
1231102 TAGAAATAAG
Statistics
Matches: 329, Mismatches: 17, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
81 4 0.01
82 73 0.22
83 247 0.75
84 5 0.02
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (83 bp):
TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAAC
AGAACCAATCATTGAATT
Found at i:1230940 original size:165 final size:166
Alignment explanation
Indices: 1230668--1231101 Score: 757
Period size: 165 Copynumber: 2.6 Consensus size: 166
1230658 ACATTAACTG
*
1230668 GAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACA
1 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACA
1230732 GAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
65 GAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
*
1230797 ATCTGATCTGGTTTGG-TA-AACAAATCATTGAATTTA
130 ATCTGATCTGG-TTGGACAGAACAAATCATTGAATTTA
*
1230833 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAATAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAG
*
1230898 AACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTGTTTGAGTTA
66 AACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
1230963 TCTGATCTGGTTGGACAGAACCAATCATTGAATTTA
131 TCTGATCTGGTTGGACAGAACAAATCATTGAATTTA
*
1230999 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAG
* *
1231064 AACCAATCATTGAATTTGGAAGATGATTTTGCTCATAG
66 AACCAATCATTGAATTTGGAAGATGAATGTGCTCATAG
1231102 TAGAAATAAG
Statistics
Matches: 257, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
164 5 0.02
165 136 0.53
166 116 0.45
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (166 bp):
GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAG
AACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCTGATCTGGTTGGACAGAACAAATCATTGAATTTA
Found at i:1232091 original size:113 final size:113
Alignment explanation
Indices: 1231892--1232454 Score: 803
Period size: 113 Copynumber: 5.0 Consensus size: 113
1231882 AGCAAAGATT
* * **** *
1231892 TAAATCCATCA-CTTGATGGATTAGATTTTCCAGTTCGAGTTCATGATGAGAAGAACTCATCTGA
1 TAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1231956 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG-C
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
1232004 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 T-AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
1232069 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG-C
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
1232117 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 T-AAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
1232182 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
* * * *
1232231 TGAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
* ** *
1232296 GAAGGAAGAAGAAGTTCATACTGAGAAGAATTTGTTCAATTTTTTACC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
* * * * * *
1232344 TGAATTCATCAAT-TGATGGATTATCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTAA
1 TAAATCCATC-ATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
1232407 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1232455 ATAATTCTAT
Statistics
Matches: 420, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
112 71 0.17
113 344 0.82
114 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCC
Found at i:1232806 original size:3 final size:3
Alignment explanation
Indices: 1232786--1232893 Score: 144
Period size: 3 Copynumber: 36.0 Consensus size: 3
1232776 GATTTATTTT
* * * * * *
1232786 TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TAA TTA CTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1232834 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1232882 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1232894 AATACATATA
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1233434 original size:15 final size:15
Alignment explanation
Indices: 1233414--1233455 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1233404 TCTCAGTAGA
1233414 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1233429 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1233444 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1233456 CTTACCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1233436 original size:20 final size:20
Alignment explanation
Indices: 1233411--1233455 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1233401 CGATCTCAGT
*
1233411 AGAAAAGAAACAGAAAAGAA-
1 AGAAAAGAAAAAG-AAAGAAG
1233431 AGAAAAGAAAAAGAAAGAAG
1 AGAAAAGAAAAAGAAAGAAG
1233451 AGAAA
1 AGAAA
1233456 CTTACCGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAAAGAAAGAAG
Found at i:1240897 original size:2 final size:2
Alignment explanation
Indices: 1240880--1240964 Score: 54
Period size: 2 Copynumber: 44.0 Consensus size: 2
1240870 AATGAATAAA
*
1240880 AT AT AT -T AA AT A- AT AT AT A- AT ACT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * * * *
1240919 AT AT AT AT TT TT AA AA AA AA ACT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
1240961 AT AT
1 AT AT
1240965 TCAAAATATT
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
1 5 0.07
2 62 0.89
3 3 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1240912 original size:17 final size:17
Alignment explanation
Indices: 1240892--1240924 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1240882 ATATTAAATA
1240892 ATATATA-ATACTATATT
1 ATATATATATA-TATATT
1240909 ATATATATATATATAT
1 ATATATATATATATAT
1240925 ATTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:1245667 original size:80 final size:78
Alignment explanation
Indices: 1245469--1245704 Score: 307
Period size: 80 Copynumber: 3.0 Consensus size: 78
1245459 TACAAATTGA
* * **
1245469 GGGGCAAAATCAAAATAAATTAAAA-TTAAAAGGCCTAAATAGGCAATGGTCCCATTATTCTTTA
1 GGGGCAAAATTAAAATAAATTAAAATTTAAAA-GCCTAAATAGGTAATTATCCCATTATTCTTTA
*
1245533 ATGATAAAAATTTT
65 ATGATAAAAAATTT
* * * * *
1245547 GGGG-AAAATT-AAACAAGTTAAAATTTAAAGGCCTAAATAGGTAATTTTCGCATTATTCTTTAA
1 GGGGCAAAATTAAAATAAATTAAAATTTAAAAGCCTAAATAGGTAATTATCCCATTATTCTTTAA
1245610 TGATAAAATAATTT
66 TGATAAAA-AATTT
* *
1245624 GGGGACAAAATTAAAATAAATCAAAATTTAAAAGCCTAAATAGGTAATTATCCCATTATTCATTA
1 GGGG-CAAAATTAAAATAAATTAAAATTTAAAAGCCTAAATAGGTAATTATCCCATTATTCTTTA
1245689 ATGATAAAAACATTT
65 ATGATAAAAA-ATTT
1245704 G
1 G
1245705 TGGGGCAGTG
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
76 48 0.35
77 18 0.13
78 4 0.03
79 7 0.05
80 59 0.43
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (78 bp):
GGGGCAAAATTAAAATAAATTAAAATTTAAAAGCCTAAATAGGTAATTATCCCATTATTCTTTAA
TGATAAAAAATTT
Found at i:1248202 original size:60 final size:60
Alignment explanation
Indices: 1248109--1248230 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 60
1248099 CCAACGCTGT
1248109 CAATCATCATCATCATAAGATGCACTCCAAGTGCAATCCTATCATTTGCACAAACGGTGC
1 CAATCATCATCATCATAAGATGCACTCCAAGTGCAATCCTATCATTTGCACAAACGGTGC
* * * *
1248169 CAATCATCATTATCATAAGATGCACTCCAAGTGCAATCCTTTCATTTGCACCAACTGTGC
1 CAATCATCATCATCATAAGATGCACTCCAAGTGCAATCCTATCATTTGCACAAACGGTGC
1248229 CA
1 CA
1248231 TACATAATGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (60 bp):
CAATCATCATCATCATAAGATGCACTCCAAGTGCAATCCTATCATTTGCACAAACGGTGC
Found at i:1255690 original size:20 final size:20
Alignment explanation
Indices: 1255654--1255703 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1255644 CAAAATGATC
*
1255654 CAATTTC-ACATTTTAACAT
1 CAATTTCAACACTTTAACAT
*
1255673 CAATTTGAACACTTTAACAT
1 CAATTTCAACACTTTAACAT
*
1255693 TAATTTCAACA
1 CAATTTCAACA
1255704 TAGTACAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (20 bp):
CAATTTCAACACTTTAACAT
Found at i:1256140 original size:28 final size:28
Alignment explanation
Indices: 1256099--1256167 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
1256089 TGATTCTACA
*
1256099 TCAATAACCCTAAAATCCATCATCAAATC
1 TCAA-AACCTTAAAATCCATCATCAAATC
1256128 TCAAAACCTTAAAATCCATCATCAAATC
1 TCAAAACCTTAAAATCCATCATCAAATC
*
1256156 TCGAAACCTTAA
1 TCAAAACCTTAA
1256168 CACCATCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 34 0.89
29 4 0.11
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (28 bp):
TCAAAACCTTAAAATCCATCATCAAATC
Found at i:1261823 original size:70 final size:69
Alignment explanation
Indices: 1261736--1261867 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 69
1261726 AAGTGCCAAT
* * *
1261736 ACACATAAGGTTGTGCCCACCATACAT-ACTAAGTTTCCTTTATATACGCCATAGTGTTAAACTG
1 ACACATAAGGTTGTGCCCA--ACACATCACTAAGTTTCCTTTATATACACCATAGTGCTAAACTG
1261800 AATATA
64 AATATA
*
1261806 ACACATAAGGTTGTGCCCAACACATGCACTAAGTTTCCTTTATATACACTATAGTGCTAAAC
1 ACACATAAGGTTGTGCCCAACACAT-CACTAAGTTTCCTTTATATACACCATAGTGCTAAAC
1261868 CGGATATACA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
68 5 0.09
70 51 0.91
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (69 bp):
ACACATAAGGTTGTGCCCAACACATCACTAAGTTTCCTTTATATACACCATAGTGCTAAACTGAA
TATA
Found at i:1262533 original size:17 final size:18
Alignment explanation
Indices: 1262504--1262540 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1262494 TATTATCTTT
*
1262504 AAACCATCCAAACTTTCC
1 AAACCATCCAAACTTACC
1262522 AAACCA-CCAAACTTACC
1 AAACCATCCAAACTTACC
1262539 AA
1 AA
1262541 TCTTCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (18 bp):
AAACCATCCAAACTTACC
Found at i:1275018 original size:3 final size:3
Alignment explanation
Indices: 1274960--1275009 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
1274950 CCTTTTTCTT
* *
1274960 TTA TTA TTA TTA ATA ATA TGTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
1275006 TTA T
1 TTA T
1275010 AAATTATTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1277967 original size:36 final size:36
Alignment explanation
Indices: 1277918--1277987 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1277908 GATATGCACT
* *
1277918 CAAAGATCATGTTATATTAATACCAAAAGTATTCCA
1 CAAAGATCATGTTAGATTAATACCAAAAGCATTCCA
* *
1277954 CAAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 CAAAGATCATGTTAGATTAATACCAAAAGCATTC
1277988 TACGGTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (36 bp):
CAAAGATCATGTTAGATTAATACCAAAAGCATTCCA
Found at i:1281265 original size:72 final size:72
Alignment explanation
Indices: 1281148--1281282 Score: 234
Period size: 72 Copynumber: 1.9 Consensus size: 72
1281138 ACACAATAAA
*
1281148 GCTTGAGTTATCCCCCTAAAGCAATAGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTACT
1 GCTTGAGTTATCCCCCTAAAGCAATAGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTACT
1281213 CTGTTAT
66 CTGTTAT
* * *
1281220 GCTTGAGTTATTCCCCTAAATCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTA
1 GCTTGAGTTATCCCCCTAAAGCAATAGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTA
1281283 GCATGTTATA
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:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGCAATAGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTACT
CTGTTAT
Found at i:1283336 original size:75 final size:75
Alignment explanation
Indices: 1283230--1283397 Score: 257
Period size: 75 Copynumber: 2.2 Consensus size: 75
1283220 CTCACACCAA
* * *
1283230 CAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCGCATTTTGAACG
1 CAAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATTAGAATATTGGCACATTTTGAACG
*
1283295 -TCTGTATTAG
66 TTC-ATATTAG
* *
1283305 CAAATGCTGGGGCATGCTAAAAGCCCTTTTCAATCAGAAATTAGAATTTTGGCACATTTTGAACG
1 CAAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATTAGAATATTGGCACATTTTGAACG
1283370 TTCATATTAG
66 TTCATATTAG
*
1283380 CAAATACTGGGGCATGCT
1 CAAATGCTGGGGCATGCT
1283398 GAAGGCCTAC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
75 83 0.98
76 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (75 bp):
CAAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATTAGAATATTGGCACATTTTGAACG
TTCATATTAG
Found at i:1284349 original size:54 final size:54
Alignment explanation
Indices: 1284263--1284640 Score: 481
Period size: 54 Copynumber: 7.0 Consensus size: 54
1284253 AAGAGCTTCA
* * *
1284263 CTACGAACATCTGTGCAGAAGCCACACGAAAGGATGAATGTGTTATCAAATGTT
1 CTACGAACATCTGTACAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
* * *
1284317 CTACGAACATTTGTACAGAAGCCACAGAAAAGGATAAATGTGTTGTCAAATGTT
1 CTACGAACATCTGTACAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
* * *
1284371 CTATGAACATCTGTACCGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTT
1 CTACGAACATCTGTACAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
* *
1284425 CTACGAACATCTGTACAGAAGCCACAGGAAAGGATAAATGTATTGTCAAATGTT
1 CTACGAACATCTGTACAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
* *
1284479 TTACGAACATCTG-AGCAGAAGCCACAGGAAAGGATGAATATGTTGTCAAATGTT
1 CTACGAACATCTGTA-CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
* * ** *
1284533 CTACGAACATCTGTATAGAAGCCACGGGAAACAATGAATGTGTTGTCAAATATT
1 CTACGAACATCTGTACAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
* * * * * * * * *
1284587 TTACGAGCATCTG-AGCAAAAACCATATGAGATGATGAATGAGTTGTCAAATGTT
1 CTACGAACATCTGTA-CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
1284641 TTATGAACTA
Statistics
Matches: 280, Mismatches: 41, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
53 2 0.01
54 277 0.99
55 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (54 bp):
CTACGAACATCTGTACAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTT
Done.