Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 13 of 125
Found at i:2064249 original size:4 final size:4
Alignment explanation
Indices: 2064231--2064279 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
2064221 TATATGTATT
* * *
2064231 TTTA TTTA TCT- TTTA TTTA TCTA TTTA TTTA TTTT TTTA TTTA TCTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
2064279 T
1 T
2064280 AATATTATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
3 2 0.05
4 31 0.84
5 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:2064652 original size:9 final size:10
Alignment explanation
Indices: 2064628--2064653 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2064618 TTAGCAAAAC
2064628 ATTTTTGGAG
1 ATTTTTGGAG
2064638 ATTTTTGGAG
1 ATTTTTGGAG
2064648 ATTTTT
1 ATTTTT
2064654 TTTTGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (10 bp):
ATTTTTGGAG
Found at i:2065264 original size:6 final size:6
Alignment explanation
Indices: 2065253--2065318 Score: 61
Period size: 6 Copynumber: 11.8 Consensus size: 6
2065243 TTTATCTTTC
* * *
2065253 TTTTAT TTTTAT TTTT-G TTTTAC TTTT-T TTTTA- TTCTA- TTTTA-
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
2065296 TTTTAT TTTTAT TTTTAC TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTA
2065319 CTTTGTTACT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
5 21 0.41
6 30 0.59
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:2065267 original size:11 final size:11
Alignment explanation
Indices: 2065215--2065310 Score: 74
Period size: 11 Copynumber: 8.9 Consensus size: 11
2065205 TAATTTGTTT
2065215 TTTTTATTTTA
1 TTTTTATTTTA
**
2065226 GGTTTA-TTTA
1 TTTTTATTTTA
* * *
2065236 ATATTCTTTTA
1 TTTTTATTTTA
* *
2065247 TCTTTCTTTTA
1 TTTTTATTTTA
2065258 TTTTTATTTT-
1 TTTTTATTTTA
2065268 TGTTTTACTTTT-
1 T-TTTTA-TTTTA
*
2065280 TTTTTATTCTA
1 TTTTTATTTTA
2065291 -TTTTATTTTA
1 TTTTTATTTTA
2065301 TTTTTATTTT
1 TTTTTATTTT
2065311 TACTTTTACT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
10 19 0.28
11 43 0.64
12 5 0.07
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:2065322 original size:6 final size:5
Alignment explanation
Indices: 2065212--2065310 Score: 65
Period size: 5 Copynumber: 18.8 Consensus size: 5
2065202 AATTAATTTG
* * * * *
2065212 TTTT- TTTTA TTTTA GGTTTA TTTAA TATTC TTTTA TCTTTC TTTTA TTTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA -TTTTA
* * *
2065264 TTTTTG TTTTA CTTTTT TTTTA TTCTA TTTTA TTTTA TTTTTA TTTT
1 -TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
2065311 TACTTTTACT
Statistics
Matches: 73, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
4 4 0.05
5 42 0.58
6 27 0.37
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:2065330 original size:14 final size:12
Alignment explanation
Indices: 2065241--2065322 Score: 70
Period size: 11 Copynumber: 7.3 Consensus size: 12
2065231 ATTTAATATT
*
2065241 CTTTTATCTTT-
1 CTTTTATTTTTA
2065252 CTTTTATTTTTA
1 CTTTTATTTTTA
2065264 -TTTT-TGTTTTA
1 CTTTTAT-TTTTA
2065275 CTTTT-TTTTTA
1 CTTTTATTTTTA
*
2065286 -TTCTA-TTTTA
1 CTTTTATTTTTA
2065296 -TTTTATTTTTA
1 CTTTTATTTTTA
* *
2065307 TTTTTACTTTTA
1 CTTTTATTTTTA
2065319 CTTT
1 CTTT
2065323 GTTACTTTCT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
10 13 0.22
11 29 0.48
12 18 0.30
ACGTcount: A:0.13, C:0.09, G:0.01, T:0.77
Consensus pattern (12 bp):
CTTTTATTTTTA
Found at i:2065421 original size:58 final size:57
Alignment explanation
Indices: 2065348--2065737 Score: 473
Period size: 58 Copynumber: 6.7 Consensus size: 57
2065338 GAAAAATAAA
2065348 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
** * *
2065405 AAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAATTTTC
1 AAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
* * * *
2065463 AAAAAA-AGGGTTTTTAAGGAAAAGTTGATAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAATA---TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTC
* * *
2065523 CAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTTC
1 AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
* * *
2065580 AAAAAAAAAGTTTTTGAGGAAAAGTTGAAAGTATCCATTTTCCTTAAAAATCAAAGTTCTC
1 -AAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATT-TC
**
2065641 AAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTC
1 AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAA-TTTC
* *
2065699 TAAAAATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTT
2065738 TCCTGCACAA
Statistics
Matches: 290, Mismatches: 28, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
57 15 0.05
58 136 0.47
59 111 0.38
60 25 0.09
61 3 0.01
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
Found at i:2065468 original size:117 final size:117
Alignment explanation
Indices: 2065346--2065737 Score: 526
Period size: 117 Copynumber: 3.4 Consensus size: 117
2065336 AAGAAAAATA
*
2065346 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTCAAAAA
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAA
** *
2065410 AGGGTTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAATTTTC
66 A-TATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*** * * * *
2065463 AAAAAAAGGGTTTTTAAGGAAAAGTTGATAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAA
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAA
*
2065528 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTTTC
66 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
2065580 AAAAAAAA-AGTTTTTGAGGAAAAGTTGAAAGTATCCATTTTCCTTAAAAATCAAAGTTCTCAAA
1 AAAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTT-TCAAA
** *
2065644 AAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTC
64 AAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* *
2065699 --TAAAAATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTT
2065738 TCCTGCACAA
Statistics
Matches: 242, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
116 3 0.01
117 172 0.71
118 60 0.25
119 7 0.03
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.34
Consensus pattern (117 bp):
AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAA
ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:2065803 original size:13 final size:12
Alignment explanation
Indices: 2065770--2065803 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
2065760 TTTTCTTCTC
2065770 TTTTTTTATTTT
1 TTTTTTTATTTT
2065782 TTATTTTTATTTT
1 TT-TTTTTATTTT
2065795 TTTTCTTTA
1 TTTT-TTTA
2065804 AATAATCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTATTTT
Found at i:2067540 original size:22 final size:22
Alignment explanation
Indices: 2067515--2067593 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
2067505 AACTTTTTAG
*
2067515 TAAAT-CAGTAATAATACAATAA
1 TAAATACA-TAATAATATAATAA
* * *
2067537 TAAATACATAATATTTTAATAG
1 TAAATACATAATAATATAATAA
* *
2067559 TAAAT-CAATTATAATATAATTA
1 TAAATAC-ATAATAATATAATAA
*
2067581 TAAATGCATAATA
1 TAAATACATAATA
2067594 GCATAATACT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
21 1 0.02
22 40 0.91
23 3 0.07
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
TAAATACATAATAATATAATAA
Found at i:2067601 original size:44 final size:44
Alignment explanation
Indices: 2067512--2067606 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 44
2067502 AATAACTTTT
* ***
2067512 TAGTAAATCAGTAATAATACAATAATAAATACATAATATTTTAA
1 TAGTAAATCAATAATAATACAATAATAAATACATAATAGCATAA
* * * *
2067556 TAGTAAATCAATTATAATATAATTATAAATGCATAATAGCATAA
1 TAGTAAATCAATAATAATACAATAATAAATACATAATAGCATAA
*
2067600 TACTAAA
1 TAGTAAA
2067607 ATAAGGATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (44 bp):
TAGTAAATCAATAATAATACAATAATAAATACATAATAGCATAA
Found at i:2067702 original size:22 final size:21
Alignment explanation
Indices: 2067632--2067738 Score: 79
Period size: 22 Copynumber: 4.8 Consensus size: 21
2067622 CAAAAATAAT
* * *
2067632 TGATAACTTAGTAGTTAATTA
1 TGATAATTTAATAGTAAATTA
* * *
2067653 TTGATAACTTAGTAATAAAAGTTAA
1 -TGATAATTTAATAGT-AAA-TT-A
2067678 TGATAATTTTAATAGTAAATTA
1 TGATAA-TTTAATAGTAAATTA
2067700 TGATAATTTAATAGTAAATTA
1 TGATAATTTAATAGTAAATTA
** *
2067721 GTTTTAGTTTAATAGTAA
1 -TGATAATTTAATAGTAA
2067739 TTAATTAATA
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.21
22 35 0.49
23 4 0.06
24 11 0.15
25 7 0.10
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (21 bp):
TGATAATTTAATAGTAAATTA
Found at i:2067750 original size:22 final size:22
Alignment explanation
Indices: 2067685--2067750 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
2067675 TAATGATAAT
* *
2067685 TTTAATAGTAAATT-ATGATAA
1 TTTAATAGTAAATTAATTATAG
* *
2067706 TTTAATAGTAAATTAGTTTTAG
1 TTTAATAGTAAATTAATTATAG
2067728 TTTAATAGT-AATTAATTAATAG
1 TTTAATAGTAAATTAATT-ATAG
2067750 T
1 T
2067751 ACTAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.57
22 16 0.43
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTAATAGTAAATTAATTATAG
Found at i:2067790 original size:25 final size:23
Alignment explanation
Indices: 2067763--2067847 Score: 81
Period size: 22 Copynumber: 3.8 Consensus size: 23
2067753 TAAATAAAAA
2067763 AAAACTTAGTAGTAAATTAATTAT
1 AAAACTTAGTAGTAAATTAATT-T
2067787 AAAA--TAGTAGTAAA-TAA-TT
1 AAAACTTAGTAGTAAATTAATTT
* * *
2067806 AATAATTTAGTAGT-TATTCATTT
1 AA-AACTTAGTAGTAAATTAATTT
*
2067829 AAAACTTAATAGTAAATTA
1 AAAACTTAGTAGTAAATTA
2067848 TTGATAACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 4 0.08
22 28 0.57
23 7 0.14
24 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (23 bp):
AAAACTTAGTAGTAAATTAATTT
Found at i:2067810 original size:22 final size:22
Alignment explanation
Indices: 2067736--2067819 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
2067726 AGTTTAATAG
* *
2067736 TAATTAAT-TAATAGTACTAAA
1 TAATTAATAAAATAGTAGTAAA
*
2067757 TAA--AAAAAAACTTAGTAGTAAA
1 TAATTAATAAAA--TAGTAGTAAA
2067779 TTAATT-ATAAAATAGTAGTAAA
1 -TAATTAATAAAATAGTAGTAAA
**
2067801 TAATTAATAATTTAGTAGT
1 TAATTAATAAAATAGTAGT
2067820 TATTCATTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 8 0.16
22 30 0.60
23 3 0.06
24 5 0.10
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (22 bp):
TAATTAATAAAATAGTAGTAAA
Found at i:2067860 original size:22 final size:22
Alignment explanation
Indices: 2067835--2067892 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2067825 ATTTAAAACT
*
2067835 TAATAGTAAATTATTGATAACA
1 TAATAGTAAATTATTGACAACA
* * * * *
2067857 TAATAGTTAATCAATGACCACT
1 TAATAGTAAATTATTGACAACA
2067879 TAATAGTAAATTAT
1 TAATAGTAAATTAT
2067893 GCATAATTTA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATAGTAAATTATTGACAACA
Found at i:2067905 original size:44 final size:43
Alignment explanation
Indices: 2067832--2067914 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
2067822 TTCATTTAAA
*
2067832 ACTTAATAGTAAATTATTGATAACATAATAGTTAATCAATGACC
1 ACTTAATAGTAAATTATTGATAACATAATA-TAAATCAATGACC
**
2067876 ACTTAATAGTAAATTA-TGCATAATTTAATATAAATCAAT
1 ACTTAATAGTAAATTATTG-ATAACATAATATAAATCAAT
2067915 AATAACTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 10 0.29
44 25 0.71
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (43 bp):
ACTTAATAGTAAATTATTGATAACATAATATAAATCAATGACC
Found at i:2067962 original size:22 final size:22
Alignment explanation
Indices: 2067895--2068129 Score: 77
Period size: 22 Copynumber: 10.8 Consensus size: 22
2067885 TAAATTATGC
* *
2067895 ATAATTTAAT-ATAAATCAATA
1 ATAATTTAGTAATAAATCAATG
* *
2067916 ATAACTTT-GTAATGAATC-TTAG
1 ATAA-TTTAGTAATAAATCAAT-G
*
2067938 ATAATTTAGTAATAAATCAGTG
1 ATAATTTAGTAATAAATCAATG
* * *
2067960 ATAATTTTA-TAACAGAT-AATT
1 ATAA-TTTAGTAATAAATCAATG
* * *
2067981 AAAATTAAGTAATAAATAAATG
1 ATAATTTAGTAATAAATCAATG
* * *
2068003 ATAATATAATAATAAAT-ATATA
1 ATAATTTAGTAATAAATCA-ATG
* * ** * * *
2068025 AAAATATAGTAGCAAATTACTA
1 ATAATTTAGTAATAAATCAATG
* * * *
2068047 ATAATTTAGTAGTAAATTACTA
1 ATAATTTAGTAATAAATCAATG
* * * * * *
2068069 ATAATGTAATAGTAAATTACTA
1 ATAATTTAGTAATAAATCAATG
* ** *
2068091 ATAATTTATTTGTAAAACAATG
1 ATAATTTAGTAATAAATCAATG
2068113 ATAATTTAGTAATAAAT
1 ATAATTTAGTAATAAAT
2068130 TAGTTAATCA
Statistics
Matches: 163, Mismatches: 41, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.02
21 21 0.13
22 133 0.82
23 6 0.04
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
ATAATTTAGTAATAAATCAATG
Found at i:2068027 original size:43 final size:43
Alignment explanation
Indices: 2067940--2068029 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 43
2067930 AATCTTAGAT
* * * * * *
2067940 AATTTAGTAATAAATCAGTGATAATTTTATAACAGATAATTAA
1 AATTAAGTAATAAATAAATGATAATATAATAACAAATAATTAA
* *
2067983 AATTAAGTAATAAATAAATGATAATATAATAATAAATATATAAA
1 AATTAAGTAATAAATAAATGATAATATAATAACAAATA-ATTAA
2068027 AAT
1 AAT
2068030 ATAGTAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 31 0.82
44 7 0.18
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (43 bp):
AATTAAGTAATAAATAAATGATAATATAATAACAAATAATTAA
Found at i:2068051 original size:44 final size:44
Alignment explanation
Indices: 2068003--2068095 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
2067993 TAAATAAATG
*
2068003 ATAATATAATAATAAATATA-TAAAAATATAGTAGCAAATTACTA
1 ATAATATAATAATAAAT-TACTAAAAATATAATAGCAAATTACTA
* * * * * *
2068047 ATAATTTAGTAGTAAATTACTAATAATGTAATAGTAAATTACTA
1 ATAATATAATAATAAATTACTAAAAATATAATAGCAAATTACTA
2068091 ATAAT
1 ATAAT
2068096 TTATTTGTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.05
44 39 0.95
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (44 bp):
ATAATATAATAATAAATTACTAAAAATATAATAGCAAATTACTA
Found at i:2068117 original size:44 final size:44
Alignment explanation
Indices: 2068038--2068131 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
2068028 ATATAGTAGC
** * *
2068038 AAATTACTAATAATTTAGTAGTAAATTACTAATAATGTAATAGT
1 AAATTACTAATAATTTAGTAGTAAAACAATAATAATGTAATAAT
* * * * *
2068082 AAATTACTAATAATTTATTTGTAAAACAATGATAATTTAGTAAT
1 AAATTACTAATAATTTAGTAGTAAAACAATAATAATGTAATAAT
2068126 AAATTA
1 AAATTA
2068132 GTTAATCATT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.39
Consensus pattern (44 bp):
AAATTACTAATAATTTAGTAGTAAAACAATAATAATGTAATAAT
Found at i:2068155 original size:32 final size:32
Alignment explanation
Indices: 2068117--2068178 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2068107 ACAATGATAA
* *
2068117 TTTAGT-AATAAATTAGTTAATCATTAATAATT
1 TTTAGTAAAT-AATTAGTAAATCAGTAATAATT
*
2068149 TTTAGTAAATAATTGGTAAATCAGTAATAA
1 TTTAGTAAATAATTAGTAAATCAGTAATAA
2068179 ATTAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (32 bp):
TTTAGTAAATAATTAGTAAATCAGTAATAATT
Found at i:2068198 original size:22 final size:23
Alignment explanation
Indices: 2068173--2068261 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 23
2068163 GGTAAATCAG
*
2068173 TAATAAATTAATT-ATAACTTTA
1 TAATAAATTAATTAATAACTTAA
*
2068195 TAATAAA-TATTTAATAACTTAA
1 TAATAAATTAATTAATAACTTAA
* * * *
2068217 TGATAAA-TCATCAATAATTTAA
1 TAATAAATTAATTAATAACTTAA
* **
2068239 TATTAAATT-ATGCATAACTTAA
1 TAATAAATTAATTAATAACTTAA
2068261 T
1 T
2068262 GACAAATCAT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 4 0.08
22 48 0.91
23 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAATTAATTAATAACTTAA
Found at i:2068268 original size:22 final size:22
Alignment explanation
Indices: 2068251--2068316 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
2068241 TTAAATTATG
*
2068251 CATAACTTAAT-GACAAATCATT
1 CATAAATTAATAG-CAAATCATT
*
2068273 CATAAATTAATAGCAAATTATT
1 CATAAATTAATAGCAAATCATT
* *
2068295 CATAAATTAATAGTACATCATT
1 CATAAATTAATAGCAAATCATT
2068317 GATAGTTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 37 0.97
23 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (22 bp):
CATAAATTAATAGCAAATCATT
Found at i:2068299 original size:44 final size:44
Alignment explanation
Indices: 2068208--2068305 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
2068198 TAAATATTTA
* * **
2068208 ATAACTTAATGATAAATCATCAATAATTTAATATTAAATTATGC
1 ATAACTTAATGACAAATCATCAATAAATTAATAGCAAATTATGC
*
2068252 ATAACTTAATGACAAATCATTC-ATAAATTAATAGCAAATTATTC
1 ATAACTTAATGACAAATCA-TCAATAAATTAATAGCAAATTATGC
*
2068296 ATAAATTAAT
1 ATAACTTAAT
2068306 AGTACATCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 45 0.96
45 2 0.04
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (44 bp):
ATAACTTAATGACAAATCATCAATAAATTAATAGCAAATTATGC
Found at i:2068847 original size:21 final size:22
Alignment explanation
Indices: 2068605--2068945 Score: 173
Period size: 22 Copynumber: 15.5 Consensus size: 22
2068595 AACATATTAG
*
2068605 TAAATCAATGATAAGTTAATAA
1 TAAATCAATGATAATTTAATAA
* * *
2068627 AAAAT-AAGTGATAACTTAGTAA
1 TAAATCAA-TGATAATTTAATAA
*
2068649 TTAAT-AATTGATAATTTAATAA
1 TAAATCAA-TGATAATTTAATAA
* * *
2068671 TAAATCAATAATAACTTAACAA
1 TAAATCAATGATAATTTAATAA
* * * * * *
2068693 TAAATTAGTAATTACTTAATAG
1 TAAATCAATGATAATTTAATAA
* * **
2068715 TAAATTAGTTTTAATTTAATAA
1 TAAATCAATGATAATTTAATAA
* * * *
2068737 T-AATTAATTGAAAATTTTAGTAG
1 TAAATCAA-TGATAA-TTTAATAA
* *
2068760 TAAGT-AATAAATAA-TTAAT-A
1 TAAATCAAT-GATAATTTAATAA
*
2068780 TAAAATCAATGATAATTTAGTAA
1 T-AAATCAATGATAATTTAATAA
* * * *
2068803 TTAATCATTGAAAATTTAAAAA
1 TAAATCAATGATAATTTAATAA
*
2068825 TAAATCAAT-ATAATTTAGTAA
1 TAAATCAATGATAATTTAATAA
* *
2068846 TAGTTAATC-ATAATAACTTAATAA
1 TA---AATCAATGATAATTTAATAA
* * *
2068870 TTAATCAATGACAACTTAATAA
1 TAAATCAATGATAATTTAATAA
*
2068892 TAAAT-TATGAATAATTTAAT-A
1 TAAATCAATG-ATAATTTAATAA
*
2068913 TAAATCAATAATAATTTAATAA
1 TAAATCAATGATAATTTAATAA
*
2068935 TGAAT-AATGAT
1 TAAATCAATGAT
2068946 TAAGTTTGTA
Statistics
Matches: 242, Mismatches: 59, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.00
21 57 0.24
22 149 0.62
23 18 0.07
24 17 0.07
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.37
Consensus pattern (22 bp):
TAAATCAATGATAATTTAATAA
Found at i:2068919 original size:43 final size:43
Alignment explanation
Indices: 2068769--2068944 Score: 153
Period size: 43 Copynumber: 4.0 Consensus size: 43
2068759 GTAAGTAATA
* *
2068769 AATAA-TTAATATAAAATCAATGATAATTTAGTAATTAATCATTG
1 AATAATTTAATAT-AAATCAATGATAATTTAATAATAAATCA-TG
* *
2068813 AA-AATTTAAAAATAAATCAAT-ATAATTTAGTAATAGTTAATCAT-
1 AATAATTT-AATATAAATCAATGATAATTTAATAATA---AATCATG
* * * * *
2068857 AATAACTTAATAATTAATCAATGACAACTTAATAATAAATTATG
1 AATAATTTAAT-ATAAATCAATGATAATTTAATAATAAATCATG
* * *
2068901 AATAATTTAATATAAATCAATAATAATTTAATAATGAATAATG
1 AATAATTTAATATAAATCAATGATAATTTAATAATAAATCATG
2068944 A
1 A
2068945 TTAAGTTTGT
Statistics
Matches: 107, Mismatches: 16, Indels: 19
0.75 0.11 0.13
Matches are distributed among these distances:
43 47 0.44
44 26 0.24
45 18 0.17
46 16 0.15
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (43 bp):
AATAATTTAATATAAATCAATGATAATTTAATAATAAATCATG
Found at i:2068933 original size:11 final size:11
Alignment explanation
Indices: 2068659--2068935 Score: 54
Period size: 11 Copynumber: 25.2 Consensus size: 11
2068649 TTAATAATTG
2068659 ATAATTTAATA
1 ATAATTTAATA
* *
2068670 ATAAATCAATA
1 ATAATTTAATA
* *
2068681 ATAACTTAACA
1 ATAATTTAATA
* *
2068692 ATAAATTAGTA
1 ATAATTTAATA
* *
2068703 ATTACTTAATA
1 ATAATTTAATA
* * * *
2068714 GTAAATTAGTT
1 ATAATTTAATA
*
2068725 TTAATTTAATA
1 ATAATTTAATA
2068736 ATAA-TTAATTGA
1 ATAATTTAA-T-A
*
2068748 A-AATTTTAGTA
1 ATAA-TTTAATA
* *
2068759 GTAA-GTAATAA
1 ATAATTTAAT-A
2068770 ATAA-TTAAT-
1 ATAATTTAATA
* * *
2068779 ATAAAATCAATG
1 AT-AATTTAATA
*
2068791 ATAATTTAGTA
1 ATAATTTAATA
* *
2068802 ATTAA-TCATTGA
1 A-TAATTTAAT-A
*
2068814 A-AATTTAAAA
1 ATAATTTAATA
* *
2068824 ATAAATCAAT-
1 ATAATTTAATA
*
2068834 ATAATTTAGTA
1 ATAATTTAATA
* *
2068845 ATAGTTAATCATA
1 ATAATT--TAATA
*
2068858 ATAACTTAATA
1 ATAATTTAATA
* *
2068869 ATTAA-TCAATG
1 A-TAATTTAATA
* *
2068880 ACAACTTAATA
1 ATAATTTAATA
*
2068891 ATAAATT-ATGA
1 ATAATTTAAT-A
2068902 ATAATTTAAT-
1 ATAATTTAATA
* *
2068912 ATAAATCAATA
1 ATAATTTAATA
2068923 ATAATTTAATA
1 ATAATTTAATA
2068934 AT
1 AT
2068936 GAATAATGAT
Statistics
Matches: 184, Mismatches: 61, Indels: 42
0.64 0.21 0.15
Matches are distributed among these distances:
9 2 0.01
10 32 0.17
11 123 0.67
12 17 0.09
13 10 0.05
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (11 bp):
ATAATTTAATA
Found at i:2068982 original size:65 final size:65
Alignment explanation
Indices: 2068843--2068982 Score: 160
Period size: 65 Copynumber: 2.2 Consensus size: 65
2068833 TATAATTTAG
* *
2068843 TAATAGTTAATCATAATAACTTAATAATTAATCAATGACAACTTAATAATAAATTATGAATAATT
1 TAATAGTAAATCATAATAACTTAATAATGAATCAATGACAACTTAATAATAAATTATGAATAATT
* * * ** *
2068908 TAATA-TAAATCAATAATAATTTAATAATGAAT-AATGATTAAGTTTGTAATAAATTATG-ATGA
1 TAATAGTAAATC-ATAATAACTTAATAATGAATCAATGA-CAACTTAATAATAAATTATGAATAA
2068970 TT
64 TT
*
2068972 TTATAGTAAAT
1 TAATAGTAAAT
2068983 AATCGAAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
64 19 0.30
65 44 0.70
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.39
Consensus pattern (65 bp):
TAATAGTAAATCATAATAACTTAATAATGAATCAATGACAACTTAATAATAAATTATGAATAATT
Found at i:2069036 original size:22 final size:22
Alignment explanation
Indices: 2069009--2069050 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2068999 GTAAATCAAA
2069009 ATGATAACATAACAGTAAATAC
1 ATGATAACATAACAGTAAATAC
*
2069031 ATGATAACATAATAGTAAAT
1 ATGATAACATAACAGTAAAT
2069051 CATTGACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (22 bp):
ATGATAACATAACAGTAAATAC
Found at i:2069086 original size:22 final size:22
Alignment explanation
Indices: 2069068--2069116 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2069058 AATTTAGATA
*
2069068 TAAATTATTAATAACTTAGTAG
1 TAAATTACTAATAACTTAGTAG
* *
2069090 TAAATTACTAATAATTTAGTTG
1 TAAATTACTAATAACTTAGTAG
2069112 TAAAT
1 TAAAT
2069117 CGGTGATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (22 bp):
TAAATTACTAATAACTTAGTAG
Found at i:2069171 original size:22 final size:22
Alignment explanation
Indices: 2069143--2069236 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 22
2069133 TAAATAAATT
*
2069143 AATTATTAATAACTTTACAATA
1 AATTATTAATAACTTTATAATA
* * * *
2069165 AATTATTGATAAATTAATAGTA
1 AATTATTAATAACTTTATAATA
*
2069187 AATCAATT-ATAACTTTATAATA
1 AAT-TATTAATAACTTTATAATA
* *
2069209 AATTATCAGTAAC-TTAGTAATA
1 AATTATTAATAACTTTA-TAATA
2069231 AATTAT
1 AATTAT
2069237 CAACAATATA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
21 5 0.09
22 49 0.86
23 3 0.05
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTATTAATAACTTTATAATA
Found at i:2069248 original size:22 final size:22
Alignment explanation
Indices: 2069204--2069257 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2069194 TATAACTTTA
**
2069204 TAATAAATTATCAGTAACTTAG
1 TAATAAATTATCAACAACTTAG
2069226 TAATAAATTATCAACAA-TATAG
1 TAATAAATTATCAACAACT-TAG
*
2069248 TAGTAAATTA
1 TAATAAATTA
2069258 GTTATAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (22 bp):
TAATAAATTATCAACAACTTAG
Found at i:2069286 original size:22 final size:23
Alignment explanation
Indices: 2069248--2069344 Score: 69
Period size: 22 Copynumber: 4.3 Consensus size: 23
2069238 AACAATATAG
* *
2069248 TAGTAAATTAGTT-ATAACTTAT
1 TAGTAAATCAGTTAATAACTTAA
* *
2069270 TAGTAAATCA-TTAATAAATCAA
1 TAGTAAATCAGTTAATAACTTAA
* *
2069292 TAGTAAATCA---AAGCTAATTTAG
1 TAGTAAATCAGTTAA--TAACTTAA
* *
2069314 TAGTAAATCAGTTTATAGCTTAA
1 TAGTAAATCAGTTAATAACTTAA
2069337 TAGTAAAT
1 TAGTAAAT
2069345 TGCTGACAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
20 2 0.03
21 2 0.03
22 40 0.69
23 13 0.22
25 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.37
Consensus pattern (23 bp):
TAGTAAATCAGTTAATAACTTAA
Found at i:2069287 original size:11 final size:11
Alignment explanation
Indices: 2069268--2069301 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2069258 GTTATAACTT
2069268 ATTAGTAAATC
1 ATTAGTAAATC
*
2069279 ATTAATAAATC
1 ATTAGTAAATC
*
2069290 AATAGTAAATC
1 ATTAGTAAATC
2069301 A
1 A
2069302 AAGCTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (11 bp):
ATTAGTAAATC
Found at i:2069759 original size:21 final size:21
Alignment explanation
Indices: 2069729--2069786 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2069719 TTTATAAAAA
*
2069729 TTACCAAAATTGTATCAATGAG
1 TTACCAAAATTGTATC-ATAAG
* *
2069751 -TATCAAAATTATATCATAAG
1 TTACCAAAATTGTATCATAAG
2069771 TTACCAAAATTGTATC
1 TTACCAAAATTGTATC
2069787 GAGTATTACC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (21 bp):
TTACCAAAATTGTATCATAAG
Found at i:2069795 original size:21 final size:20
Alignment explanation
Indices: 2069727--2069822 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 20
2069717 ATTTTATAAA
2069727 AATTACCAAAATTGTATCAAT
1 AATTACCAAAATTGTATC-AT
* * * *
2069748 GAGTATCAAAATTATATCAT
1 AATTACCAAAATTGTATCAT
2069768 AAGTTACCAAAATTGTATCGAGT
1 AA-TTACCAAAATTGTATC-A-T
* * *
2069791 -ATTACCGAAATTTTATCAA
1 AATTACCAAAATTGTATCAT
*
2069810 AGATTATCAAAAT
1 A-ATTACCAAAAT
2069823 CAAAATTATA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
20 4 0.07
21 50 0.88
22 2 0.04
23 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (20 bp):
AATTACCAAAATTGTATCAT
Found at i:2069802 original size:42 final size:42
Alignment explanation
Indices: 2069714--2069822 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
2069704 AGAGGTTATT
* * *
2069714 AAAATTTTAT-AAAAATTACCAAAATTGTATCAATGAGTATC
1 AAAATTATATCAAAGATTACCAAAATTGTATCAATGAGTACC
* *
2069755 AAAATTATATCATAAG-TTACCAAAATTGTATCGA-GTATTACC
1 AAAATTATATCA-AAGATTACCAAAATTGTATCAATG-AGTACC
* * *
2069797 GAAATTTTATCAAAGATTATCAAAAT
1 AAAATTATATCAAAGATTACCAAAAT
2069823 CAAAATTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
41 13 0.23
42 41 0.73
43 2 0.04
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (42 bp):
AAAATTATATCAAAGATTACCAAAATTGTATCAATGAGTACC
Found at i:2072988 original size:13 final size:13
Alignment explanation
Indices: 2072972--2072996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2072962 AAAAGTTACG
2072972 AAAAAAAAAAAGT
1 AAAAAAAAAAAGT
2072985 AAAAAAAAAAAG
1 AAAAAAAAAAAG
2072997 AGTAGGCATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAAGT
Found at i:2073192 original size:31 final size:28
Alignment explanation
Indices: 2073132--2073202 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 28
2073122 TTTTTTTTAT
2073132 AAAAAAAAAAAACAGGTTTGAAACATAA
1 AAAAAAAAAAAACAGGTTTGAAACATAA
*
2073160 AAAAAAAGGAAAAATAGGTTTGAAA-AGTTAA
1 AAAAAAA--AAAAACAGGTTTGAAACA--TAA
*
2073191 AACAAAAAAAAA
1 AAAAAAAAAAAA
2073203 GTTTTGATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 7 0.19
29 6 0.16
30 15 0.41
31 9 0.24
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.14
Consensus pattern (28 bp):
AAAAAAAAAAAACAGGTTTGAAACATAA
Found at i:2073241 original size:27 final size:28
Alignment explanation
Indices: 2073211--2073273 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
2073201 AAGTTTTGAT
2073211 AAAAAAACTTTGAAAAG-CAAAAAAAAA
1 AAAAAAACTTTGAAAAGTCAAAAAAAAA
* * *
2073238 AAAAAAGCTTTGAAATGTTAAAAAAAAA
1 AAAAAAACTTTGAAAAGTCAAAAAAAAA
2073266 AAAGAAAA
1 AAA-AAAA
2073274 GACAACTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 15 0.50
28 12 0.40
29 3 0.10
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (28 bp):
AAAAAAACTTTGAAAAGTCAAAAAAAAA
Found at i:2073848 original size:187 final size:187
Alignment explanation
Indices: 2073644--2074019 Score: 725
Period size: 187 Copynumber: 2.0 Consensus size: 187
2073634 ATAATTTCAA
2073644 TTTAAAAATGTTTTTTTAGAAAAAGGATTTTAGAAATTAAAATGGAATAATAGTTTTTTTAATGA
1 TTTAAAAATGTTTTTTTAGAAAAAGGATTTTAGAAATTAAAATGGAATAATAGTTTTTTTAATGA
*
2073709 AATACAATGACTTTGAAAACTTTGCCTAGATATTGAAGGAAATTTAAATCGTGTTTTGAAAATTT
66 AATACAATGACTTTGAAAACTTTGCCTAGATATTGAAGGAAATTCAAATCGTGTTTTGAAAATTT
2073774 TAATTCTACCTAAATGTTAGAGAATTAAAGAATTAAAACTAAAAAAAATTAATTAAG
131 TAATTCTACCTAAATGTTAGAGAATTAAAGAATTAAAACTAAAAAAAATTAATTAAG
*
2073831 TTTAAAAATGTTTTTTTAGAAAGAGGATTTTAGAAATTAAAATGGAATAATAGTTTTTTTAATGA
1 TTTAAAAATGTTTTTTTAGAAAAAGGATTTTAGAAATTAAAATGGAATAATAGTTTTTTTAATGA
*
2073896 AATACAATGACTTTGAAAACTTTGCCTAGATATTGAAGGAAATTCAAATTGTGTTTTGAAAATTT
66 AATACAATGACTTTGAAAACTTTGCCTAGATATTGAAGGAAATTCAAATCGTGTTTTGAAAATTT
2073961 TAATTCTACCTAAATGTTAGAGAATTAAAGAATTAAAACTAAAAAAAATTAATTAAG
131 TAATTCTACCTAAATGTTAGAGAATTAAAGAATTAAAACTAAAAAAAATTAATTAAG
2074018 TT
1 TT
2074020 AAATTAAATT
Statistics
Matches: 186, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
187 186 1.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.37
Consensus pattern (187 bp):
TTTAAAAATGTTTTTTTAGAAAAAGGATTTTAGAAATTAAAATGGAATAATAGTTTTTTTAATGA
AATACAATGACTTTGAAAACTTTGCCTAGATATTGAAGGAAATTCAAATCGTGTTTTGAAAATTT
TAATTCTACCTAAATGTTAGAGAATTAAAGAATTAAAACTAAAAAAAATTAATTAAG
Found at i:2078179 original size:27 final size:29
Alignment explanation
Indices: 2078148--2078206 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2078138 AAACACCAGT
* *
2078148 AAAATAAAAT-AAA-AAACTTAAAAAATA
1 AAAATAAAATAAAACAAAATCAAAAAATA
2078175 AAAATAAAATAAAACAAAATCAAAAAATA
1 AAAATAAAATAAAACAAAATCAAAAAATA
2078204 AAA
1 AAA
2078207 TGAAAATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.36
28 3 0.11
29 15 0.54
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (29 bp):
AAAATAAAATAAAACAAAATCAAAAAATA
Found at i:2079105 original size:3 final size:3
Alignment explanation
Indices: 2079087--2079123 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2079077 AAACATAAAA
2079087 AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2079124 GCTATACCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2079583 original size:120 final size:119
Alignment explanation
Indices: 2079391--2079703 Score: 294
Period size: 120 Copynumber: 2.6 Consensus size: 119
2079381 GATTGAGGCG
* * * * * *
2079391 AGATTGAATGATCGAGATAAAATCATGAG-TCAAAAGATAAAAATGA-CTAGAACCGAGTCAAGG
1 AGATTGAATGATCGAGATAAACT-ATGAGTTAAAAAGAT-AAAGTGACCAAG-ATCGAGTTAAGG
* * * * * * ** *
2079454 TTAAAGATGGTTGATCGTGACGGAATC-ATAAGCTAGGAAATGATCTGGACGGAACCA
63 TTGAAGATGGTTGATCATGA-GGAAACTACAAGCTAGAAAATGATCTAGACAAAAACA
* * *
2079511 AGATTGAATGATCGGGATGAAACTATGAGTTGAAAAGATAAAGTGACCAAGATCGAGTTAAGGTC
1 AGATTGAATGATCGAGAT-AAACTATGAGTTAAAAAGATAAAGTGACCAAGATCGAGTTAAGGTT
* * *
2079576 GAAGATGGTTGATCATGATGAAACTACAAGTTAGAAAATGATCTAGATAAAAACA
65 GAAGATGGTTGATCATGAGGAAACTACAAGCTAGAAAATGATCTAGACAAAAACA
* * * * *
2079631 AGATAGAATGATCGAGACAAAACCATGAGTCAAAAAGAT--AGTGACCAAGATTGAGTTAAGGTT
1 AGATTGAATGATCGAGA-TAAACTATGAGTTAAAAAGATAAAGTGACCAAGATCGAGTTAAGGTT
*
2079694 GAAAATGGTT
65 GAAGATGGTT
2079704 AACCAAGATG
Statistics
Matches: 159, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
118 31 0.19
119 4 0.03
120 109 0.69
121 15 0.09
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.22
Consensus pattern (119 bp):
AGATTGAATGATCGAGATAAACTATGAGTTAAAAAGATAAAGTGACCAAGATCGAGTTAAGGTTG
AAGATGGTTGATCATGAGGAAACTACAAGCTAGAAAATGATCTAGACAAAAACA
Found at i:2080254 original size:17 final size:17
Alignment explanation
Indices: 2080232--2080265 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2080222 TAAGATTCCA
*
2080232 AGTTTCACAAAGGTTCT
1 AGTTTCACAAAGATTCT
2080249 AGTTTCACAAAGATTCT
1 AGTTTCACAAAGATTCT
2080266 TGGTTCGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (17 bp):
AGTTTCACAAAGATTCT
Found at i:2080277 original size:86 final size:86
Alignment explanation
Indices: 2080040--2080278 Score: 252
Period size: 86 Copynumber: 2.8 Consensus size: 86
2080030 TCTCAAGCAT
* * * * * * *
2080040 GAAAGCTTCATAAGATTTCAAGTTTCACAGAGATTCTAGATTTGCAAATA-TCTTAGGTTCGTAA
1 GAAAGATTCGTAAGATTCCAAGTTTCACAAAGGTTCTAGATTTGCAAAGATTCTT-GGTTCGCAA
*
2080104 GAACTTTCAGATTTGCAAGAAA
65 GGACTTTCAGATTTGCAAGAAA
* * * * * * *
2080126 GAAAGATTCGCAAGACTCTAAGTTTCGCAAAGGTTCTAGATTTGTAAAGATT-TCAGGTTTGCAA
1 GAAAGATTCGTAAGATTCCAAGTTTCACAAAGGTTCTAGATTTGCAAAGATTCT-TGGTTCGCAA
* *
2080190 GGACTTTTAGATTCT-TAAGAAA
65 GGACTTTCAGATT-TGCAAGAAA
*
2080212 GAAAGATTCGTAAGATTCCAAGTTTCACAAAGGTTCTAG-TTTCACAAAGATTCTTGGTTCGCAA
1 GAAAGATTCGTAAGATTCCAAGTTTCACAAAGGTTCTAGATTT-GCAAAGATTCTTGGTTCGCAA
2080276 GGA
65 GGA
2080279 TGAATGATTC
Statistics
Matches: 123, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
85 3 0.02
86 117 0.95
87 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (86 bp):
GAAAGATTCGTAAGATTCCAAGTTTCACAAAGGTTCTAGATTTGCAAAGATTCTTGGTTCGCAAG
GACTTTCAGATTTGCAAGAAA
Found at i:2080673 original size:60 final size:61
Alignment explanation
Indices: 2080564--2080681 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 61
2080554 TAAAAGCGGC
* * * ** *
2080564 CAAGATCGAGTTGAAGTTATAGATGAATGATCGAGATGATGTTATGAGTCT-AAAAATGAT
1 CAAGATCGAGTTCAAGTCATAGATGAATGATCGAGACGATGCCACGAGTCTGAAAAATGAT
*
2080624 CAAGATCGAG-TCAAGGTCATAGATGAATGATCGGGACGATGCCACGAGTCTGAAAAAT
1 CAAGATCGAGTTCAA-GTCATAGATGAATGATCGAGACGATGCCACGAGTCTGAAAAAT
2080682 AATCTAGCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.06
60 40 0.82
61 6 0.12
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (61 bp):
CAAGATCGAGTTCAAGTCATAGATGAATGATCGAGACGATGCCACGAGTCTGAAAAATGAT
Found at i:2081837 original size:18 final size:18
Alignment explanation
Indices: 2081816--2081850 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2081806 TATCCCATCA
*
2081816 ATTTTTGTTATTTTTTTC
1 ATTTTTGCTATTTTTTTC
*
2081834 ATTTTTGCTCTTTTTTT
1 ATTTTTGCTATTTTTTT
2081851 TTTATGGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (18 bp):
ATTTTTGCTATTTTTTTC
Found at i:2084810 original size:39 final size:39
Alignment explanation
Indices: 2084743--2084829 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
2084733 TATATACAAT
*
2084743 AAATAAATAAATAAATAAGCAAGCATAAGCAATGAAAAG
1 AAATAAATAAATAAATAAGAAAGCATAAGCAATGAAAAG
* *
2084782 AAATAAATAAATAATTAAGAAAGTATAAGCAATGAAAAG
1 AAATAAATAAATAAATAAGAAAGCATAAGCAATGAAAAG
2084821 AAATAAATA
1 AAATAAATA
2084830 GGAAAGACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (39 bp):
AAATAAATAAATAAATAAGAAAGCATAAGCAATGAAAAG
Found at i:2085810 original size:19 final size:19
Alignment explanation
Indices: 2085771--2085848 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
2085761 CAATAAAATT
*
2085771 AAATAAAAACTAAAA--ACA
1 AAATAAAAA-TAAAATCAAA
* *
2085789 AAATAAAAA-AAACTTAAGA
1 AAATAAAAATAAAATCAA-A
2085808 AAATAAAAATAAAATCAAA
1 AAATAAAAATAAAATCAAA
*
2085827 AAAT-AAAATGAAAATGAAA
1 AAATAAAAAT-AAAATCAAA
2085846 AAA
1 AAA
2085849 AAGAAACCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.06
18 15 0.30
19 26 0.52
20 6 0.12
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (19 bp):
AAATAAAAATAAAATCAAA
Found at i:2085847 original size:13 final size:11
Alignment explanation
Indices: 2085765--2085850 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
2085755 TTTAACCAAT
*
2085765 AAAATTAAATA
1 AAAATAAAATA
2085776 AAAACTAAAA-A
1 AAAA-TAAAATA
*
2085787 CAAAATAAAAAA
1 -AAAATAAAATA
*
2085799 AACTTAAGAAAATA
1 AA---AATAAAATA
2085813 AAAATAAAATCAA
1 AAAATAAAAT--A
*
2085826 AAAATAAAATG
1 AAAATAAAATA
2085837 AAAATGAAAA-A
1 AAAAT-AAAATA
2085848 AAA
1 AAA
2085851 GAAACCTATG
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
11 27 0.45
12 13 0.22
13 11 0.18
14 9 0.15
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:2095128 original size:8 final size:8
Alignment explanation
Indices: 2095115--2095142 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2095105 AAACAAACCA
2095115 AAAACAAT
1 AAAACAAT
2095123 AAAACAAT
1 AAAACAAT
2095131 AAAACAAT
1 AAAACAAT
2095139 AAAA
1 AAAA
2095143 AGAGACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAACAAT
Found at i:2096280 original size:34 final size:34
Alignment explanation
Indices: 2096216--2096301 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
2096206 ATCCCAATCA
* * * *
2096216 TCTTTATCTTTTAACTTACAGTTTAGTCCTGATTG
1 TCTTTAT-TTCTAACTTACAATTCAATCCTGATTG
2096251 TCTTTATTTCTAACTTACAATTCAATCCTGATTG
1 TCTTTATTTCTAACTTACAATTCAATCCTGATTG
2096285 -CTTTTATTCTCTAACTT
1 TC-TTTATT-TCTAACTT
2096302 GGTCTCTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 1 0.02
34 29 0.64
35 15 0.33
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (34 bp):
TCTTTATTTCTAACTTACAATTCAATCCTGATTG
Found at i:2096942 original size:35 final size:34
Alignment explanation
Indices: 2096903--2097037 Score: 94
Period size: 35 Copynumber: 3.9 Consensus size: 34
2096893 TTAATTTATC
*
2096903 AACTTGTGATTCAATCCTGGTCATTTTTATTTTT
1 AACTTGTGATTCAATCCTGATCATTTTTATTTTT
* * * * **
2096937 GAACTTGAGATTCAGTCCCGATCATCTTTACCCTTT
1 -AACTTGTGATTCAATCCTGATCATTTTTA-TTTTT
* *** * *
2096973 AAGTTACAATT-AAGTCCTGGTCATTTTTATTTCTC
1 AACTTGTGATTCAA-TCCTGATCATTTTTATTT-TT
2097008 AACTTGTGATTCAAT-CTCGATCATTTTTAT
1 AACTTGTGATTCAATCCT-GATCATTTTTAT
2097038 CCCAACTTAC
Statistics
Matches: 72, Mismatches: 23, Indels: 10
0.69 0.22 0.10
Matches are distributed among these distances:
34 4 0.06
35 63 0.88
36 5 0.07
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (34 bp):
AACTTGTGATTCAATCCTGATCATTTTTATTTTT
Found at i:2097701 original size:35 final size:35
Alignment explanation
Indices: 2097662--2097763 Score: 87
Period size: 35 Copynumber: 3.1 Consensus size: 35
2097652 CTTATTTTTC
2097662 AACTTACGATTCAATCCTGATTGTTTTTATTCTCT
1 AACTTACGATTCAATCCTGATTGTTTTTATTCTCT
* *
2097697 AACTTGC-AGTTCAATCC----T-TTATT-TTC-C-
1 AACTTACGA-TTCAATCCTGATTGTTTTTATTCTCT
* *
2097724 AACTTATGATTCAATCCTGATTGTTTTTAGTCTCT
1 AACTTACGATTCAATCCTGATTGTTTTTATTCTCT
*
2097759 GACTT
1 AACTT
2097764 GTGATTTAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 20
0.65 0.09 0.26
Matches are distributed among these distances:
27 13 0.26
28 2 0.04
29 3 0.06
30 4 0.08
31 2 0.04
32 4 0.08
33 2 0.04
34 2 0.04
35 18 0.36
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.47
Consensus pattern (35 bp):
AACTTACGATTCAATCCTGATTGTTTTTATTCTCT
Found at i:2097777 original size:62 final size:62
Alignment explanation
Indices: 2097649--2097764 Score: 189
Period size: 62 Copynumber: 1.9 Consensus size: 62
2097639 AATCTTAGTC
* *
2097649 ATCC-TTATTTTTCAACTTACGATTCAATCCTGATTGTTTTTATTCTCTAACTTGCAGTTCA
1 ATCCTTTATTTTCCAACTTACGATTCAATCCTGATTGTTTTTAGTCTCTAACTTGCAGTTCA
* *
2097710 ATCCTTTATTTTCCAACTTATGATTCAATCCTGATTGTTTTTAGTCTCTGACTTG
1 ATCCTTTATTTTCCAACTTACGATTCAATCCTGATTGTTTTTAGTCTCTAACTTG
2097765 TGATTTAGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
61 4 0.08
62 46 0.92
ACGTcount: A:0.22, C:0.21, G:0.09, T:0.48
Consensus pattern (62 bp):
ATCCTTTATTTTCCAACTTACGATTCAATCCTGATTGTTTTTAGTCTCTAACTTGCAGTTCA
Found at i:2097821 original size:35 final size:35
Alignment explanation
Indices: 2097758--2097826 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
2097748 TTTTAGTCTC
* * *
2097758 TGACTTGTGATTTAGTCCTTGTCGTTTTTATTTCT
1 TGACTTGTGATTTAATCCTTATCATTTTTATTTCT
2097793 TGACTTGTGATTTAAT-CTTAATCATTTTTATTTC
1 TGACTTGTGATTTAATCCTT-ATCATTTTTATTTC
2097827 CCGACTGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 3 0.10
35 27 0.90
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (35 bp):
TGACTTGTGATTTAATCCTTATCATTTTTATTTCT
Found at i:2097958 original size:35 final size:35
Alignment explanation
Indices: 2097911--2098000 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
2097901 TGTGGTTCAA
* * *
2097911 TCTCGATTGTTTTTATTTTTTGACTTGCAATTTAG
1 TCTCGATCGTTTTTATTTTTTGACTTACAAGTTAG
*
2097946 TCTC-AGTCGTTTTCATTTTTTGACTTACAAGTTAG
1 TCTCGA-TCGTTTTTATTTTTTGACTTACAAGTTAG
*
2097981 TCTCGATCGTCTTTATTTTT
1 TCTCGATCGTTTTTATTTTT
2098001 CAACCTATGG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 1 0.02
35 45 0.96
36 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.13, T:0.54
Consensus pattern (35 bp):
TCTCGATCGTTTTTATTTTTTGACTTACAAGTTAG
Found at i:2098197 original size:3 final size:3
Alignment explanation
Indices: 2098189--2098251 Score: 108
Period size: 3 Copynumber: 20.3 Consensus size: 3
2098179 ACCTAAAAAT
2098189 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2098237 ATA GATAA ATA ATA A
1 ATA -AT-A ATA ATA A
2098252 ATAGTTTTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 53 0.91
4 4 0.07
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2099834 original size:24 final size:24
Alignment explanation
Indices: 2099802--2099871 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 24
2099792 GGAGAAGGAG
*
2099802 AAAAAAAAGTAAT-AAAAAGAAAA
1 AAAAAAAAGGAATGAAAAAGAAAA
*
2099825 AAAAATAAAGGAATGAAATAGCAAAA
1 AAAAA-AAAGGAATGAAAAAG-AAAA
2099851 AAAGAAAAA-GAA-G-AAAAGAAA
1 AAA-AAAAAGGAATGAAAAAGAAA
2099872 GAGAGAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 3 0.08
23 9 0.22
24 8 0.20
25 8 0.20
26 10 0.25
27 2 0.05
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.07
Consensus pattern (24 bp):
AAAAAAAAGGAATGAAAAAGAAAA
Found at i:2099995 original size:15 final size:15
Alignment explanation
Indices: 2099977--2100007 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2099967 AAGTCAAAAC
2099977 AAAAAAAT-TTTGAA
1 AAAAAAATCTTTGAA
2099991 AAAAAAATCTTTGAA
1 AAAAAAATCTTTGAA
2100006 AA
1 AA
2100008 GTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAAAAATCTTTGAA
Found at i:2100019 original size:23 final size:23
Alignment explanation
Indices: 2099989--2100040 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
2099979 AAAAATTTTG
*
2099989 AAAAAAAAATCTTTGAAA-AGTA
1 AAAAAAAAAACTTTGAAACAGTA
*
2100011 AAAAAAAAAACTTTGAAACATTA
1 AAAAAAAAAACTTTGAAACAGTA
2100034 AAAAAAA
1 AAAAAAA
2100041 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAAAAAAAACTTTGAAACAGTA
Found at i:2103977 original size:9 final size:9
Alignment explanation
Indices: 2103963--2104011 Score: 55
Period size: 9 Copynumber: 5.1 Consensus size: 9
2103953 TTTTTCCCTC
2103963 ATTTTTATT
1 ATTTTTATT
2103972 ATTTTTATT
1 ATTTTTATT
2103981 AATAATTTTAGTT
1 -AT--TTTTA-TT
2103994 A-TTTTATT
1 ATTTTTATT
2104002 ATTTTTATT
1 ATTTTTATT
2104011 A
1 A
2104012 ATAATTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 22 0.63
10 2 0.06
12 6 0.17
13 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (9 bp):
ATTTTTATT
Found at i:2104004 original size:33 final size:33
Alignment explanation
Indices: 2103963--2104034 Score: 123
Period size: 30 Copynumber: 2.3 Consensus size: 33
2103953 TTTTTCCCTC
2103963 ATTTTTATTATTTTTATTAATAA-TTTTAGTT-
1 ATTTTTATTATTTTTATTAATAATTTTTAGTTA
2103994 A-TTTTATTATTTTTATTAATAATTTTTAGTTA
1 ATTTTTATTATTTTTATTAATAATTTTTAGTTA
2104026 ATTTTTATT
1 ATTTTTATT
2104035 TTATTTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 21 0.55
31 9 0.24
32 1 0.03
33 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (33 bp):
ATTTTTATTATTTTTATTAATAATTTTTAGTTA
Found at i:2104160 original size:6 final size:6
Alignment explanation
Indices: 2104136--2104177 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2104126 ATATTTAATT
* *
2104136 ATAAAA CTAAATA AT-AAA ATAAAA ATAAAA GTAAAA ATAAAA
1 ATAAAA ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
2104178 CAATAGGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 3 0.10
6 25 0.83
7 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:2104170 original size:12 final size:11
Alignment explanation
Indices: 2104136--2104177 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
2104126 ATATTTAATT
2104136 ATAAAACTAAATA
1 ATAAAA-TAAA-A
2104149 ATAAAATAAAA
1 ATAAAATAAAA
2104160 ATAAAAGTAAAA
1 ATAAAA-TAAAA
2104172 ATAAAA
1 ATAAAA
2104178 CAATAGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.25
12 15 0.54
13 6 0.21
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:2105206 original size:21 final size:20
Alignment explanation
Indices: 2105168--2105207 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2105158 GCATGTCAGA
*
2105168 AAATAATTTTTCAATGAAAT
1 AAATAATTTTTAAATGAAAT
*
2105188 AAATCATTTTTAAAGTGAAA
1 AAATAATTTTTAAA-TGAAA
2105208 GATAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
AAATAATTTTTAAATGAAAT
Found at i:2106983 original size:27 final size:26
Alignment explanation
Indices: 2106944--2106997 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 26
2106934 ATAATTTGAT
2106944 TTTAATTGAATTAATCGATCGAATCAA
1 TTTAATTGAATTAATCGATC-AATCAA
2106971 TTTAATTCG-ATTAATCGATCAATCAA
1 TTTAATT-GAATTAATCGATCAATCAA
2106997 T
1 T
2106998 CAATCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.27
27 18 0.69
28 1 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (26 bp):
TTTAATTGAATTAATCGATCAATCAA
Found at i:2107284 original size:15 final size:17
Alignment explanation
Indices: 2107253--2107285 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2107243 AATTTAAAAG
2107253 TTTAAAGTATAATTTAT
1 TTTAAAGTATAATTTAT
2107270 TTTAAA-TAT-ATTTAT
1 TTTAAAGTATAATTTAT
2107285 T
1 T
2107286 ATTCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTAAAGTATAATTTAT
Found at i:2112825 original size:1 final size:1
Alignment explanation
Indices: 2112819--2112843 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2112809 ATTTGAAAGT
2112819 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2112844 CCTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2113796 original size:2 final size:2
Alignment explanation
Indices: 2113789--2113827 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2113779 AATAAACTTC
*
2113789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2113828 AAACTTGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2124237 original size:20 final size:20
Alignment explanation
Indices: 2124212--2124255 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
2124202 AAAGATGTGC
2124212 AAAAAA-AAAGTAAAAACAGAA
1 AAAAAACAAAG-AAAAA-AGAA
2124233 AAAAAACAAAGAAAAAAGAA
1 AAAAAACAAAGAAAAAAGAA
2124253 AAA
1 AAA
2124256 CTTAAACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 11 0.50
22 4 0.18
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (20 bp):
AAAAAACAAAGAAAAAAGAA
Found at i:2124237 original size:22 final size:20
Alignment explanation
Indices: 2124212--2124255 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
2124202 AAAGATGTGC
2124212 AAAAAAAAAGTAAAAACAGAAA
1 AAAAAAAAAG-AAAAA-AGAAA
*
2124234 AAAAACAAAGAAAAAAGAAA
1 AAAAAAAAAGAAAAAAGAAA
2124254 AA
1 AA
2124256 CTTAAACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAGAAA
Found at i:2125350 original size:46 final size:46
Alignment explanation
Indices: 2125299--2125397 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
2125289 TAAAAAGGAC
* **
2125299 CTTTGAAACTTTGGATATGAATAT-CTAAAATTTTTTGAATGAAAAT
1 CTTTGAAACTTTGGATAGGAAT-TCCTAAAATTTTTCAAATGAAAAT
* * *
2125345 CTTTGAAATTTTGGATGGGAATTCCTATAATTTTTCAAATGAAAAT
1 CTTTGAAACTTTGGATAGGAATTCCTAAAATTTTTCAAATGAAAAT
2125391 CTTTGAA
1 CTTTGAA
2125398 TTCTAGAGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 1 0.02
46 45 0.98
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.41
Consensus pattern (46 bp):
CTTTGAAACTTTGGATAGGAATTCCTAAAATTTTTCAAATGAAAAT
Found at i:2126251 original size:43 final size:43
Alignment explanation
Indices: 2126105--2126525 Score: 355
Period size: 43 Copynumber: 9.7 Consensus size: 43
2126095 TATTTAAAAT
* * * * * *
2126105 TTTTAAAATTGTTTAGCCTCTAAATATAAGAGTTTATTTCTTAA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTTCTT-A
* * * ** *
2126149 TTTTAAAGGTGTTTACCCTCTATATAAAGGAATTCATTTTTTAA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTTCTT-A
* * * *
2126193 TTTTAAAATTATTTAGCCTCTATATAGAGGAGTTTATTTCTTA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTTCTTA
* * * ** *
2126236 TTTTAAAGTGGTTTAGCCTTTGTATAGATAAGCCCATTTCTTA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTTCTTA
* * * * *
2126279 TTTTAAAGTTATTTAGCCTCTGTTTAGAAGAACTCATTTCTTAA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTTCTT-A
* * * *
2126323 TTTTAAAGTTGTTTAGCCTCTATATAAAGAAACAT-ATTTCCTA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGC-TCATTTCTTA
* * *
2126366 TTTTAAAGTTGTTTAGGCTCTATATAAAGGAGCTCATTTCCTA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTTCTTA
* * ** *
2126409 TTTTTAAGTTATTTAGCCTC-ACTATAGAAAAGCCCATTTCTTA
1 TTTTAAAGTTGTTTAGCCTCTA-TATAGAGGAGCTCATTTCTTA
* * *
2126452 TTTTAAAGTTGTTTAACCTTTATATAAAGGAGCTCAATTT-TTA
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTC-ATTTCTTA
* * *
2126495 ATTTAAATTTCTTT-GCCTCTATATAGAGGAG
1 TTTTAAAGTTGTTTAGCCTCTATATAGAGGAG
2126526 TTTAATTTGT
Statistics
Matches: 304, Mismatches: 67, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
42 16 0.05
43 179 0.59
44 108 0.36
45 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.45
Consensus pattern (43 bp):
TTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTTCTTA
Found at i:2126328 original size:130 final size:130
Alignment explanation
Indices: 2126105--2126484 Score: 374
Period size: 130 Copynumber: 2.9 Consensus size: 130
2126095 TATTTAAAAT
* * * *** * * *
2126105 TTTTAAAATTGTTTAGCCTCTAAATATAAG-AGTTTATTTCTTAATTTTAAAGGTGTTTACCCTC
1 TTTTAAAGTGGTTTAGCCTCTATATA-AAGAAGCCCATTTCTT-ATTTTAAAGTTATTTAGCCTC
* * * * * **
2126169 TATATA-AAGGAATTCATTTTTTAATTTTAAAATTATTTAGCCTCTATATAGAGGAGTTTATTTC
64 TATATAGAA-GAACTCATTTCTTAATTTTAAAGTTGTTTAGCCTCTATATAAAGGAGCATATTTC
*
2126233 TTA
128 CTA
* * * * *
2126236 TTTTAAAGTGGTTTAGCCTTTGTATAGATAAGCCCATTTCTTATTTTAAAGTTATTTAGCCTCTG
1 TTTTAAAGTGGTTTAGCCTCTATATAAAGAAGCCCATTTCTTATTTTAAAGTTATTTAGCCTCTA
* * *
2126301 TTTAGAAGAACTCATTTCTTAATTTTAAAGTTGTTTAGCCTCTATATAAAGAAACATATTTCCTA
66 TATAGAAGAACTCATTTCTTAATTTTAAAGTTGTTTAGCCTCTATATAAAGGAGCATATTTCCTA
* * * * * *
2126366 TTTTAAAGTTGTTTAGGCTCTATATAAAGGAGCTCATTTCCTATTTTTAAGTTATTTAGCCTC-A
1 TTTTAAAGTGGTTTAGCCTCTATATAAAGAAGCCCATTTCTTATTTTAAAGTTATTTAGCCTCTA
* * *
2126430 CTATAGAA-AAGCCCATTTCTT-ATTTTAAAGTTGTTTAACCTTTATATAAAGGAGC
66 -TATAGAAGAA-CTCATTTCTTAATTTTAAAGTTGTTTAGCCTCTATATAAAGGAGC
2126485 TCAATTTTTA
Statistics
Matches: 203, Mismatches: 42, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
129 32 0.16
130 139 0.68
131 32 0.16
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (130 bp):
TTTTAAAGTGGTTTAGCCTCTATATAAAGAAGCCCATTTCTTATTTTAAAGTTATTTAGCCTCTA
TATAGAAGAACTCATTTCTTAATTTTAAAGTTGTTTAGCCTCTATATAAAGGAGCATATTTCCTA
Found at i:2127354 original size:4 final size:4
Alignment explanation
Indices: 2127345--2127383 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
2127335 TAGTTTTAAC
* *
2127345 TTTA TTTA TTTA ATTA TTTTA TTTA TTTA ATTA TTTA TT
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TT
2127384 ATTCTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:2127367 original size:17 final size:17
Alignment explanation
Indices: 2127345--2127380 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2127335 TAGTTTTAAC
2127345 TTTATTTATTTAATTAT
1 TTTATTTATTTAATTAT
2127362 TTTATTTATTTAATTAT
1 TTTATTTATTTAATTAT
2127379 TT
1 TT
2127381 ATTATTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTATTTAATTAT
Found at i:2129235 original size:13 final size:14
Alignment explanation
Indices: 2129217--2129255 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2129207 TATTTTAAAA
2129217 AATTAAAA-AAATC
1 AATTAAAATAAATC
*
2129230 AATTAAAATAAATA
1 AATTAAAATAAATC
*
2129244 AAATAAAATAAA
1 AATTAAAATAAA
2129256 CACAAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AATTAAAATAAATC
Found at i:2130306 original size:6 final size:6
Alignment explanation
Indices: 2130297--2130328 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2130287 TAATAATAAT
*
2130297 AATATA AATATA AATATA AATGTA AATATA AA
1 AATATA AATATA AATATA AATATA AATATA AA
2130329 ACAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:2135538 original size:12 final size:12
Alignment explanation
Indices: 2135517--2135547 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2135507 AAATTCTAAA
*
2135517 TATATTTTATAT
1 TATATATTATAT
2135529 TATATATTATAT
1 TATATATTATAT
2135541 TATATAT
1 TATATAT
2135548 ACCTACAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATATTATAT
Found at i:2137369 original size:12 final size:12
Alignment explanation
Indices: 2137347--2137378 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2137337 GTGTGATTAT
2137347 TATAT-TATAAA
1 TATATATATAAA
2137358 TATATATATAAA
1 TATATATATAAA
2137370 TATATATAT
1 TATATATAT
2137379 TTTTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATATAAA
Found at i:2139840 original size:37 final size:33
Alignment explanation
Indices: 2139789--2139865 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 33
2139779 ATGGGAAAGT
2139789 AAAAAAAAGATTATGCAAAAAAACTCTTGAAG-GAA
1 AAAAAAAAGATTATGC--AAAAACTC-TGAAGAGAA
*
2139824 AAAAAATAGAGATTATGCAGAAACTCTGAAGAGAA
1 AAAAAA-A-AGATTATGCAAAAACTCTGAAGAGAA
2139859 AAAAAAA
1 AAAAAAA
2139866 GTTTGTCTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
34 6 0.16
35 22 0.58
36 1 0.03
37 9 0.24
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (33 bp):
AAAAAAAAGATTATGCAAAAACTCTGAAGAGAA
Found at i:2140321 original size:16 final size:16
Alignment explanation
Indices: 2140288--2140349 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
2140278 ATTTTTTTGA
2140288 TTTT-ATTTATTTTATAT
1 TTTTAATTTA-TTT-TAT
*
2140305 TTTTAACTTATTTTAT
1 TTTTAATTTATTTTAT
* *
2140321 TTTCAATTTCTTTTAT
1 TTTTAATTTATTTTAT
2140337 TTTATAATTTATT
1 TTT-TAATTTATT
2140350 CTACCTCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
16 19 0.51
17 14 0.38
18 4 0.11
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATTTATTTTAT
Found at i:2140705 original size:17 final size:18
Alignment explanation
Indices: 2140683--2140720 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2140673 TTTTAGGGTT
2140683 AATTTT-TAATATTA-AAA
1 AATTTTGTAA-ATTATAAA
2140700 AATTTTGTAAATTATAAA
1 AATTTTGTAAATTATAAA
2140718 AAT
1 AAT
2140721 GATCAAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AATTTTGTAAATTATAAA
Found at i:2141770 original size:46 final size:47
Alignment explanation
Indices: 2141693--2141800 Score: 159
Period size: 46 Copynumber: 2.3 Consensus size: 47
2141683 TATTTTTTTT
* *
2141693 TTTTTTTTTTTATTTCTAAATTTTTCTCCATTTTGG-CTAATTTAAAA
1 TTTTTCTTTTTATTTCTAAATTTTTCACCATTTTGGTCT-ATTTAAAA
2141740 -TTTTCTTTTTGATTTCTAAA-TTTTCACCATTTTGGTCTATTTAAAA
1 TTTTTCTTTTT-ATTTCTAAATTTTTCACCATTTTGGTCTATTTAAAA
2141786 TTTTTCTTTTTATTT
1 TTTTTCTTTTTATTT
2141801 TTGAAAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
46 35 0.62
47 21 0.38
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (47 bp):
TTTTTCTTTTTATTTCTAAATTTTTCACCATTTTGGTCTATTTAAAA
Found at i:2144288 original size:13 final size:13
Alignment explanation
Indices: 2144270--2144295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2144260 CGATTTTTGA
2144270 TATTTTTTATTTT
1 TATTTTTTATTTT
2144283 TATTTTTTATTTT
1 TATTTTTTATTTT
2144296 AAATTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:2144438 original size:19 final size:19
Alignment explanation
Indices: 2144425--2144488 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
2144415 AAAAAATATT
2144425 TAAAAAATTAAAAACATAA
1 TAAAAAATTAAAAACATAA
* *
2144444 TAAAAAA-TAATAA-ATGA
1 TAAAAAATTAAAAACATAA
2144461 TAAACAAATTAATAAA-ATTAA
1 TAAA-AAATTAA-AAACA-TAA
2144482 TAAAAAA
1 TAAAAAA
2144489 AATCCCCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 7 0.19
18 8 0.22
19 10 0.27
20 6 0.16
21 6 0.16
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAAAATTAAAAACATAA
Found at i:2144448 original size:10 final size:10
Alignment explanation
Indices: 2144413--2144488 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
2144403 TAAAATATGT
2144413 ATAAAAAATA
1 ATAAAAAATA
*
2144423 TTTAAAAAAT-
1 -ATAAAAAATA
2144433 -TAAAAACATA
1 ATAAAAA-ATA
2144443 ATAAAAAATA
1 ATAAAAAATA
**
2144453 ATAAATGATA
1 ATAAAAAATA
* *
2144463 A-ACAAATTA
1 ATAAAAAATA
*
2144472 AT-AAAATTA
1 ATAAAAAATA
2144481 ATAAAAAA
1 ATAAAAAA
2144489 AATCCCCAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
8 6 0.12
9 15 0.29
10 16 0.31
11 14 0.27
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:2144850 original size:3 final size:3
Alignment explanation
Indices: 2144830--2144875 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
2144820 TTAAAGTTAG
2144830 AAT AA- AAT AA- AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2144874 AA
1 AA
2144876 AAATGGAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2148186 original size:11 final size:11
Alignment explanation
Indices: 2148168--2148201 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2148158 TTCTTTCAAG
2148168 TTTCTCTTTTT
1 TTTCTCTTTTT
*
2148179 TTTTTCTTTTT
1 TTTCTCTTTTT
2148190 TTTCTCTTTTT
1 TTTCTCTTTTT
2148201 T
1 T
2148202 GGGTTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTCTTTTT
Found at i:2152579 original size:25 final size:27
Alignment explanation
Indices: 2152522--2152579 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
2152512 TCAAATGAGT
*
2152522 TAAAAAGATTAATTCTATTATCACTTA
1 TAAAATGATTAATTCTATTATCACTTA
* * *
2152549 TTAAATGATT-ATTCTCTTTTCA-TTA
1 TAAAATGATTAATTCTATTATCACTTA
2152574 TAAAAT
1 TAAAAT
2152580 TAATTTATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 8 0.31
26 10 0.38
27 8 0.31
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (27 bp):
TAAAATGATTAATTCTATTATCACTTA
Found at i:2153081 original size:17 final size:20
Alignment explanation
Indices: 2153054--2153093 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2153044 GAGCTTTAAA
2153054 AAAATATTTT-AAT-AAATT
1 AAAATATTTTAAATCAAATT
2153072 AAAA-ATTTTAAATCAAATT
1 AAAATATTTTAAATCAAATT
2153091 AAA
1 AAA
2153094 TTCGAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 7 0.35
19 8 0.40
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATATTTTAAATCAAATT
Found at i:2155239 original size:19 final size:20
Alignment explanation
Indices: 2155217--2155255 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2155207 ATATTATTTT
2155217 TTAATAAAAATTT-TTAAAA
1 TTAATAAAAATTTATTAAAA
*
2155236 TTAATTAAAATTTATTAAAA
1 TTAATAAAAATTTATTAAAA
2155256 GAAGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATAAAAATTTATTAAAA
Found at i:2155413 original size:14 final size:15
Alignment explanation
Indices: 2155396--2155428 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2155386 ATATGATTTT
2155396 TTTAATATTTT-AAA
1 TTTAATATTTTAAAA
*
2155410 TTTAATTTTTTAAAA
1 TTTAATATTTTAAAA
2155425 TTTA
1 TTTA
2155429 TTTATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATATTTTAAAA
Found at i:2156033 original size:19 final size:21
Alignment explanation
Indices: 2155999--2156037 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
2155989 TCCATTATCA
2155999 TTATTATTTTTCATATTGTTT
1 TTATTATTTTTCATATTGTTT
2156020 TTATT-TTTTT-ATATTGTT
1 TTATTATTTTTCATATTGTT
2156038 AAAATAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (21 bp):
TTATTATTTTTCATATTGTTT
Found at i:2156396 original size:18 final size:18
Alignment explanation
Indices: 2156375--2156415 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2156365 ATATTATATT
*
2156375 TTTTAGGTCTATATTTTA
1 TTTTAAGTCTATATTTTA
* *
2156393 TTTTAATTCTATTTTTTA
1 TTTTAAGTCTATATTTTA
2156411 TTTTA
1 TTTTA
2156416 TTTATTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAAGTCTATATTTTA
Found at i:2156494 original size:15 final size:14
Alignment explanation
Indices: 2156472--2156552 Score: 62
Period size: 15 Copynumber: 5.9 Consensus size: 14
2156462 CAATAATAAT
2156472 AAAAAATAAAAACA
1 AAAAAATAAAAACA
2156486 AACAAAATAAATAACA
1 AA-AAAATAAA-AACA
* * *
2156502 TAAAAATCAACACA
1 AAAAAATAAAAACA
*
2156516 AAATAAATAAAATC-
1 AAA-AAATAAAAACA
*
2156530 --AAAATCAAAAC-
1 AAAAAATAAAAACA
2156541 AAAAAATAAAAA
1 AAAAAATAAAAA
2156553 AATAAAAGGA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
11 8 0.15
12 1 0.02
13 9 0.17
14 7 0.13
15 22 0.42
16 5 0.10
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAATAAAAACA
Found at i:2156498 original size:26 final size:24
Alignment explanation
Indices: 2156460--2156559 Score: 94
Period size: 26 Copynumber: 3.9 Consensus size: 24
2156450 AGCATAAAAT
*
2156460 AACAATAATAATAAAAAATAAAAACA
1 AACAA-AATAA-ATAAAATAAAAACA
*
2156486 AACAAAATAAATAACATAAAAATCA
1 AACAAAATAAATAAAATAAAAA-CA
*
2156511 ACACAAAATAAATAAAATCAAAATCAA
1 A-ACAAAATAAATAAAAT-AAAAAC-A
2156538 AACAAAAAATAAA-AAAATAAAA
1 AAC--AAAATAAATAAAATAAAA
2156560 GGAAAAACTT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
24 10 0.16
25 8 0.12
26 27 0.42
27 11 0.17
28 8 0.12
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (24 bp):
AACAAAATAAATAAAATAAAAACA
Found at i:2157454 original size:3 final size:3
Alignment explanation
Indices: 2157448--2157472 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2157438 TGTAAGAAGA
2157448 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2157473 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2162940 original size:2 final size:2
Alignment explanation
Indices: 2162935--2162962 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2162925 AAAAAAAGTA
2162935 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2162963 GGAGGTAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2186865 original size:13 final size:13
Alignment explanation
Indices: 2186847--2186871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2186837 TGATTACAAA
2186847 TAAAAAGGAAAAG
1 TAAAAAGGAAAAG
2186860 TAAAAAGGAAAA
1 TAAAAAGGAAAA
2186872 TTTGATGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (13 bp):
TAAAAAGGAAAAG
Found at i:2195460 original size:20 final size:20
Alignment explanation
Indices: 2195423--2195460 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2195413 TATAAATAAA
*
2195423 TTTTCAAAATAAATATTTTT
1 TTTTCAAAATAAAAATTTTT
2195443 TTTTCAAAA-AATAAATTT
1 TTTTCAAAATAA-AAATTT
2195461 CATAAGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATAAAAATTTTT
Found at i:2200996 original size:33 final size:33
Alignment explanation
Indices: 2200959--2201024 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2200949 TCCAAAAAGT
* *
2200959 CTCAAAACTTCTTGAATATTCATTTTTGAAAAA
1 CTCAAAACTTCTCGAATATTCATTTTCGAAAAA
** *
2200992 CTCAAATTTTCTCGAATATTTATTTTCGAAAAA
1 CTCAAAACTTCTCGAATATTCATTTTCGAAAAA
2201025 GTTGAGTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (33 bp):
CTCAAAACTTCTCGAATATTCATTTTCGAAAAA
Found at i:2204642 original size:34 final size:34
Alignment explanation
Indices: 2204608--2204676 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
2204598 TTTTAAATTA
*
2204608 TATTAT-TT-TTATATTTTATATTTATATCATAT
1 TATTATATTATTATATTTTATAATTATATCATAT
2204640 TATTATATTATTATATTTTATAATTATATCATAT
1 TATTATATTATTATATTTTATAATTATATCATAT
2204674 TAT
1 TAT
2204677 CAATCTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 6 0.18
33 2 0.06
34 26 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (34 bp):
TATTATATTATTATATTTTATAATTATATCATAT
Found at i:2204656 original size:13 final size:13
Alignment explanation
Indices: 2204604--2204676 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
2204594 AAAATTTTAA
2204604 ATTATATTATT-T
1 ATTATATTATTAT
2204616 -TTATATT-TTAT
1 ATTATATTATTAT
*
2204627 ATTTATATCA-TATT
1 A-TTATATTATTA-T
2204641 ATTATATTATTAT
1 ATTATATTATTAT
* *
2204654 ATTTTATAATTAT
1 ATTATATTATTAT
*
2204667 ATCATATTAT
1 ATTATATTAT
2204677 CAATCTAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
10 2 0.04
11 8 0.17
13 34 0.71
14 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATTATTAT
Found at i:2205459 original size:30 final size:30
Alignment explanation
Indices: 2205418--2205474 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2205408 TAATATTTTA
2205418 AATGATAATTTTCTTTCTCAAGATACTCTT
1 AATGATAATTTTCTTTCTCAAGATACTCTT
* * *
2205448 AATGATCATTTTCTTTCTTAATATACT
1 AATGATAATTTTCTTTCTCAAGATACT
2205475 TCTTCTCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (30 bp):
AATGATAATTTTCTTTCTCAAGATACTCTT
Found at i:2219544 original size:20 final size:20
Alignment explanation
Indices: 2219508--2219545 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2219498 TTTCATGAAA
*
2219508 AAGAAAACATAGCAGACTTT
1 AAGAAAACATAGAAGACTTT
2219528 AAGAAAA-ATGAGAAGACT
1 AAGAAAACAT-AGAAGACT
2219546 ATACAGGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.55, C:0.11, G:0.18, T:0.16
Consensus pattern (20 bp):
AAGAAAACATAGAAGACTTT
Found at i:2227032 original size:81 final size:81
Alignment explanation
Indices: 2226897--2227060 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
2226887 AAGGCTTCAA
2226897 GTCTGACTCAGATAGTTGTTTTTTCCCCTACAATTGCTGTGCAGACACTTGATGACGTAGTTGGA
1 GTCTGACTCAGATAGTTGTTTTTTCCCCTACAATTGCTGTGCAGACACTTGATGACGTAGTTGGA
2226962 TATTACAGAAATACAT
66 TATTACAGAAATACAT
2226978 GTCTGACTCAGATAGTTGTTTTTTCCCCTACAATTGCTGTGCAGACACTTGATGACGTAGTTGGA
1 GTCTGACTCAGATAGTTGTTTTTTCCCCTACAATTGCTGTGCAGACACTTGATGACGTAGTTGGA
2227043 TATTACAGAAATACAT
66 TATTACAGAAATACAT
2227059 GT
1 GT
2227061 AACATGCTTC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (81 bp):
GTCTGACTCAGATAGTTGTTTTTTCCCCTACAATTGCTGTGCAGACACTTGATGACGTAGTTGGA
TATTACAGAAATACAT
Found at i:2249217 original size:30 final size:33
Alignment explanation
Indices: 2249136--2249220 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 33
2249126 TTGATATATA
*
2249136 TATATATATTTATTATTATTATTATTTATTTAAT
1 TATATATATTTA-TATTTTTATTATTTATTTAAT
2249170 TATATATATACATTATATTTTTA-TATTTATTTAAT
1 TATATATAT---TTATATTTTTATTATTTATTTAAT
2249205 T-T-TATATTTATATTTT
1 TATATATATTTATATTTT
2249221 AAAAAATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
30 9 0.19
33 5 0.11
34 10 0.21
35 13 0.28
36 7 0.15
37 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (33 bp):
TATATATATTTATATTTTTATTATTTATTTAAT
Found at i:2252357 original size:2 final size:2
Alignment explanation
Indices: 2252350--2252400 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2252340 ATTGCTAATT
*
2252350 TA TA TA TA TA TA TA TA TA TA TG 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 TA TA TA TA TA TA
2252392 TA TA TA TA T
1 TA TA TA TA T
2252401 CCTATCAGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2252876 original size:16 final size:18
Alignment explanation
Indices: 2252851--2252883 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2252841 CTTCTCTAAT
2252851 TTTTTCTTAC-AAGATTA
1 TTTTTCTTACTAAGATTA
2252868 TTTTT-TTACTAAGATT
1 TTTTTCTTACTAAGATT
2252884 GTTTAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTTTCTTACTAAGATTA
Found at i:2258037 original size:21 final size:23
Alignment explanation
Indices: 2257998--2258069 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
2257988 TAAATAACTC
2257998 TTTTAAATA-ACATATAAGATAATT
1 TTTTAAATATA-A-ATAAGATAATT
*
2258022 TTTTAAA-A-AAATAAGATAGTTT
1 TTTTAAATATAAATAAGATA-ATT
*
2258044 CTTTTAAATATAAATTAGATAATT
1 -TTTTAAATATAAATAAGATAATT
2258068 TT
1 TT
2258070 AAATTTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 8 0.20
22 3 0.07
23 11 0.27
24 10 0.24
25 9 0.22
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (23 bp):
TTTTAAATATAAATAAGATAATT
Found at i:2258058 original size:25 final size:23
Alignment explanation
Indices: 2257991--2258067 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 23
2257981 GTTTATGTAA
*
2257991 ATAACTCTTTTAAATAACATATAAG
1 ATAATTCTTTTAAATAA-A-ATAAG
2258016 ATAATT-TTTTAAA-AAAATAAG
1 ATAATTCTTTTAAATAAAATAAG
* *
2258037 ATAGTTTCTTTTAAATATAAATTAG
1 ATA-ATTCTTTTAAATA-AAATAAG
2258062 ATAATT
1 ATAATT
2258068 TTAAATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 8 0.18
22 3 0.07
23 9 0.20
24 10 0.23
25 14 0.32
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (23 bp):
ATAATTCTTTTAAATAAAATAAG
Found at i:2258188 original size:20 final size:20
Alignment explanation
Indices: 2258163--2258212 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2258153 TGAAATATGG
2258163 ATTTTATTTTTTAAT-AAATA
1 ATTTTATTTTTT-ATCAAATA
*
2258183 ATTTTAGTTGTTTATCAAATA
1 ATTTTA-TTTTTTATCAAATA
2258204 ATTTTATTT
1 ATTTTATTT
2258213 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
ATTTTATTTTTTATCAAATA
Found at i:2258381 original size:30 final size:31
Alignment explanation
Indices: 2258337--2258396 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2258327 AAGATTTACG
* *
2258337 TAAGATATTAAAAATTC-AAATAATTTTATA
1 TAAGATATTAAAAATCCAAAAAAATTTTATA
* *
2258367 TAAGATTTTGAAAATCCAAAAAAATTTTAT
1 TAAGATATTAAAAATCCAAAAAAATTTTAT
2258397 CTTAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (31 bp):
TAAGATATTAAAAATCCAAAAAAATTTTATA
Found at i:2258702 original size:54 final size:54
Alignment explanation
Indices: 2258619--2258725 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
2258609 TGTTTTGCAT
*
2258619 CAATTTTTTTTAATTTTTTAGTAACTTTTTTCAAGGTATATTCTATTACTATTG
1 CAATTTTTTTTAATTTTTTAGTAACTTTTTTCAAGATATATTCTATTACTATTG
* * *
2258673 CAATTTGTTTTT-TTTTTTTA-TAACTTTTTTTCAAGATATATTTTATTATTATT
1 CAATTT-TTTTTAATTTTTTAGTAAC-TTTTTTCAAGATATATTCTATTACTATT
2258726 ACAGTTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 4 0.09
54 38 0.81
55 5 0.11
ACGTcount: A:0.25, C:0.07, G:0.06, T:0.62
Consensus pattern (54 bp):
CAATTTTTTTTAATTTTTTAGTAACTTTTTTCAAGATATATTCTATTACTATTG
Found at i:2260008 original size:21 final size:21
Alignment explanation
Indices: 2259984--2260027 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2259974 TTTACTTGAG
2259984 AAAATATATAAAATTTAATTTA
1 AAAAT-TATAAAATTTAATTTA
* *
2260006 AAAATTTTCAAATTTAATTTA
1 AAAATTATAAAATTTAATTTA
2260027 A
1 A
2260028 TGGATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTATAAAATTTAATTTA
Found at i:2262393 original size:22 final size:22
Alignment explanation
Indices: 2262367--2262408 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2262357 TGTAAGCCTA
2262367 AAATTTAAATTTTAAAATTATT
1 AAATTTAAATTTTAAAATTATT
* *
2262389 AAATTTTATTTTTAAAATTA
1 AAATTTAAATTTTAAAATTA
2262409 ATTTCATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATTTAAATTTTAAAATTATT
Done.