Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008165.1 Hibiscus syriacus cultivar Beakdansim tig00110745_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: 2894944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:242070 original size:19 final size:20
Alignment explanation
Indices: 242038--242080 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
242028 AATAGTTTCT
242038 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
242058 GAAACTT-AAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
242077 GAAA
1 GAAA
242081 ATGACTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:242092 original size:20 final size:20
Alignment explanation
Indices: 242067--242115 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
242057 CGAAACTTAA
242067 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
242087 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
242107 ATCGCAACG
1 ATCGCAACG
242116 GGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:242156 original size:14 final size:14
Alignment explanation
Indices: 242137--242167 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
242127 ATGCGAAATA
242137 AAAATCGCAACGAG
1 AAAATCGCAACGAG
*
242151 AAAATCGCAACGCG
1 AAAATCGCAACGAG
242165 AAA
1 AAA
242168 CTAAATTCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.23, G:0.19, T:0.06
Consensus pattern (14 bp):
AAAATCGCAACGAG
Found at i:242157 original size:33 final size:34
Alignment explanation
Indices: 242107--242172 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
242097 GAATTTGACT
* * *
242107 ATCGCAACGGGATAATCGCAATGCGAAA-TAAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACTAAAA
242140 ATCGCAACGAGAAAATCGCAACGCGAAACTAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAACTAAA
242173 TTCGCGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAACGCGAAACTAAAA
Found at i:244141 original size:12 final size:12
Alignment explanation
Indices: 244124--244148 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
244114 TTAAAATCGC
244124 AACACGAAAATG
1 AACACGAAAATG
244136 AACACGAAAATG
1 AACACGAAAATG
244148 A
1 A
244149 CTATCGCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (12 bp):
AACACGAAAATG
Found at i:244211 original size:19 final size:19
Alignment explanation
Indices: 244184--244236 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
244174 GCAACGAGAT
*
244184 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
244203 AATCGCAACACGAAAATGAC
1 AATCGCAACGCG-AAATGAA
*
244223 TATCGCAACGCGAA
1 AATCGCAACGCGAA
244237 TTAAACTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:244649 original size:22 final size:22
Alignment explanation
Indices: 244615--244679 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
244605 TCTGAGAGAT
244615 GGAGAT-A-GACGGATTTCGCC
1 GGAGATGAGGACGGATTTCGCC
* *
244635 GGAGATGGGGACGGATTTCGTC
1 GGAGATGAGGACGGATTTCGCC
*
244657 GGAGATGAGGACGGATGTCGCC
1 GGAGATGAGGACGGATTTCGCC
244679 G
1 G
244680 TAGAGAGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 6 0.16
22 32 0.84
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.18
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGCC
Found at i:244850 original size:21 final size:21
Alignment explanation
Indices: 244817--245096 Score: 285
Period size: 21 Copynumber: 13.6 Consensus size: 21
244807 CACTTTGAAA
* * *
244817 ATCGCATTACGATTTTGTATT
1 ATCGCGTTGCGATTATGTATT
**
244838 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
244858 ATCGCGTTGCGATTATGT-TT
1 ATCGCGTTGCGATTATGTATT
**
244878 ATCGCGTTGCGA-TA-GTTAGA
1 ATCGCGTTGCGATTATG-TATT
244898 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
244919 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
* *
244939 ATAGCGTTGTGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
244960 ATCGCGTTGCGA-TA-GTCAAA
1 ATCGCGTTGCGATTATGT-ATT
244980 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
245001 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
*
245022 ATTGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
245043 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
*
245063 ATTGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
245084 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
245097 AGTCAGAATT
Statistics
Matches: 212, Mismatches: 31, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.00
19 11 0.05
20 80 0.38
21 111 0.52
22 9 0.04
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:244933 original size:41 final size:41
Alignment explanation
Indices: 244816--245113 Score: 456
Period size: 41 Copynumber: 7.3 Consensus size: 41
244806 GCACTTTGAA
* * *
244816 AATCGCATTACGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
*
244857 AATCGCGTTGCGATTATGT-TTATCGCGTTGCGATAGTTAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
244897 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
* * *
244938 AATAGCGTTGTGATTATGTATTATCGCGTTGCGATAGTCAA
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
*
244979 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATTATGT-AT
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGA-TA-GTCAG
* *
245021 TATTGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
*
245062 AATTGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
*
245103 AATTGCGTTGC
1 AATCGCGTTGC
245114 AATTTACATA
Statistics
Matches: 238, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
40 41 0.17
41 160 0.67
42 35 0.15
43 2 0.01
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (41 bp):
AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
Found at i:245070 original size:124 final size:122
Alignment explanation
Indices: 244826--245113 Score: 470
Period size: 124 Copynumber: 2.3 Consensus size: 122
244816 AATCGCATTA
*
244826 CGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTTTATCGCGTTGCGAT
1 CGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTTTATCGCGTTGCGAT
244891 AGTTAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATAGCGTTG
66 AGTTAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATAGCGTTG
* *
244948 TGATTATGTATTATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTATGTATTATCGCGTTGCGA
1 CGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGT-TTATCGCGTTGCGA
** * *
245013 TTA-TGTATTATTGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATTGCGTTG
65 -TAGT-TAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATAGCGTTG
*
245072 CGATTATGTATTATCGCGTTGCGATAGTCAGAATTGCGTTGC
1 CGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGC
245114 AATTTACATA
Statistics
Matches: 153, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
122 47 0.31
123 15 0.10
124 91 0.59
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.38
Consensus pattern (122 bp):
CGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTTTATCGCGTTGCGAT
AGTTAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATAGCGTTG
Found at i:245701 original size:2 final size:2
Alignment explanation
Indices: 245694--245726 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
245684 TCCGTATTAT
245694 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
245727 ATTAAAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:246711 original size:23 final size:23
Alignment explanation
Indices: 246673--246746 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 23
246663 GTGCTTTAGA
246673 ACTGATATACTAAAGTGTCTTAAC
1 ACTGATA-ACTAAAGTGTCTTAAC
* * *
246697 ACTGATAACTAAAGTTTTTTATC
1 ACTGATAACTAAAGTGTCTTAAC
* * *
246720 ATTG--AACTAAAGTGCCTTAGC
1 ACTGATAACTAAAGTGTCTTAAC
246741 ACTGAT
1 ACTGAT
246747 TTGGAATATA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 16 0.41
23 16 0.41
24 7 0.18
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (23 bp):
ACTGATAACTAAAGTGTCTTAAC
Found at i:251224 original size:23 final size:23
Alignment explanation
Indices: 251180--251224 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
251170 ATTAAAAAAG
** *
251180 AAAATAAAAAACAGTAATTAAAT
1 AAAATAAAAAACAAAAAGTAAAT
*
251203 AAAATAAGAAACAAAAAGTAAA
1 AAAATAAAAAACAAAAAGTAAA
251225 ATATATATAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (23 bp):
AAAATAAAAAACAAAAAGTAAAT
Found at i:253164 original size:34 final size:35
Alignment explanation
Indices: 253090--253184 Score: 165
Period size: 35 Copynumber: 2.7 Consensus size: 35
253080 CGAAGGTTTG
* *
253090 GTGTTTCAAGAGAAACATTTTCAAGGGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
253125 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
253160 -TGTTTCAAGAGAAACAATTTCAAAG
1 GTGTTTCAAGAGAAACAATTTCAAAG
253185 ATTGGTGCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
34 25 0.43
35 33 0.57
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
Found at i:253293 original size:65 final size:65
Alignment explanation
Indices: 253157--253303 Score: 149
Period size: 65 Copynumber: 2.2 Consensus size: 65
253147 AAAGGTTTTT
* ** * *
253157 TTTTGTTTCAAGAGAAACAATTTCAAAGATTGGTGCTTCAAGAGAAATTGTCTCGAGAGAGACGA
1 TTTTGTTTAAAGAGAAACAATTTCAAAGATTGGTGCTTCAAGAGAAACCGTCTCAAGAGAGACAA
* * *
253222 TATTTGTTTAAAG-GAAA-ACATATTCAAAGATT-TTGTTTCAAGGGAAACCGTCTCAAGAGAGA
1 T-TTTGTTTAAAGAGAAACA-AT-TTCAAAGATTGGTGCTTCAAGAGAAACCGTCTCAAGAGAGA
253284 CAAA
63 C-AA
253288 TTTTGTTTTAAA-AGAA
1 TTTTG-TTTAAAGAGAA
253304 TTTGTCTCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
64 1 0.01
65 36 0.53
66 31 0.46
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (65 bp):
TTTTGTTTAAAGAGAAACAATTTCAAAGATTGGTGCTTCAAGAGAAACCGTCTCAAGAGAGACAA
Found at i:253311 original size:36 final size:35
Alignment explanation
Indices: 253253--253644 Score: 255
Period size: 36 Copynumber: 11.2 Consensus size: 35
253243 ATTCAAAGAT
* * *
253253 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAA
* ** * *
253288 TTTTGTTTTAAAAGAATTTGTCTCAAGGGAGGCGAAA
1 -TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC-AAA
* *
253325 TTTGTTTTAAG-GAAAAATAGAT-TC-A-A-AG---AT
1 TTTGTTTTAAGAG-AAACT-G-TCTCAAGAGAGACAAA
* *
253355 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAA
* *
253389 TTTGTTTTAAGAGAAAATGTCTCAAGAAAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC-AAA
*
253425 TTTGTTTTAAGAGAAACTGTCTCGAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC-AAA
** ** **
253461 TTTGTTACAAG-GAAAACAAAT-TC-A-A-AG---TT
1 TTTGTTTTAAGAG-AAAC-TGTCTCAAGAGAGACAAA
*
253490 TTTGTTTCAATGA-AAACTGAT-TCAAGAGAGACAAAA
1 TTTGTTTTAA-GAGAAACTG-TCTCAAGAGAGAC-AAA
* *
253526 GTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC--AAA
*
253563 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC--AAA
*
253600 TTTGTTTTAAGAGAAACTGTCTCGAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC-AAA
253636 CTTTGTTTT
1 -TTTGTTTT
253645 GAGTAAATTA
Statistics
Matches: 287, Mismatches: 40, Indels: 57
0.75 0.10 0.15
Matches are distributed among these distances:
28 1 0.00
29 19 0.07
30 18 0.06
31 3 0.01
32 4 0.01
33 2 0.01
34 32 0.11
35 6 0.02
36 116 0.40
37 85 0.30
38 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (35 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAA
Found at i:253379 original size:102 final size:99
Alignment explanation
Indices: 253199--253440 Score: 333
Period size: 100 Copynumber: 2.4 Consensus size: 99
253189 GTGCTTCAAG
* * *
253199 AGAAATTGTCTCGAGAGAGACGATATTTGTTTAAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAATTGTCTCAAGAGAGACGAAATTTGTTTTAAGGAAAACATATTCAAAGATTTTGTTTCAAG
253264 GGAAACCGTCTCAAGAGAGACAAATTTTGTTTTAAA
66 GGAAACCGTCTCAAGAGAGAC-AA-TTTGTTTTAAA
* * *
253300 AGAATTTGTCTCAAGGGAGGCGAAATTTGTTTTAAGGAAAA-ATAGATTCAAAGATTTTGTTTCA
1 AGAAATTGTCTCAAGAGAGACGAAATTTGTTTTAAGGAAAACAT--ATTCAAAGATTTTGTTTCA
* *
253364 AGGGAAACTGTCTCAAGAGAGACAATTTGTTTTAAG
64 AGGGAAACCGTCTCAAGAGAGACAATTTGTTTTAAA
* * *
253400 AGAAAATGTCTCAAGAAAGACAAAATTTGTTTTAAGAGAAA
1 AGAAATTGTCTCAAGAGAGACGAAATTTGTTTTAAG-GAAA
253441 CTGTCTCGAG
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
100 42 0.34
101 41 0.33
102 41 0.33
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (99 bp):
AGAAATTGTCTCAAGAGAGACGAAATTTGTTTTAAGGAAAACATATTCAAAGATTTTGTTTCAAG
GGAAACCGTCTCAAGAGAGACAATTTGTTTTAAA
Found at i:253568 original size:37 final size:37
Alignment explanation
Indices: 253511--253644 Score: 225
Period size: 37 Copynumber: 3.6 Consensus size: 37
253501 GAAAACTGAT
*
253511 TCAAGAGAGAC-AAAAGTTGTTTTAAGAGAAAATGTC
1 TCAAGAGAGACAAAAATTTGTTTTAAGAGAAAATGTC
253547 TCAAGAGAGACAAAAATTTGTTTTAAGAGAAAATGTC
1 TCAAGAGAGACAAAAATTTGTTTTAAGAGAAAATGTC
*
253584 TCAAGAGAGACAAAAATTTGTTTTAAGAGAAACTGTC
1 TCAAGAGAGACAAAAATTTGTTTTAAGAGAAAATGTC
* *
253621 TCGAGAGAGACAAAACTTTGTTTT
1 TCAAGAGAGACAAAAATTTGTTTT
253645 GAGTAAATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 11 0.12
37 82 0.88
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.28
Consensus pattern (37 bp):
TCAAGAGAGACAAAAATTTGTTTTAAGAGAAAATGTC
Found at i:253575 original size:20 final size:20
Alignment explanation
Indices: 253552--253613 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
253542 ATGTCTCAAG
253552 AGAGACAAAAATTTGTTTTA
1 AGAGACAAAAATTTGTTTTA
**
253572 AGAG---AAAA--TGTCTCAA
1 AGAGACAAAAATTTGT-TTTA
253588 GAGAGACAAAAATTTGTTTTA
1 -AGAGACAAAAATTTGTTTTA
253609 AGAGA
1 AGAGA
253614 AACTGTCTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
15 3 0.10
16 2 0.06
17 8 0.26
20 13 0.42
21 2 0.06
22 3 0.10
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.27
Consensus pattern (20 bp):
AGAGACAAAAATTTGTTTTA
Found at i:253674 original size:33 final size:33
Alignment explanation
Indices: 253634--253699 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
253624 AGAGAGACAA
253634 AACTTTGTTTTGAGTAAATTAGTCTTGAGCGAG
1 AACTTTGTTTTGAGTAAATTAGTCTTGAGCGAG
253667 AACTTTGTTTTGAGTAAATTAGTCTTGAGCGAG
1 AACTTTGTTTTGAGTAAATTAGTCTTGAGCGAG
253700 GCGACCCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.39
Consensus pattern (33 bp):
AACTTTGTTTTGAGTAAATTAGTCTTGAGCGAG
Found at i:255078 original size:83 final size:86
Alignment explanation
Indices: 254979--255206 Score: 266
Period size: 95 Copynumber: 2.6 Consensus size: 86
254969 GGCTAGGTGA
* * *
254979 ATCCATAAAGCTGGGGCATTTAACCAATTACTCTAGAGGGACAACTCAATAT-GTA-AAT-ACCT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATAGTATAATCACCT
* *
255041 TTATCAGGTTAGCTGAATCTT
66 TTATCAGGCTAGCTGAATATT
*
255062 ATCCATAAAGCCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A---TATAGT
*
255126 ATAATCACCTTTATCATGCTAGCTGAATATT
56 ATAATCACCTTTATCAGGCTAGCTGAATATT
*
255157 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCAAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAT
255207 CTTTATTGTA
Statistics
Matches: 122, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
82 1 0.01
83 41 0.34
84 1 0.01
86 1 0.01
89 2 0.02
92 3 0.02
93 3 0.02
94 4 0.03
95 65 0.53
96 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (86 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATAGTATAATCACCT
TTATCAGGCTAGCTGAATATT
Found at i:255205 original size:95 final size:95
Alignment explanation
Indices: 255037--255218 Score: 294
Period size: 95 Copynumber: 1.9 Consensus size: 95
255027 ATATGTAAAT
* * *
255037 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAAAGGG
*
255102 ACAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
*
255132 ACCTTTATCATGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAAAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAAAGG
*
255196 GACAACTCAATCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
255219 TAAATAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 2 0.03
95 78 0.98
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAAAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:259371 original size:2 final size:2
Alignment explanation
Indices: 259359--259399 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
259349 ATTAAGAAAA
*
259359 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
259400 AAAGGATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:259475 original size:19 final size:19
Alignment explanation
Indices: 259451--259489 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
259441 ATATATAATA
*
259451 AGATAAAATAAAGTAAATC
1 AGATAAAATAAAGAAAATC
259470 AGATAAAATAAAGAAAATC
1 AGATAAAATAAAGAAAATC
259489 A
1 A
259490 TAACATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (19 bp):
AGATAAAATAAAGAAAATC
Found at i:259563 original size:19 final size:20
Alignment explanation
Indices: 259530--259569 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
259520 AATACTATCT
259530 AAATACATAAAAAAAAATGA
1 AAATACATAAAAAAAAATGA
* *
259550 AAATA-ATAATAAAATATGA
1 AAATACATAAAAAAAAATGA
259569 A
1 A
259570 GGGACTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (20 bp):
AAATACATAAAAAAAAATGA
Found at i:259621 original size:24 final size:23
Alignment explanation
Indices: 259584--259629 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
259574 CTGAATTGAA
259584 TAAAAAAAAATAGGGGATGAATTT
1 TAAAAAAAAATA-GGGATGAATTT
* *
259608 TAAAAGAAATTAGGGATGAATT
1 TAAAAAAAAATAGGGATGAATT
259630 CGATGAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (23 bp):
TAAAAAAAAATAGGGATGAATTT
Found at i:262052 original size:27 final size:27
Alignment explanation
Indices: 262021--262086 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
262011 AAAACAGTGT
262021 TGAATGATTCAGCACAAAAGTACATTC
1 TGAATGATTCAGCACAAAAGTACATTC
*
262048 TGAATGATTCAGCACAGAAGTACATTC
1 TGAATGATTCAGCACAAAAGTACATTC
262075 TGAATGATTCAG
1 TGAATGATTCAG
262087 AGTCATTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (27 bp):
TGAATGATTCAGCACAAAAGTACATTC
Found at i:263434 original size:20 final size:20
Alignment explanation
Indices: 263398--263435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
263388 ATCCTATTCC
**
263398 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
263418 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
263436 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:275122 original size:67 final size:68
Alignment explanation
Indices: 275040--275178 Score: 190
Period size: 67 Copynumber: 2.1 Consensus size: 68
275030 TCATGATTAT
* *
275040 CAAAAGGCTATACAGTTCATCAAGGATCTCAATGAAATTAACATATTACTTAATTTCAATTTGCA
1 CAAAAGGCTACACAGTTCATCAAGAATCTCAATGAAATTAACATATTACTTAATTTCAATTTGCA
275105 A-A
66 AGA
** * * * * *
275107 CAAAAGGCTACACAGTTTGTTAAGAATCTCAATGGAATTAACATATTACTTCATTTCGATTTTCA
1 CAAAAGGCTACACAGTTCATCAAGAATCTCAATGAAATTAACATATTACTTAATTTCAATTTGCA
275172 AGA
66 AGA
275175 CAAA
1 CAAA
275179 TACCCTAACT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
67 57 0.92
68 5 0.08
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (68 bp):
CAAAAGGCTACACAGTTCATCAAGAATCTCAATGAAATTAACATATTACTTAATTTCAATTTGCA
AGA
Found at i:277005 original size:19 final size:18
Alignment explanation
Indices: 276960--277010 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
276950 TAAGTACAAG
276960 TGTAGAAAACAGACTGTA
1 TGTAGAAAACAGACTGTA
*
276978 -GAAAGAAAACAGACTGTA
1 TG-TAGAAAACAGACTGTA
276996 TTGTAGAAAACAGAC
1 -TGTAGAAAACAGAC
277011 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.04
18 15 0.54
19 11 0.39
20 1 0.04
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.18
Consensus pattern (18 bp):
TGTAGAAAACAGACTGTA
Found at i:280978 original size:19 final size:18
Alignment explanation
Indices: 280932--280983 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
280922 ACCTGATACC
280932 ATGTAGAAAACAGACTGT
1 ATGTAGAAAACAGACTGT
*
280950 A-GAAAGAAAACAGACTGT
1 ATG-TAGAAAACAGACTGT
280968 ATTGTAGAAAACAGAC
1 A-TGTAGAAAACAGAC
280984 AAGTCTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 1 0.03
18 16 0.55
19 11 0.38
20 1 0.03
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (18 bp):
ATGTAGAAAACAGACTGT
Found at i:282667 original size:14 final size:14
Alignment explanation
Indices: 282648--282675 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
282638 CAATCGTATA
282648 TGAAAAATTATAAC
1 TGAAAAATTATAAC
282662 TGAAAAATTATAAC
1 TGAAAAATTATAAC
282676 ATGTCATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TGAAAAATTATAAC
Found at i:289164 original size:14 final size:14
Alignment explanation
Indices: 289145--289172 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
289135 AATCGGTATA
289145 TGAAAAATTATAAC
1 TGAAAAATTATAAC
289159 TGAAAAATTATAAC
1 TGAAAAATTATAAC
289173 ATGTCATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TGAAAAATTATAAC
Found at i:299001 original size:32 final size:31
Alignment explanation
Indices: 298965--299035 Score: 115
Period size: 32 Copynumber: 2.3 Consensus size: 31
298955 TTGTAATAAG
*
298965 AAAGGAAAATATATCAGGGAAATGAAAATGT
1 AAAGGAAAATATACCAGGGAAATGAAAATGT
*
298996 AAAAGGAAAATCTACCAGGGAAATGAAAATGT
1 -AAAGGAAAATATACCAGGGAAATGAAAATGT
299028 AAAGGAAA
1 AAAGGAAA
299036 GAAAAGTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (31 bp):
AAAGGAAAATATACCAGGGAAATGAAAATGT
Found at i:300882 original size:31 final size:29
Alignment explanation
Indices: 300800--300886 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
300790 TGAATACTTA
* *
300800 AAGTACATATTTTGATAAAAAAAATATTTT
1 AAGTACCTATTTTGA-AAAAAAAAAATTTT
300830 AAGTACCTATTTTGAACAAAAATATAAATTTT
1 AAGTACCTATTTTGAA-AAAAA-A-AAATTTT
* *
300862 AA-TGCTTATTTTGACAAAAAAAAAA
1 AAGTACCTATTTTGA-AAAAAAAAAA
300887 CACTTTAGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
29 4 0.08
30 20 0.41
31 16 0.33
32 9 0.18
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (29 bp):
AAGTACCTATTTTGAAAAAAAAAAATTTT
Found at i:301393 original size:6 final size:6
Alignment explanation
Indices: 301382--301408 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
301372 TTATATCCAC
301382 CATTCA CATTCA CATTCA CATTCA CAT
1 CATTCA CATTCA CATTCA CATTCA CAT
301409 ACATGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
CATTCA
Found at i:309284 original size:20 final size:22
Alignment explanation
Indices: 309239--309292 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 22
309229 CTGTTGAAGA
*
309239 GGTATCGATA-CTGTAAGGGGT
1 GGTATCGATACCTGTAAGGGAT
309260 GGTATCGATACCTG-AA-GGAT
1 GGTATCGATACCTGTAAGGGAT
309280 GGTATCGATACCT
1 GGTATCGATACCT
309293 TGAAACAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 16 0.52
21 12 0.39
22 3 0.10
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCTGTAAGGGAT
Found at i:317841 original size:55 final size:55
Alignment explanation
Indices: 317676--318061 Score: 526
Period size: 55 Copynumber: 7.1 Consensus size: 55
317666 TGATATGGTC
* * * *
317676 ATTCACAAACTCATTGTGAATTACGT-AGGTTGCTCACATAGTGCCAATAC-GATA
1 ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGA-A
* * * *
317730 ATTCACAAACTCATTATGAATTAC-TTAGGTTGCACACATAGTGCCAATATGGAA
1 ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGAA
* * * * *
317784 ATTCAAAAACTCATTATGAATTTTGTGGGGTTGCATACATAGTGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGAA
* * * *
317839 ATTTATAAACTCATTATAAATTTCGTGGGGTTGCACACATAGTTCCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGAA
*
317894 ATTCATAAACTCATTATGAATTTCGTAAGGTTGCACACATAGTGCCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGAA
* *
317949 ATTCATAAACTCATTATGAATTTCATGAAGTTGCACACATAGTGCCAATACGGAA
1 ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGAA
* * * *
318004 ATTCATAAACTCATTACGAATTTCATGAAGTTGCACACATAGTGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGAA
318059 ATT
1 ATT
318062 GCAACATATA
Statistics
Matches: 301, Mismatches: 28, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 67 0.22
55 233 0.77
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (55 bp):
ATTCATAAACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATACGGAA
Found at i:323756 original size:22 final size:22
Alignment explanation
Indices: 323701--323760 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
323691 TGAAATACAT
*
323701 CTAAGGCATTTTAGTATCAGTG
1 CTAAGGCACTTTAGTATCAGTG
* * *
323723 CTAATGCGCTTTCGTATCAGTG
1 CTAAGGCACTTTAGTATCAGTG
* *
323745 TTGAGGCACTTTAGTA
1 CTAAGGCACTTTAGTA
323761 CTAATGTCAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (22 bp):
CTAAGGCACTTTAGTATCAGTG
Found at i:324093 original size:29 final size:28
Alignment explanation
Indices: 324060--324124 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
324050 GTAAAATTAT
* *
324060 AAAGTTAGTGACCAAAGTATAAACTTTGA
1 AAAGTTAGTGACCAAAATAT-AACTTTAA
* *
324089 AAAGTTTATTGACCAAAATATAATTTTAA
1 AAAG-TTAGTGACCAAAATATAACTTTAA
324118 AAAGTTA
1 AAAGTTA
324125 CAAATGGGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 3 0.10
29 14 0.45
30 14 0.45
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (28 bp):
AAAGTTAGTGACCAAAATATAACTTTAA
Found at i:326012 original size:31 final size:31
Alignment explanation
Indices: 325974--326038 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
325964 GAGTCGATGG
*
325974 TTACCTATGTTCTTC-GATACATATGGACAAA
1 TTACCTATGTTCTTCGGA-ACATATGAACAAA
*
326005 TTACCTATGTTCTTCGGAACATATGAACATA
1 TTACCTATGTTCTTCGGAACATATGAACAAA
326036 TTA
1 TTA
326039 TTATACGAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGAACAAA
Found at i:331428 original size:29 final size:29
Alignment explanation
Indices: 331395--331476 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
331385 ATTATAGTGA
*
331395 GTGACCAAATTGTAAATTTATAAAGTTT-G
1 GTGACCAAAATGTAAATTTA-AAAGTTTAG
* *
331424 GTGACCAAAGTATAAACTTTGAAAAGTTTAG
1 GTGACCAAAATGTAAA-TTT-AAAAGTTTAG
* *
331455 G-GATCAAAATGTAATTTTAAAA
1 GTGACCAAAATGTAAATTTAAAA
331477 AGTTACAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.09
29 17 0.39
30 20 0.45
31 3 0.07
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (29 bp):
GTGACCAAAATGTAAATTTAAAAGTTTAG
Found at i:331452 original size:30 final size:29
Alignment explanation
Indices: 331395--331452 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
331385 ATTATAGTGA
* *
331395 GTGACCAAATTGTAAATTTATAAAGTTTG
1 GTGACCAAAGTATAAATTTATAAAGTTTG
331424 GTGACCAAAGTATAAACTTTGA-AAAGTTT
1 GTGACCAAAGTATAAA-TTT-ATAAAGTTT
331453 AGGGATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.56
30 10 0.40
31 1 0.04
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (29 bp):
GTGACCAAAGTATAAATTTATAAAGTTTG
Found at i:333354 original size:31 final size:31
Alignment explanation
Indices: 333316--333472 Score: 237
Period size: 31 Copynumber: 5.1 Consensus size: 31
333306 AGTCGAGGGA
*
333316 TACCTATGTTCTTCGGGACATATGGACAGTT
1 TACCTATGTTCTTCGGGACATATGGACAGAT
*
333347 TACCTATGTTCTTCTGGACATATGGACA-ATT
1 TACCTATGTTCTTCGGGACATATGGACAGA-T
* *
333378 TACCTATGTTATTTC-GGACATATGGACAGAA
1 TACCTATGTT-CTTCGGGACATATGGACAGAT
333409 TACCTATGTTCTTCGGGACATATGGACAGAT
1 TACCTATGTTCTTCGGGACATATGGACAGAT
*
333440 TACCTATGTTCTTCGGGACATATGAACAGAT
1 TACCTATGTTCTTCGGGACATATGGACAGAT
333471 TA
1 TA
333473 TTATACGAGT
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
30 3 0.03
31 108 0.94
32 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTTCGGGACATATGGACAGAT
Found at i:337396 original size:28 final size:31
Alignment explanation
Indices: 337356--337417 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
337346 ATGTTTGAAC
*
337356 TTTTCTGGACA-T-TTCGAACCAAATCTATTT
1 TTTTCTGGACATTGTTCGAACCAAAT-TAATT
337386 TTTTCT-G-CATTGTTCGAACCAAATTAATT
1 TTTTCTGGACATTGTTCGAACCAAATTAATT
337415 TTT
1 TTT
337418 CTTTACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.07
29 9 0.31
30 18 0.62
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTTCTGGACATTGTTCGAACCAAATTAATT
Found at i:337532 original size:39 final size:37
Alignment explanation
Indices: 337462--337534 Score: 101
Period size: 39 Copynumber: 1.9 Consensus size: 37
337452 TGCTCGAATC
* *
337462 TGCTAAAAAAATAAAATAAATAGAATGAAATAAAGTT
1 TGCTAAAAAAATAAAATAAATAAAATAAAATAAAGTT
*
337499 TGCTAAAAAAATAAAAATGTAATAAAATAAAATAAA
1 TGCTAAAAAAAT-AAAAT-AAATAAAATAAAATAAA
337535 ACAAAAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 12 0.39
38 5 0.16
39 14 0.45
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (37 bp):
TGCTAAAAAAATAAAATAAATAAAATAAAATAAAGTT
Found at i:343011 original size:19 final size:19
Alignment explanation
Indices: 342994--343038 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
342984 TGAAAAGATT
342994 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
* *
343014 TAATAAATAAAA-GGAAAA
1 TAATAAATAAAATAGATAA
343032 TAATAAA
1 TAATAAA
343039 ATAATCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.48
19 8 0.35
20 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:345661 original size:49 final size:51
Alignment explanation
Indices: 345606--345737 Score: 137
Period size: 51 Copynumber: 2.6 Consensus size: 51
345596 TGCTGTGTAT
* * * * *
345606 TTTTCTGCACTA-TTCGAACTAAA-TTTTTTCTACGCTGTTCTGTTTGAGC
1 TTTTCTGCACTAGTTCAAACCAAACTTTTTTCTACACTGTTCTGTTCGAAC
*
345655 TTTTCTGCA-TAGTTCAAACCAAATCTTTTTTCTATACTGTTCTGTTCGAAC
1 TTTTCTGCACTAGTTCAAACCAAA-CTTTTTTCTACACTGTTCTGTTCGAAC
**
345706 TTTTCTGCAC-AGTTTGAACCAAATCTATTTTT
1 TTTTCTGCACTAGTTCAAACCAAA-CT-TTTTT
345738 TTCTGCATTG
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
48 2 0.03
49 18 0.26
51 45 0.64
52 5 0.07
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.46
Consensus pattern (51 bp):
TTTTCTGCACTAGTTCAAACCAAACTTTTTTCTACACTGTTCTGTTCGAAC
Found at i:345688 original size:51 final size:51
Alignment explanation
Indices: 345629--345737 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
345619 TCGAACTAAA
* * * *
345629 TTTTTTCTACGCTGTTCTGTTTGAGCTTTTCTGCATAGTTCAAACCAAATC
1 TTTTTTCTACACTGTTCTGTTCGAACTTTTCTGCACAGTTCAAACCAAATC
* **
345680 TTTTTTCTATACTGTTCTGTTCGAACTTTTCTGCACAGTTTGAACCAAATC
1 TTTTTTCTACACTGTTCTGTTCGAACTTTTCTGCACAGTTCAAACCAAATC
345731 TATTTTT
1 T-TTTTT
345738 TTCTGCATTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 45 0.90
52 5 0.10
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (51 bp):
TTTTTTCTACACTGTTCTGTTCGAACTTTTCTGCACAGTTCAAACCAAATC
Found at i:345740 original size:30 final size:28
Alignment explanation
Indices: 345706--345773 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 28
345696 CTGTTCGAAC
* *
345706 TTTTCTGCACAGTTTGAACCAAATCTATTT
1 TTTTCTGCACAGTTCGAACCAAAT-TA-AT
**
345736 TTTTCTGCATTGTTCGAACCAAATTAAT
1 TTTTCTGCACAGTTCGAACCAAATTAAT
345764 TTTTCTGCAC
1 TTTTCTGCAC
345774 TATTTTGTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 10 0.30
29 2 0.06
30 21 0.64
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (28 bp):
TTTTCTGCACAGTTCGAACCAAATTAAT
Found at i:351464 original size:19 final size:19
Alignment explanation
Indices: 351447--351505 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
351437 TGAAAAGATT
351447 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
** *
351467 TAATAAATAAAAGGGAAAA
1 TAATAAATAAAATAGATAA
* *
351486 TAATAAA-ATAATAAATAA
1 TAATAAATAAAATAGATAA
351504 TA
1 TA
351506 GTAGTAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 8 0.26
19 19 0.61
20 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:351520 original size:27 final size:26
Alignment explanation
Indices: 351448--351520 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 26
351438 GAAAAGATTT
*
351448 AATAAAA--TAAAATAGATAATAATA
1 AATAAAAGGTAAAATAGAAAATAATA
* *
351472 AATAAAAGGGAAAATAATAAAATAATA
1 AATAAAAGGTAAAAT-AGAAAATAATA
*
351499 AATAATAGTAGTAAAATA-AAAA
1 AATAAAAG--GTAAAATAGAAAA
351521 GGGGTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 7 0.18
26 5 0.13
27 20 0.51
28 1 0.03
29 6 0.15
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (26 bp):
AATAAAAGGTAAAATAGAAAATAATA
Found at i:351584 original size:13 final size:13
Alignment explanation
Indices: 351563--351592 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
351553 AGATAAAAAT
*
351563 TAAATTAAATAAA
1 TAAAATAAATAAA
351576 TAAAATAAATAAA
1 TAAAATAAATAAA
351589 TAAA
1 TAAA
351593 TCGAGATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:352253 original size:72 final size:76
Alignment explanation
Indices: 352168--352319 Score: 215
Period size: 72 Copynumber: 2.1 Consensus size: 76
352158 TAAAACATCT
* *
352168 TAAATCCTAATTAAAATACTTAAAA-ATATTTAAACTAAAATACCT-AAAC-AA-ATAATAT-TT
1 TAAATCCTAATTAAAATAC-TAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
352228 AAAATAATATTC
65 AAAATAATATCC
* *
352240 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTCAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
352305 AAATAATATCC
66 AAATAATATCC
352316 TAAA
1 TAAA
352320 CTTGAGTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
71 5 0.07
72 37 0.53
73 4 0.06
74 2 0.03
75 6 0.09
76 16 0.23
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.30
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:353854 original size:3 final size:3
Alignment explanation
Indices: 353846--353908 Score: 94
Period size: 3 Copynumber: 21.7 Consensus size: 3
353836 TTGTTTTTAA
*
353846 TAT TAT TAT TA- TAC TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
353892 TAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
353909 CAAACAGGCC
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
2 4 0.07
3 51 0.93
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:357645 original size:43 final size:44
Alignment explanation
Indices: 357578--357664 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
357568 TGGCTTTAGA
* *
357578 GAAGTTAGGAGGGAAGGTTATCCCCTATATAT-AAAGTTTTGTT
1 GAAGTTAGGAGGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
** * *
357621 GAAGTTAGGATTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGAGGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
357665 TGATGCACAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 26 0.70
44 11 0.30
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (44 bp):
GAAGTTAGGAGGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
Found at i:357754 original size:21 final size:21
Alignment explanation
Indices: 357729--357773 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
357719 GAGTAACACC
357729 TTTTCATAC-ATGCATTTGCAT
1 TTTTCAT-CTATGCATTTGCAT
* *
357750 TTTTCATCTTTGCATTTTCAT
1 TTTTCATCTATGCATTTGCAT
357771 TTT
1 TTT
357774 ACTTTTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTCATCTATGCATTTGCAT
Found at i:361037 original size:14 final size:15
Alignment explanation
Indices: 361005--361058 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
360995 TCATTCATAA
*
361005 AAAAATGAAAAAGAAG
1 AAAAA-GAAAAAAAAG
*
361021 AAAAAG-GAAAAAAG
1 AAAAAGAAAAAAAAG
*
361035 AAAACGAAAAAAAAG
1 AAAAAGAAAAAAAAG
*
361050 AAAGAGAAA
1 AAAAAGAAA
361059 GAGAAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 11 0.35
15 15 0.48
16 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:365831 original size:22 final size:23
Alignment explanation
Indices: 365803--365859 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 23
365793 ACATCTACAC
365803 TCTTCAAAGATGATAGATTCT-T
1 TCTTCAAAGATGATAGATTCTCT
365825 TCTTCAAAGATGATAGATTCTCT
1 TCTTCAAAGATGATAGATTCTCT
*
365848 T-TTCAAATATGA
1 TCTTCAAAGATGA
365860 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (23 bp):
TCTTCAAAGATGATAGATTCTCT
Found at i:366429 original size:113 final size:113
Alignment explanation
Indices: 366215--366497 Score: 505
Period size: 113 Copynumber: 2.5 Consensus size: 113
366205 TAGCAAAGAT
* * *
366215 TCGAATCCATCACTCGATGGATCAACATCTCCAGAGAAAGTTCAT-ATGAGAATAACTCATTTGA
1 TCGAATCCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
366279 AGAAGGAAGGAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGC
366327 TCGAATCCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATCCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
366392 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGC
*
366440 TCGAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT
1 TCGAATCCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT
366498 TGTTCAACCT
Statistics
Matches: 164, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
112 44 0.27
113 120 0.73
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (113 bp):
TCGAATCCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAAAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGC
Found at i:366490 original size:73 final size:73
Alignment explanation
Indices: 366403--366569 Score: 307
Period size: 73 Copynumber: 2.3 Consensus size: 73
366393 GAAGGAAGAA
366403 AAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACAT
1 AAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACAT
366468 TTCCAGAG
66 TTCCAGAG
* *
366476 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCTATGGATCAACAT
1 AAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACAT
366541 TTCCAGAG
66 TTCCAGAG
*
366549 AAAATTCATAATGAGAAGAAC
1 AAAGTTCATAATGAGAAGAAC
366570 TCATCTGAAG
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (73 bp):
AAAGTTCATAATGAGAAGAACATGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACAT
TTCCAGAG
Found at i:366992 original size:3 final size:3
Alignment explanation
Indices: 366984--367043 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
366974 TTGTTTTTAA
*
366984 TAT TAT TAT TA- TAC TAT TAT TAT TA- TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
367028 TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TA
367044 CAAACAGGTC
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:367003 original size:8 final size:8
Alignment explanation
Indices: 366987--367043 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
366977 TTTTTAATAT
366987 TATTATTA
1 TATTATTA
*
366995 TACTA-T-
1 TATTATTA
367001 TATTATTA
1 TATTATTA
367009 TATTATT-
1 TATTATTA
367016 TATTA-T-
1 TATTATTA
367022 TATTATTA
1 TATTATTA
367030 TTATTATTA
1 -TATTATTA
367039 TATTA
1 TATTA
367044 CAAACAGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
6 10 0.24
7 8 0.19
8 16 0.38
9 8 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTATTA
Found at i:368976 original size:29 final size:28
Alignment explanation
Indices: 368936--368992 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
368926 TTTTAAATTA
368936 ATTACTAATTAGAT-ATTTAATTTTAATAT
1 ATTACTAATTAG-TCA-TTAATTTTAATAT
*
368965 ATTA-TAATTTAGTCATTGATTTTAATAT
1 ATTACTAA-TTAGTCATTAATTTTAATAT
368993 TTTCATTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTACTAATTAGTCATTAATTTTAATAT
Found at i:369335 original size:23 final size:22
Alignment explanation
Indices: 369284--369335 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
369274 CATTTTCTGA
369284 TATTTTTAAATAATAAATATCT
1 TATTTTTAAATAATAAATATCT
* * *
369306 TACTTTTTAAATTATATAATTTTT
1 TA-TTTTTAAATAATA-AATATCT
369330 TATTTT
1 TATTTT
369336 AGATAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 16 0.64
24 7 0.28
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTAAATAATAAATATCT
Found at i:369635 original size:2 final size:2
Alignment explanation
Indices: 369628--369680 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
369618 ATCTCATCTT
*
369628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
369670 TA TA TA TA TA T
1 TA TA TA TA TA T
369681 TTATCATGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:370100 original size:14 final size:14
Alignment explanation
Indices: 370078--370107 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
370068 TTCTAATCGC
*
370078 CACTGAAATCGCAT
1 CACTAAAATCGCAT
370092 CACTAAAATCGCAT
1 CACTAAAATCGCAT
370106 CA
1 CA
370108 TTTTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (14 bp):
CACTAAAATCGCAT
Found at i:370281 original size:75 final size:75
Alignment explanation
Indices: 370167--370311 Score: 263
Period size: 75 Copynumber: 1.9 Consensus size: 75
370157 GGGTATGTAT
* *
370167 AAAAGTATTCGCCACTAATGTCATACATATTATATTCTATGCTCATGCTACTATGGTCAACATCT
1 AAAAGTATTCGCCACTAAGGTCATACATATTATATTCTATGCTCATGCAACTATGGTCAACATCT
370232 AGTATACTCA
66 AGTATACTCA
*
370242 AAAAGTATTCGCCACTAAGGTCATACATATTATATTCTATGCTCATGCAACTATGGTCTACATCT
1 AAAAGTATTCGCCACTAAGGTCATACATATTATATTCTATGCTCATGCAACTATGGTCAACATCT
370307 AGTAT
66 AGTAT
370312 GCCCATGTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (75 bp):
AAAAGTATTCGCCACTAAGGTCATACATATTATATTCTATGCTCATGCAACTATGGTCAACATCT
AGTATACTCA
Found at i:372263 original size:2 final size:2
Alignment explanation
Indices: 372256--372289 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
372246 GATTCAATCA
372256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
372290 TATTTTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:372713 original size:22 final size:22
Alignment explanation
Indices: 372673--372715 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
372663 GTCTTAACAT
* * *
372673 ATATATATATTTTTTTTAATTA
1 ATATATATATATATATTAATTA
372695 ATATATATATATATATTAATT
1 ATATATATATATATATTAATT
372716 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATATATATATATATTAATTA
Found at i:372723 original size:26 final size:26
Alignment explanation
Indices: 372671--372723 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
372661 TAGTCTTAAC
** *
372671 ATATATATATATTTTTTTTAATTAAT
1 ATATATATATATTTAATTTAATAAAT
372697 ATATATATATATATTAATTTAA-AAAT
1 ATATATATATAT-TTAATTTAATAAAT
372723 A
1 A
372724 ATTAACAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATATATATATTTAATTTAATAAAT
Found at i:373486 original size:21 final size:23
Alignment explanation
Indices: 373450--373491 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
373440 AAGCTTTCTT
373450 TCTTCTCTGCCTTCTTATCCACG
1 TCTTCTCTGCCTTCTTATCCACG
*
373473 TCTTCT-TG-CTTCTTCTCCA
1 TCTTCTCTGCCTTCTTATCCA
373492 TTTTCACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 2 0.11
23 6 0.33
ACGTcount: A:0.07, C:0.38, G:0.07, T:0.48
Consensus pattern (23 bp):
TCTTCTCTGCCTTCTTATCCACG
Found at i:377643 original size:5 final size:5
Alignment explanation
Indices: 377633--377693 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
377623 TTGTTTATAT
*
377633 TTTTA TTTTA TTTTA TTTT- TTTATA TTTTG TTATT- TTATTA GTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TT-TTA TT-TTA -TTTTA
*
377680 TTTTC TTTTA TTTT
1 TTTTA TTTTA TTTT
377694 CAGGCCATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 3 0.06
5 35 0.73
6 8 0.17
7 2 0.04
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:377653 original size:18 final size:18
Alignment explanation
Indices: 377626--377688 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
377616 ACCCGACTTG
*
377626 TTTATATTTTTATTTTAT
1 TTTATTTTTTTATTTTAT
377644 TTTATTTTTTTATATTT-T
1 TTTATTTTTTTAT-TTTAT
* *
377662 GTTATTTTATTAGTTTTAT
1 TTTATTTTTTTA-TTTTAT
*
377681 TTTCTTTT
1 TTTATTTT
377689 ATTTTCAGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 26 0.70
19 11 0.30
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTATTTTTTTATTTTAT
Found at i:377678 original size:26 final size:25
Alignment explanation
Indices: 377626--377678 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
377616 ACCCGACTTG
*
377626 TTTATATTTTTATTTTATTTTATTTT
1 TTTATATTTTTATTTTA-TTTAGTTT
377652 TTTATATTTTGTTATTTTA-TTAGTTT
1 TTTATA-TTT-TTATTTTATTTAGTTT
377678 T
1 T
377679 ATTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 13 0.54
27 3 0.12
28 8 0.33
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTATATTTTTATTTTATTTAGTTT
Found at i:394021 original size:18 final size:19
Alignment explanation
Indices: 393993--394031 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
393983 CGGTTTTGAG
*
393993 CTACTACCAGAATGAGTGA
1 CTACTACCAGAACGAGTGA
394012 CTAC-ACCAGAACGAGTGA
1 CTACTACCAGAACGAGTGA
394030 CT
1 CT
394032 TCTCCAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (19 bp):
CTACTACCAGAACGAGTGA
Found at i:397230 original size:12 final size:12
Alignment explanation
Indices: 397213--397237 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
397203 AGACAATAAG
397213 TGAAATATTTAT
1 TGAAATATTTAT
397225 TGAAATATTTAT
1 TGAAATATTTAT
397237 T
1 T
397238 ACTGCTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGAAATATTTAT
Found at i:405843 original size:11 final size:11
Alignment explanation
Indices: 405829--405869 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
405819 AAGAAATAAA
405829 AAATAAAAAAT
1 AAATAAAAAAT
**
405840 AAATAAAAAGG
1 AAATAAAAAAT
405851 AAATAAATAAAT
1 AAATAAA-AAAT
405863 AAATAAA
1 AAATAAA
405870 TCAAAGAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:405844 original size:27 final size:31
Alignment explanation
Indices: 405813--405870 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
405803 TTAGTTGATA
405813 AAAT-AAAA-GAAATAAA-AAATAAA-AAAT
1 AAATAAAAAGGAAATAAATAAATAAATAAAT
405840 AAATAAAAAGGAAATAAATAAATAAATAAAT
1 AAATAAAAAGGAAATAAATAAATAAATAAAT
405871 CAAAGAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 8 0.30
30 7 0.26
31 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (31 bp):
AAATAAAAAGGAAATAAATAAATAAATAAAT
Found at i:405845 original size:4 final size:4
Alignment explanation
Indices: 405822--405870 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
405812 AAAATAAAAG
**
405822 AAAT AAA- AAAT AAA- AAAT AAAT AAA- AAGG AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
405867 AAAT
1 AAAT
405871 CAAAGAAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
3 8 0.21
4 31 0.79
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:405858 original size:19 final size:18
Alignment explanation
Indices: 405817--405865 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
405807 TTGATAAAAT
* *
405817 AAAAGAAATAAAAAATAA
1 AAAATAAATAAAAAAGAA
*
405835 AAAATAAATAAAAAGGAA
1 AAAATAAATAAAAAAGAA
405853 ATAAATAAATAAA
1 A-AAATAAATAAA
405866 TAAATCAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAATAAATAAAAAAGAA
Found at i:405864 original size:8 final size:8
Alignment explanation
Indices: 405822--405870 Score: 59
Period size: 7 Copynumber: 6.5 Consensus size: 8
405812 AAAATAAAAG
405822 AAATAAA-
1 AAATAAAT
405829 AAATAAA-
1 AAATAAAT
405836 AAATAAAT
1 AAATAAAT
**
405844 AAA-AAGG
1 AAATAAAT
405851 AAATAAAT
1 AAATAAAT
405859 AAATAAAT
1 AAATAAAT
405867 AAAT
1 AAAT
405871 CAAAGAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
7 19 0.53
8 17 0.47
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (8 bp):
AAATAAAT
Found at i:405879 original size:29 final size:26
Alignment explanation
Indices: 405829--405884 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 26
405819 AAGAAATAAA
405829 AAATAAAAAATAAATAAAAAGGAAAT
1 AAATAAAAAATAAATAAAAAGGAAAT
405855 AAATAAATAAATAAATCAAAGAAGGAAAT
1 AAATAAA-AAATAAAT-AAA-AAGGAAAT
405884 A
1 A
405885 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.26
27 8 0.30
28 3 0.11
29 9 0.33
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (26 bp):
AAATAAAAAATAAATAAAAAGGAAAT
Found at i:405981 original size:7 final size:8
Alignment explanation
Indices: 405959--405991 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
405949 AAATTTCAAG
405959 AAAAATAAT
1 AAAAA-AAT
405968 AAAAAAAT
1 AAAAAAAT
405976 AAAAAAAT
1 AAAAAAAT
405984 AAAAAAAT
1 AAAAAAAT
405992 GTTAAAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:405989 original size:62 final size:61
Alignment explanation
Indices: 405855--405989 Score: 141
Period size: 62 Copynumber: 2.2 Consensus size: 61
405845 AAAAGGAAAT
** * * **
405855 AAATAAATAAATAAATCAAAGAAGGAAATATTAAATTAAAAAAATTTTATATATAAAAATATTA
1 AAATAAA-AAATAAAAAAAAGAAGAAAATATTAAATTAAAAAAA--TTATATAAAAAAATAAAA
405919 AAAT-AAAAATAAAAAAAAGAAGAAAATATTAAATTTCAAGAAAAA-TA-ATAAAAAAATAAAA
1 AAATAAAAAATAAAAAAAAGAAGAAAATATTAAA-TT-AA-AAAAATTATATAAAAAAATAAAA
405980 AAATAAAAAA
1 AAATAAAAAA
405990 ATGTTAAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
61 15 0.25
62 31 0.51
63 4 0.07
64 6 0.10
65 5 0.08
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.23
Consensus pattern (61 bp):
AAATAAAAAATAAAAAAAAGAAGAAAATATTAAATTAAAAAAATTATATAAAAAAATAAAA
Found at i:407661 original size:34 final size:33
Alignment explanation
Indices: 407586--407663 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
407576 GTTGGACCTG
407586 ATAC-ATATAATAAATATATAAATATATGTACA
1 ATACTATATAATAAATATATAAATATATGTACA
* *
407618 ATACTATATAATATAA-ATATAATATGTATGTACC
1 ATACTATATAATA-AATATATAA-ATATATGTACA
407652 ATA-TGATATAAT
1 ATACT-ATATAAT
407664 TCACATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 4 0.10
33 15 0.38
34 21 0.52
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.37
Consensus pattern (33 bp):
ATACTATATAATAAATATATAAATATATGTACA
Found at i:408463 original size:85 final size:85
Alignment explanation
Indices: 408307--408544 Score: 291
Period size: 85 Copynumber: 2.8 Consensus size: 85
408297 GCTGTTATCA
* * * * *
408307 AGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGGCAGATAACCCTTTTCACCTTGA-AGTATGT
1 AGCTGAATTGAATCGAACTCGAAGGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGA-TATGT
*
408371 TGCAAATTTGATATGCCCTTG
65 TGTAAATTTGATATGCCCTTG
* * * * * *
408392 AGCTGAATTGAATTGAACTCGAAGGTTTTGGTTGATAGATAGCCCCTCTCGCCTTGAGATATGCT
1 AGCTGAATTGAATCGAACTCGAAGGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGATATGTT
408457 GTAAATTTGATATGCCCTTG
66 GTAAATTTGATATGCCCTTG
* * * * *
408477 AGCTG-ATTATAATCAAACTTGAAGGTTTTCGTTGACAGATAACTCTTCTCGCCTTGAGTTATGT
1 AGCTGAATT-GAATCGAACTCGAAGGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGATATGT
408541 TGTA
65 TGTA
408545 CTAGGATATG
Statistics
Matches: 129, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
84 3 0.02
85 125 0.97
86 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (85 bp):
AGCTGAATTGAATCGAACTCGAAGGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGATATGTT
GTAAATTTGATATGCCCTTG
Found at i:410665 original size:19 final size:19
Alignment explanation
Indices: 410622--410665 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
410612 GAATGTAAAA
*
410622 ATGGTATCGATACCATAAT
1 ATGGTATCAATACCATAAT
* *
410641 AGGGTATCAATACCATAGT
1 ATGGTATCAATACCATAAT
410660 ATGGTA
1 ATGGTA
410666 GTATCAATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
ATGGTATCAATACCATAAT
Found at i:411160 original size:45 final size:45
Alignment explanation
Indices: 411101--411495 Score: 574
Period size: 45 Copynumber: 8.8 Consensus size: 45
411091 AATGAATGAA
*
411101 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * * * *
411146 CAAAAGAATTATGCATTTGAGTTCATTATCAGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
411191 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGCATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * ** *
411236 CAAAAGAATAATGCATATAGGTGAATTATCAACATAAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
411281 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
411326 CACAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * * *
411371 CAAAAGAATAATGCATATGAGTGGATTATTGTCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
411416 CAAAAGAATAATGAATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * ** *
411461 CAAAAGAACAATACATATAAGTGCATTATTGGCAT
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCAT
411496 AAAAAAGATG
Statistics
Matches: 308, Mismatches: 42, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 308 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (45 bp):
CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
Found at i:418143 original size:45 final size:45
Alignment explanation
Indices: 418088--418480 Score: 495
Period size: 45 Copynumber: 8.6 Consensus size: 45
418078 AATGAATGAA
* * ** * *
418088 CAAAATAATAATGGATATGGGTAAATTATCGACATGAAAGGATAC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
418133 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * * *
418178 GAAAAGAATAATGCACATGGGTGCATTATCGGCATGAAATGATTC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
418223 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
418268 CAAAAGAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
418313 CAAAAGAATAATGCATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 CAAAAG----A---ATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
** * *
418365 TGAAAGAATATTGCATAT-GGTGCATTATCGGCATGAAAGAATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * *
418409 CAAAAGAATAATGCATATGGGAGCATTATTGGCATGAATGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
**
418454 CATATCTG-A-AATGCATATGGGTGCATT
1 CA-A-AAGAATAATGCATATGGGTGCATT
418481 TTCAACATAA
Statistics
Matches: 306, Mismatches: 32, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
44 39 0.13
45 222 0.73
46 2 0.01
47 1 0.00
48 1 0.00
49 1 0.00
52 40 0.13
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (45 bp):
CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
Found at i:418337 original size:52 final size:52
Alignment explanation
Indices: 418275--418425 Score: 201
Period size: 52 Copynumber: 3.1 Consensus size: 52
418265 TGCCAAAAGA
*
418275 ATAATGCATATGGGTGCATTATCGACATGAAAGGATGCCAAAAGAATAATGC
1 ATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCAAAAGAATAATGC
* **
418327 ATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCTGAAAG---AAT--
1 ATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCAAAAGAATAATGC
*
418374 AT--TGCATAT-GGTGCATTATCGGCATGAAAGAATGCCAAAAGAATAATGC
1 ATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCAAAAGAATAATGC
418423 ATA
1 ATA
418426 TGGGAGCATT
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
44 28 0.33
45 7 0.08
47 5 0.06
49 5 0.06
52 40 0.47
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (52 bp):
ATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCAAAAGAATAATGC
Found at i:423059 original size:4 final size:4
Alignment explanation
Indices: 423050--423083 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
423040 TAAAAAGGAA
*
423050 AAAT AAAT AAAT AAAT AAAT CAAAA AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT A
423084 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:423078 original size:21 final size:20
Alignment explanation
Indices: 423049--423096 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
423039 ATAAAAAGGA
423049 AAAATAAATAAATAAATAAATC
1 AAAA-AAATAAAT-AATAAATC
* *
423071 AAAAAAATAAATATTAAATT
1 AAAAAAATAAATAATAAATC
423091 AAAAAA
1 AAAAAA
423097 TGTTACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAAATAAATAATAAATC
Found at i:425725 original size:85 final size:84
Alignment explanation
Indices: 425536--425774 Score: 266
Period size: 85 Copynumber: 2.8 Consensus size: 84
425526 CGCTGTCATC
* * * *
425536 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAATATACCTTCTCGCCTTGAGCTATGCT
1 GAGCTAAATGGAATCGAACTCGAAGGTTTTTGTTGACAATATACCCTCTCACCTTGAGATATGCT
* *
425601 GTAAATTTGATATTCCCTT
66 ATAAATTTGATATGCCCTT
* * * * * *
425620 GAGCTGAATGGAATCAAACTCGAAGGTTTTGGTTGATAGATA-ACCCCTGTCACCTTGAGATATT
1 GAGCTAAATGGAATCGAACTCGAAGGTTTTTGTTGACA-ATATA-CCCTCTCACCTTGAGATATG
425684 CTATAAATTTGATATGCCCTT
64 CTATAAATTTGATATGCCCTT
* * * * * *
425705 GTGCTAAATGTAATCGAACTCGAAGGTTTTTGTTGAC-ATATAACTCTTCTCGCCTTAAGTTATG
1 GAGCTAAATGGAATCGAACTCGAAGGTTTTTGTTGACAATAT-AC-CCTCTCACCTTGAGATATG
425769 CTATAA
64 CTATAA
425775 TAGGCTGAGA
Statistics
Matches: 128, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
83 3 0.02
84 37 0.29
85 88 0.69
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (84 bp):
GAGCTAAATGGAATCGAACTCGAAGGTTTTTGTTGACAATATACCCTCTCACCTTGAGATATGCT
ATAAATTTGATATGCCCTT
Found at i:427105 original size:9 final size:9
Alignment explanation
Indices: 427091--427118 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
427081 AGTGACTATA
427091 TTGAAAATT
1 TTGAAAATT
427100 TTGAAAATT
1 TTGAAAATT
427109 TTGAAAATT
1 TTGAAAATT
427118 T
1 T
427119 AAGATTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (9 bp):
TTGAAAATT
Found at i:427990 original size:22 final size:20
Alignment explanation
Indices: 427939--428009 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
427929 TGCAAAAATG
* *
427939 GTATCGATACCATAATAAG-
1 GTATCGATACCATAGTAGGA
*
427958 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTA-GG-A
*
427980 GTATCGATACCATTGTAGGA
1 GTATCGATACCATAGTAGGA
*
428000 TTATCGATAC
1 GTATCGATAC
428010 TGAGGAGCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 15 0.35
20 11 0.26
21 2 0.05
22 15 0.35
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGA
Found at i:428482 original size:45 final size:45
Alignment explanation
Indices: 428418--428937 Score: 656
Period size: 45 Copynumber: 11.6 Consensus size: 45
428408 AACAAATGAA
* * * * *
428418 CAAAATAATAATGCATATGGCTGAATTATCGCCATGAAAGAATGT
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
428463 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAA-AGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGA-ATGC
* * *
428508 CAAAAGAATAATGCTTATGGGTGCATTATCGGCATGAAAGGATGG
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
* * *
428553 AAAAAGAATAATGC--ATGTGTGCATTATCGACATGAAAGAATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
428596 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
*
428641 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAA-AGATGT
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGA-ATGC
* * * * *
428686 TAAAAGAATAATGCATATGAGTGTATTATCAGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
** *
428731 CAAAAGAATAATGCATATGGGTGCATTATCGATATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
* * * *
428776 CAAAAGAATAATGTATATGGGTGAATTATCGGCATTAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
* * * * *
428821 CAAAAGTATAATCCATATGGGTGCGTTATTGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
* * * *
428866 CAAAAGAATAATGCATATGTGTGCATTATTGGCACGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
*
428911 C-ATAGCTAA-AATGCATATGGGTGCATT
1 CAAAAG--AATAATGCATATGGGTGCATT
428938 TTCAGCATAA
Statistics
Matches: 419, Mismatches: 48, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
43 38 0.09
44 5 0.01
45 374 0.89
46 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (45 bp):
CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGAATGC
Found at i:430384 original size:95 final size:95
Alignment explanation
Indices: 430265--430461 Score: 385
Period size: 95 Copynumber: 2.1 Consensus size: 95
430255 AAAGAACAAG
*
430265 AAAAATAATAATAATAATTGGAGGTCGACAACTAATATTGAAATTGATGACGTCACTGGTTAAAC
1 AAAAATAATAATAATAATTAGAGGTCGACAACTAATATTGAAATTGATGACGTCACTGGTTAAAC
430330 AAAAATCAAAAGAAAAGAGTAAGGTGACAC
66 AAAAATCAAAAGAAAAGAGTAAGGTGACAC
430360 AAAAATAATAATAATAATTAGAGGTCGACAACTAATATTGAAATTGATGACGTCACTGGTTAAAC
1 AAAAATAATAATAATAATTAGAGGTCGACAACTAATATTGAAATTGATGACGTCACTGGTTAAAC
430425 AAAAATCAAAAGAAAAGAGTAAGGTGACAC
66 AAAAATCAAAAGAAAAGAGTAAGGTGACAC
430455 AAAAATA
1 AAAAATA
430462 TTATGAAAAA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 101 1.00
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (95 bp):
AAAAATAATAATAATAATTAGAGGTCGACAACTAATATTGAAATTGATGACGTCACTGGTTAAAC
AAAAATCAAAAGAAAAGAGTAAGGTGACAC
Found at i:434577 original size:20 final size:21
Alignment explanation
Indices: 434552--434595 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
434542 ATTAATTAAA
*
434552 ATTTAAATAATAC-ATGATAT
1 ATTTAAATAATACAATAATAT
434572 ATTTAAATAATACAATAATAT
1 ATTTAAATAATACAATAATAT
434593 ATT
1 ATT
434596 ATCGATGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTAAATAATACAATAATAT
Found at i:434624 original size:15 final size:15
Alignment explanation
Indices: 434606--434679 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
434596 ATCGATGATT
434606 TTTTTATATAAATAA
1 TTTTTATATAAATAA
*
434621 TTTTTATTTAAAT-A
1 TTTTTATATAAATAA
* ** *
434635 -TATTAT-CGAAGAA
1 TTTTTATATAAATAA
434648 TTTTTATATAAATAA
1 TTTTTATATAAATAA
*
434663 TTTTTATTTAAATAA
1 TTTTTATATAAATAA
434678 TT
1 TT
434680 AGAATTTCAC
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
12 2 0.04
13 6 0.13
14 6 0.13
15 32 0.70
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (15 bp):
TTTTTATATAAATAA
Found at i:434665 original size:42 final size:43
Alignment explanation
Indices: 434588--434680 Score: 154
Period size: 42 Copynumber: 2.2 Consensus size: 43
434578 ATAATACAAT
* *
434588 AATATATTATCGATGATTTTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGAAGATATTTTTATATAAATAATTTTTATTTA
434631 AATATATTATCGAAGA-ATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGAAGATATTTTTATATAAATAATTTTTATTTA
434673 AATA-ATTA
1 AATATATTA
434681 GAATTTCACT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 4 0.08
42 29 0.60
43 15 0.31
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (43 bp):
AATATATTATCGAAGATATTTTTATATAAATAATTTTTATTTA
Found at i:446754 original size:52 final size:52
Alignment explanation
Indices: 446676--446804 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
446666 ACCTTAGCAC
* *
446676 TGTAAGAGCATCGAGAGATAGCCTTGGGTTTTGGTAAAACATGTATTGGCAT
1 TGTAAGAGCATCGAGAGATAGCCTTGGGTTCTGGTAAAACATGTATTGCCAT
*
446728 TGTAAGAGCATCGAGAGATAGCCTTGGGTTCTGGTAAAACATGTCTTGCCAT
1 TGTAAGAGCATCGAGAGATAGCCTTGGGTTCTGGTAAAACATGTATTGCCAT
*
446780 TGTAAGAGCATCGAGAGATACCCTT
1 TGTAAGAGCATCGAGAGATAGCCTT
446805 TTGTCTAGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (52 bp):
TGTAAGAGCATCGAGAGATAGCCTTGGGTTCTGGTAAAACATGTATTGCCAT
Found at i:448144 original size:8 final size:7
Alignment explanation
Indices: 448129--448185 Score: 53
Period size: 8 Copynumber: 7.7 Consensus size: 7
448119 CAAACAACTC
448129 TTTTTCT
1 TTTTTCT
448136 TTCTTTCT
1 TT-TTTCT
448144 TTCTTTCT
1 TT-TTTCT
*
448152 TTTCCTCT
1 TTT-TTCT
448160 TTTTT-T
1 TTTTTCT
*
448166 TTTCTTTT
1 TTT-TTCT
448174 TTTTTCT
1 TTTTTCT
448181 TTTTT
1 TTTTT
448186 TTGGTGGATC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
6 4 0.09
7 14 0.33
8 25 0.58
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:448173 original size:9 final size:10
Alignment explanation
Indices: 448129--448187 Score: 64
Period size: 10 Copynumber: 5.4 Consensus size: 10
448119 CAAACAACTC
448129 TTTTTCTTTCT
1 TTTTTCTTT-T
448140 TTCTTTCTTTCT
1 TT-TTTCTTT-T
*
448152 TTTCCTCTTTTT
1 TTT-TTC-TTTT
448164 TTTTTCTTTT
1 TTTTTCTTTT
448174 TTTTTCTTTT
1 TTTTTCTTTT
448184 TTTT
1 TTTT
448188 GGTGGATCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
10 18 0.42
11 5 0.12
12 17 0.40
13 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:448967 original size:20 final size:20
Alignment explanation
Indices: 448942--448985 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
448932 AATGGTATCG
*
448942 TACTGTATGAATAGTACCAA
1 TACTGTATGAACAGTACCAA
*
448962 TACTGTATGAACAGTACCGA
1 TACTGTATGAACAGTACCAA
448982 TACT
1 TACT
448986 ATGTGAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
TACTGTATGAACAGTACCAA
Found at i:448992 original size:20 final size:20
Alignment explanation
Indices: 448942--448994 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
448932 AATGGTATCG
* *
448942 TACTGTATGAATAGTACCAA
1 TACTATATGAACAGTACCAA
* *
448962 TACTGTATGAACAGTACCGA
1 TACTATATGAACAGTACCAA
*
448982 TACTATGTGAACA
1 TACTATATGAACA
448995 TTAGTATCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
TACTATATGAACAGTACCAA
Found at i:449123 original size:21 final size:21
Alignment explanation
Indices: 449065--449124 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
449055 CGATACTGCT
* *
449065 ACAGTATTATCGATACCAAGA
1 ACAGTAGTATCGATACTAAGA
**
449086 ACAGTAGTATCGATACTGTGA
1 ACAGTAGTATCGATACTAAGA
449107 ACAGTAGTATCGATACTA
1 ACAGTAGTATCGATACTA
449125 TCAAGCCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (21 bp):
ACAGTAGTATCGATACTAAGA
Found at i:449284 original size:20 final size:20
Alignment explanation
Indices: 449233--449284 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
449223 AGAAAATTAA
* *
449233 TCTCCAACGACTCCAAAAAT
1 TCTCTAACGGCTCCAAAAAT
449253 TCTCTAACGGCTCCAAAAAT
1 TCTCTAACGGCTCCAAAAAT
*
449273 TCTCTAATGGCT
1 TCTCTAACGGCT
449285 AGAAACGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.27
Consensus pattern (20 bp):
TCTCTAACGGCTCCAAAAAT
Found at i:454660 original size:21 final size:21
Alignment explanation
Indices: 454603--454660 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
454593 TGATTGCGGC
* *
454603 CGTCGCGGGCACTATTGCAGT
1 CGTCGCGGGCGCTATTACAGT
* * *
454624 CGTCGCGGGTGTTATTACGGT
1 CGTCGCGGGCGCTATTACAGT
*
454645 CGTCGCGGACGCTATT
1 CGTCGCGGGCGCTATT
454661 GCGGCCCTCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.26, G:0.34, T:0.28
Consensus pattern (21 bp):
CGTCGCGGGCGCTATTACAGT
Found at i:457251 original size:4 final size:4
Alignment explanation
Indices: 457242--457280 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
457232 AGCAGGTATT
*
457242 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
457281 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:457283 original size:2 final size:2
Alignment explanation
Indices: 457270--457333 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
457260 ACATACATAC
*
457270 AT AT AT AC AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
457311 AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
457334 TGTGTGTGTG
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:457302 original size:17 final size:17
Alignment explanation
Indices: 457270--457330 Score: 106
Period size: 17 Copynumber: 3.6 Consensus size: 17
457260 ACATACATAC
*
457270 ATATATACAT-ATATAT
1 ATATATATATAATATAT
457286 ATATATATATAATATAT
1 ATATATATATAATATAT
457303 ATATATATATAATATAT
1 ATATATATATAATATAT
457320 ATATATATATA
1 ATATATATATA
457331 TATTGTGTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
16 9 0.21
17 34 0.79
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATATAATATAT
Found at i:457559 original size:2 final size:2
Alignment explanation
Indices: 457554--457583 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
457544 ACACACACAC
457554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
457584 GTGTGTGTGT
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):
AT
Found at i:460158 original size:77 final size:77
Alignment explanation
Indices: 460065--460207 Score: 250
Period size: 77 Copynumber: 1.9 Consensus size: 77
460055 ATGCTGGATA
*
460065 ATCATAATTATTGAATGAGTAAAACGTTGCAGAAGATTCTTAAGACGAGGATAATTATATTAGAG
1 ATCATAATTATTGAATGAGTAAAACGTTGCAGAAGATTCTTAAGACGAGGATAATTATATAAGAG
460130 ACATGGCTGATG
66 ACATGGCTGATG
* * *
460142 ATCATAATTATTGAATGAGTAAAACGTTGCAGAAGATTCTTACGATGAGGGTAATTATATAAGAG
1 ATCATAATTATTGAATGAGTAAAACGTTGCAGAAGATTCTTAAGACGAGGATAATTATATAAGAG
460207 A
66 A
460208 GACTGTTACC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (77 bp):
ATCATAATTATTGAATGAGTAAAACGTTGCAGAAGATTCTTAAGACGAGGATAATTATATAAGAG
ACATGGCTGATG
Found at i:463571 original size:76 final size:76
Alignment explanation
Indices: 463485--463632 Score: 242
Period size: 76 Copynumber: 1.9 Consensus size: 76
463475 ACTTGACTCA
* *
463485 AAAAAATTTAAAGTCAACTCCGGGTTGTAAAATAAGACCCGTCAACTCAAATAACTCAAAATTTT
1 AAAAAATTTAAAGTCAACTCCGAGTTGTAAAATAAGACCCGTCAACTCAAATAACTCAAAATTTC
463550 GACTCGACTTG
66 GACTCGACTTG
* ** *
463561 AAAAAATTTAAAGTCAACTTCGAGTTGTAAAATAAGAGTCGTCAACTCGAATAACTCAAAATTTC
1 AAAAAATTTAAAGTCAACTCCGAGTTGTAAAATAAGACCCGTCAACTCAAATAACTCAAAATTTC
463626 GACTCGA
66 GACTCGA
463633 TTCGATCGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (76 bp):
AAAAAATTTAAAGTCAACTCCGAGTTGTAAAATAAGACCCGTCAACTCAAATAACTCAAAATTTC
GACTCGACTTG
Found at i:464196 original size:6 final size:6
Alignment explanation
Indices: 464185--464210 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
464175 TTGATTTGGT
464185 TATGAA TATGAA TATGAA TATGAA TA
1 TATGAA TATGAA TATGAA TATGAA TA
464211 GGCAAAGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
TATGAA
Found at i:464854 original size:11 final size:11
Alignment explanation
Indices: 464838--464866 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
464828 CTTAATATTA
464838 CATTTTGATTT
1 CATTTTGATTT
464849 CATTTTGATTT
1 CATTTTGATTT
464860 CATTTTG
1 CATTTTG
464867 GTCACCCGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (11 bp):
CATTTTGATTT
Found at i:466991 original size:15 final size:16
Alignment explanation
Indices: 466959--466991 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
466949 TTATTCATAC
466959 TACTAACCATATTTAA
1 TACTAACCATATTTAA
*
466975 TACTAACTATA-TTAA
1 TACTAACCATATTTAA
466990 TA
1 TA
466992 ATTTGCATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (16 bp):
TACTAACCATATTTAA
Found at i:467487 original size:30 final size:30
Alignment explanation
Indices: 467451--467509 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
467441 GCTTACCATA
467451 TGCACTAAGTGTCCTTACACACTACAGTGT
1 TGCACTAAGTGTCCTTACACACTACAGTGT
467481 TGCACTAAGTGTCCTTACACACTACAGTG
1 TGCACTAAGTGTCCTTACACACTACAGTG
467510 CCAATCCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (30 bp):
TGCACTAAGTGTCCTTACACACTACAGTGT
Found at i:469012 original size:19 final size:20
Alignment explanation
Indices: 468988--469032 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
468978 AAAATGACCA
*
468988 AATTTCA-CATTCTAACATC
1 AATTTCAGCACTCTAACATC
*
469007 AATTTCAGCACTCTAACATT
1 AATTTCAGCACTCTAACATC
469027 AATTTC
1 AATTTC
469033 CAACATAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTTCAGCACTCTAACATC
Done.