Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168169.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_408, 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: 28205
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:599 original size:1 final size:1
Alignment explanation
Indices: 593--618 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
583 TGCTGTTCAA
593 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
619 CAGTTCGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1619 original size:22 final size:22
Alignment explanation
Indices: 1588--1638 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1578 GTTGTTTTTA
*
1588 GAATTATAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
1610 GAATTCTAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
1632 -AATTCTA
1 GAATTCTA
1639 TTTAGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
GAATTCTAATTATATAAGAAAT
Found at i:2623 original size:15 final size:17
Alignment explanation
Indices: 2602--2642 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
2592 CAATATTCTT
2602 TTATTTTTTTTTA-TTC
1 TTATTTTTTTTTAGTTC
*
2618 -TATTTTTATTTAGTTC
1 TTATTTTTTTTTAGTTC
2634 TTATTTTTT
1 TTATTTTTT
2643 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
16 3 0.14
17 7 0.33
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (17 bp):
TTATTTTTTTTTAGTTC
Found at i:2713 original size:25 final size:25
Alignment explanation
Indices: 2680--2731 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2670 ATTATTTATT
*
2680 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
2705 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
2730 TT
1 TT
2732 AGGAGTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTTTAGTTTACAGTCTTCGAATGA
Found at i:2738 original size:25 final size:25
Alignment explanation
Indices: 2685--2738 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
2675 TTATTTTTTT
* ***
2685 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
2710 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
2735 AGTT
1 AGTT
2739 GGATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (25 bp):
AGTTTACAGTCTTCGAATGATTAGG
Found at i:2838 original size:15 final size:15
Alignment explanation
Indices: 2818--2867 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
2808 CATAATGATT
2818 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
2833 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
2851 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
2866 AT
1 AT
2868 ATTGTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 17 0.53
18 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
ATTTTAATATTGTTA
Found at i:2850 original size:18 final size:18
Alignment explanation
Indices: 2827--2864 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2817 TATTTTAATA
2827 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
2845 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
2863 TT
1 TT
2865 AATATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TTGTTAATTTTAATATTG
Found at i:2886 original size:17 final size:17
Alignment explanation
Indices: 2866--2899 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2856 AATATTGTTA
*
2866 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
2883 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
2900 CATTACTATA
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:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
ATATTGTATGATTTATT
Found at i:2922 original size:18 final size:18
Alignment explanation
Indices: 2901--2948 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2891 TGATTTATTC
*
2901 ATTACTATATTTTTAGTT
1 ATTACTATATTTGTAGTT
*
2919 ATTACTATATTTGTATTT
1 ATTACTATATTTGTAGTT
2937 ATTACTATATTT
1 ATTACTATATTT
2949 CATTATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (18 bp):
ATTACTATATTTGTAGTT
Found at i:2966 original size:36 final size:36
Alignment explanation
Indices: 2894--2985 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
2884 TATTGTATGA
*
2894 TTTATTCATTACTATATTT-TTAGTTATTACTATAT
1 TTTATTAATTACTATATTTCTTAGTTATTACTATAT
* *
2929 TTGTATTTATTACTATATTTCATTA-TTATTTCT-TAT
1 TT-TATTAATTACTATATTTC-TTAGTTATTACTATAT
*
2965 TTTATTAATTATTATTATTTC
1 TTTATTAATTACTA-TATTTC
2986 GTGTCGGTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
35 12 0.24
36 27 0.55
37 7 0.14
38 3 0.06
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (36 bp):
TTTATTAATTACTATATTTCTTAGTTATTACTATAT
Found at i:2982 original size:18 final size:17
Alignment explanation
Indices: 2815--2984 Score: 53
Period size: 18 Copynumber: 9.4 Consensus size: 17
2805 GTGCATAATG
* *
2815 ATTATTTTAATATTGTT
1 ATTATTTTATTATTATT
* *
2832 A--ATTTTAATATTGTT
1 ATTATTTTATTATTATT
* * *
2847 GTTAATTTTAATATTGTT
1 ATT-ATTTTATTATTATT
* *
2865 AATATTGTATTATTTATT
1 ATTATTTTATTA-TTATT
2883 A-TATTGTATGATTTATTCATT
1 ATTATT-T-T-A-TTATT-ATT
*
2904 ACTATATTT-TTAGTTATT
1 ATTAT-TTTATTA-TTATT
*
2922 ACTATATTTGTATTTATTACT
1 A-T-TATTT-TA-TTATTATT
*
2943 A-TATTTCATTATTATTT
1 ATTATTTTATTATTA-TT
*
2960 CTTATTTTATTAATTATT
1 ATTATTTTATT-ATTATT
2978 ATTATTT
1 ATTATTT
2985 CGTGTCGGTT
Statistics
Matches: 119, Mismatches: 14, Indels: 39
0.69 0.08 0.23
Matches are distributed among these distances:
15 14 0.12
16 6 0.05
17 14 0.12
18 48 0.40
19 9 0.08
20 7 0.06
21 13 0.11
22 7 0.06
23 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (17 bp):
ATTATTTTATTATTATT
Found at i:3098 original size:35 final size:35
Alignment explanation
Indices: 3059--3440 Score: 360
Period size: 35 Copynumber: 11.4 Consensus size: 35
3049 AGATATTTAT
3059 TTAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
3094 TTAAATTATATTTATAT-TT-TATATATTAAATATA
1 TTAAATTATATTTATATATTAAATATATTAAA-ATA
* * * *
3128 TTAAAATATGAAATTATAT-TTATATATATTTATAA-A
1 TTAAATTAT--ATTTATATATTAAATATA-TTAAAATA
* * * * *
3164 TTATATT-TATTTAT-TATT-TATGTATTATACA-G
1 TTAAATTATATTTATATATTAAATATATTA-AAATA
* * * *
3196 TTATA-GATA-TT-TAT-TTAAATTATATTTATATA
1 TTAAATTATATTTATATATTAAA-TATATTAAAATA
* *
3228 TTAAA-TATATTAAAATATTAAAT-TA-T---AT-
1 TTAAATTATATTTATATATTAAATATATTAAAATA
3256 TT--A-TAT-TTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
3287 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
3322 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
3357 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
3392 TGAAATTATATTTATATATTAAATATATTAAAATA
1 TTAAATTATATTTATATATTAAATATATTAAAATA
*
3427 TGAAATTATATTTA
1 TTAAATTATATTTA
3441 AATAAATATC
Statistics
Matches: 298, Mismatches: 24, Indels: 50
0.80 0.06 0.13
Matches are distributed among these distances:
25 12 0.04
26 6 0.02
27 1 0.00
28 2 0.01
29 2 0.01
30 5 0.02
31 10 0.03
32 27 0.09
33 21 0.07
34 19 0.06
35 167 0.56
36 15 0.05
37 7 0.02
38 4 0.01
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (35 bp):
TTAAATTATATTTATATATTAAATATATTAAAATA
Found at i:3240 original size:151 final size:151
Alignment explanation
Indices: 2996--3440 Score: 636
Period size: 151 Copynumber: 3.0 Consensus size: 151
2986 GTGTCGGTTC
2996 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATCACAGTTATAGATATTTATTT
1 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTAT-ACAGTTATAGATATTTATTT
3061 AAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATA
65 AAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATA
3126 TATTAAAATATGAAATTATATT
130 TATTAAAATATGAAATTATATT
3148 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATACAGTTATAGATATTTATTTA
1 TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATACAGTTATAGATATTTATTTA
3213 AATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATAT
66 AATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATAT
3278 ATTAAAATATGAAATTATATT
131 ATTAAAATATGAAATTATATT
* ** * * *
3299 TATATATTAAATATATTAAA--ATATGAAATTA-TATTTATATATTA-A-A-TATATTA-A-A-A
1 TATATA-T--ATTTA-TAAATTATATTTATTTATTATTTATGTATTATACAGT-TA-TAGATATT
* *
3355 TA-TGAAATTATATTTATATATTAAATATATTAAAATA-T-GA--A-A-TTATA-TTTATATATT
60 TATTTAAATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATT
3412 AAATATATTAAAATATGAAATTATATT
125 AAATATATTAAAATATGAAATTATATT
3439 TA
1 TA
3441 AATAAATATC
Statistics
Matches: 279, Mismatches: 8, Indels: 24
0.90 0.03 0.08
Matches are distributed among these distances:
140 39 0.14
141 5 0.02
142 1 0.00
143 1 0.00
145 1 0.00
146 1 0.00
147 34 0.12
148 2 0.01
149 2 0.01
150 4 0.01
151 116 0.42
152 57 0.20
153 8 0.03
154 4 0.01
155 4 0.01
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (151 bp):
TATATATATTTATAAATTATATTTATTTATTATTTATGTATTATACAGTTATAGATATTTATTTA
AATTATATTTATATATTAAATATATTAAAATATTAAATTATATTTATATTTTATATATTAAATAT
ATTAAAATATGAAATTATATT
Found at i:3250 original size:7 final size:8
Alignment explanation
Indices: 3225--3427 Score: 111
Period size: 8 Copynumber: 23.5 Consensus size: 8
3215 TTATATTTAT
3225 ATATTAAA
1 ATATTAAA
3233 TATATTAAA
1 -ATATTAAA
3242 ATATTAAA
1 ATATTAAA
* *
3250 TTATATTTAT
1 --ATATTAAA
* *
3260 AT-TTTAT
1 ATATTAAA
3267 ATATTAAA
1 ATATTAAA
3275 TATATTAAA
1 -ATATTAAA
*
3284 ATATGAAA
1 ATATTAAA
* *
3292 TTATATTTAT
1 --ATATTAAA
3302 ATATTAAA
1 ATATTAAA
3310 TATATTAAA
1 -ATATTAAA
*
3319 ATATGAAA
1 ATATTAAA
* *
3327 TTATATTTAT
1 --ATATTAAA
3337 ATATTAAA
1 ATATTAAA
3345 TATATTAAA
1 -ATATTAAA
*
3354 ATATGAAA
1 ATATTAAA
* *
3362 TTATATTTAT
1 --ATATTAAA
3372 ATATTAAA
1 ATATTAAA
3380 TATATTAAA
1 -ATATTAAA
*
3389 ATATGAAA
1 ATATTAAA
* *
3397 TTATATTTAT
1 --ATATTAAA
3407 ATATTAAA
1 ATATTAAA
3415 TATATTAAA
1 -ATATTAAA
3424 ATAT
1 ATAT
3428 GAAATTATAT
Statistics
Matches: 150, Mismatches: 28, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.05
8 69 0.46
9 48 0.32
10 26 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
ATATTAAA
Found at i:3459 original size:4 final size:4
Alignment explanation
Indices: 3452--3579 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
3442 ATAAATATCT
*
3452 ATAA AT-A ATATA AT-A ATAAA ATAA ACT-A ATAAA ATAA ACAA ATAA
1 ATAA ATAA ATA-A ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA
* *
3497 AT-A ATAA ATAA ATAA TTAAA ATAA ACT-A ATAAA ATAA ACAA ATAA AT-A
1 ATAA ATAA ATAA ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA ATAA
*
3545 AGAA ATAA AT-A ATAA ATAA AT-A ATACA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA A
3580 AAAAACAAAG
Statistics
Matches: 99, Mismatches: 8, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
3 22 0.22
4 57 0.58
5 20 0.20
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:3462 original size:35 final size:35
Alignment explanation
Indices: 3232--3440 Score: 370
Period size: 35 Copynumber: 6.0 Consensus size: 35
3222 TATATATTAA
* *
3232 ATATATTAAA-ATATTAAATTAT--ATTTATATTTT
1 ATATATTAAATATATTAAAATATGAAATTATA-TTT
3265 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
3300 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
3335 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
3370 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
3405 ATATATTAAATATATTAAAATATGAAATTATATTT
1 ATATATTAAATATATTAAAATATGAAATTATATTT
3440 A
1 A
3441 AATAAATATC
Statistics
Matches: 171, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
33 10 0.06
34 11 0.06
35 144 0.84
36 6 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (35 bp):
ATATATTAAATATATTAAAATATGAAATTATATTT
Found at i:3474 original size:13 final size:13
Alignment explanation
Indices: 3465--3542 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
3455 AATAATATAA
3465 TAATAAAATAAAC
1 TAATAAAATAAAC
3478 TAATAAAATAAAC
1 TAATAAAATAAAC
3491 -----AAATAAA-
1 TAATAAAATAAAC
3498 TAAT-AAATAAA-
1 TAATAAAATAAAC
3509 TAATTAAAATAAAC
1 TAA-TAAAATAAAC
3523 TAATAAAATAAAC
1 TAATAAAATAAAC
*
3536 AAATAAA
1 TAATAAA
3543 TAAGAAATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
8 7 0.12
11 10 0.18
12 1 0.02
13 36 0.63
14 3 0.05
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (13 bp):
TAATAAAATAAAC
Found at i:3579 original size:45 final size:44
Alignment explanation
Indices: 3458--3575 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 44
3448 ATCTATAAAT
*
3458 AATATAATAATAAAATAAACTAATAAAATAAACAAATAAATAATA
1 AATA-AATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
3503 AATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATAAGA
1 AATAAATAA-TAAAATAAACTAATAAAATAAACAAATAAATAAGA
*
3548 AATAAATAAT-AAATAAA-TAATACAATAA
1 AATAAATAATAAAATAAACTAATAAAATAA
3576 TAAAAAAAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
42 10 0.14
43 7 0.10
44 6 0.09
45 47 0.67
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (44 bp):
AATAAATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
Found at i:5698 original size:30 final size:30
Alignment explanation
Indices: 5664--5943 Score: 560
Period size: 30 Copynumber: 9.3 Consensus size: 30
5654 AAATGGTGTT
5664 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5694 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5724 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5754 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5784 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5814 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5844 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5874 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5904 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
5934 CCATTGTCGT
1 CCATTGTCGT
5944 TAACTAGTCT
Statistics
Matches: 250, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 250 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (30 bp):
CCATTGTCGTCAAATGGTGGTCTTCCATTG
Found at i:5984 original size:18 final size:18
Alignment explanation
Indices: 5957--6191 Score: 388
Period size: 18 Copynumber: 13.1 Consensus size: 18
5947 CTAGTCTCCA
*
5957 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
5975 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
5993 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
6011 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
6029 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
6047 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
6065 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
6083 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
*
6101 TTTGTTTATTCACTATA-G
1 TTT-TTCATTCACTATAGG
6119 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
6137 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
6155 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
6173 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
6191 T
1 T
6192 CTCGATTCTG
Statistics
Matches: 211, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
17 14 0.07
18 183 0.87
19 14 0.07
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.51
Consensus pattern (18 bp):
TTTTTCATTCACTATAGG
Found at i:6530 original size:18 final size:18
Alignment explanation
Indices: 6507--6544 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6497 TTTTTTGCGC
6507 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
6525 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
6543 AT
1 AT
6545 GGAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
ATTGCATACGGCTTTACA
Found at i:8479 original size:78 final size:78
Alignment explanation
Indices: 8350--8518 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
8340 AGTAAAAAGA
* *
8350 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
8415 TTATCTTAATAAT
66 TTATCTTAATAAT
8428 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
8493 TTATCTTAATAAT
66 TTATCTTAATAAT
8506 ATGTAATATTATA
1 ATGTAATATTATA
8519 ATATGTAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (78 bp):
ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
TTATCTTAATAAT
Found at i:8521 original size:15 final size:15
Alignment explanation
Indices: 8501--8533 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
8491 TCTTATCTTA
8501 ATAATATGTAATATT
1 ATAATATGTAATATT
8516 ATAATATGTAATATT
1 ATAATATGTAATATT
8531 ATA
1 ATA
8534 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:8614 original size:15 final size:15
Alignment explanation
Indices: 8594--8626 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
8584 TCTTATCTTA
8594 ATAATATGTAATATT
1 ATAATATGTAATATT
8609 ATAATATGTAATATT
1 ATAATATGTAATATT
8624 ATA
1 ATA
8627 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:8715 original size:93 final size:93
Alignment explanation
Indices: 8423--8699 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
8413 TCTTATCTTA
8423 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
8488 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
8516 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
8581 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
8609 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
8674 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
8700 ATGGTCTTAA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 184 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (93 bp):
ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
TGGTCTTATCTTAATAATATGTAATATT
Found at i:11105 original size:21 final size:20
Alignment explanation
Indices: 11088--11139 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
11078 TTATATAATT
*
11088 ATATAAATA-ATATATATAA
1 ATATAAATATAAATATATAA
11107 ATATAAATATAAATAATATAA
1 ATATAAATATAAAT-ATATAA
11128 ATATAAATATAA
1 ATATAAATATAA
11140 TTTCAAGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 9 0.30
20 3 0.10
21 18 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAATATAAATATATAA
Found at i:11112 original size:6 final size:6
Alignment explanation
Indices: 11088--11139 Score: 65
Period size: 6 Copynumber: 9.0 Consensus size: 6
11078 TTATATAATT
*
11088 ATATAA ATAATAT ATATAA ATATAA ATAT-A A-AT-A ATATAA ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
11134 ATATAA
1 ATATAA
11140 TTTCAAGATC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 28 0.68
7 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:13105 original size:23 final size:23
Alignment explanation
Indices: 13079--13124 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
13069 TATATTGTAA
13079 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
13102 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
13125 GGGGAGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (23 bp):
CCAATCATTTATCTTATTACTTG
Found at i:18632 original size:21 final size:21
Alignment explanation
Indices: 18608--18651 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
18598 GATTCTTTGC
18608 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
18629 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
18650 TT
1 TT
18652 ATAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTGAGATTTTATCTGATCTA
Found at i:18659 original size:21 final size:21
Alignment explanation
Indices: 18608--18659 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
18598 GATTCTTTGC
*
18608 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
18629 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
18650 TTAT-AAATTT
1 TT-TGAAATTT
18660 GTATATCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTGAAATTTTATCTGATCTA
Found at i:18855 original size:20 final size:20
Alignment explanation
Indices: 18830--18908 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
18820 AACAATCAAA
18830 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
***
18850 TAAAATGAAAATAAAA-AAA
1 TAAAATGAAAATAAAATTTT
*
18869 AAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
18889 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
18909 CGCGGGCGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.30
20 35 0.70
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAATGAAAATAAAATTTT
Found at i:19183 original size:24 final size:25
Alignment explanation
Indices: 19140--19203 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
19130 TGGAGCCTTA
**
19140 ATTTAATATTTAATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
19165 ATTTAATAAA-AATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
19189 ATTTAATAAATAATA
1 ATTTAATAAATAATA
19204 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAATAAATAATAAAAATTTAAT
Found at i:19198 original size:18 final size:18
Alignment explanation
Indices: 19139--19177 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
19129 ATGGAGCCTT
19139 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
19157 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
19175 AAT
1 AAT
19178 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATATTTAATAAA
Found at i:19204 original size:14 final size:14
Alignment explanation
Indices: 19185--19212 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19175 AATAAAAATT
19185 TAATATTTAATAAA
1 TAATATTTAATAAA
19199 TAATATTTAATAAA
1 TAATATTTAATAAA
19213 AAAATTTGTT
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:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTTAATAAA
Found at i:19217 original size:18 final size:18
Alignment explanation
Indices: 19143--19217 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
19133 AGCCTTAATT
**
19143 TAATATTTAATAAAAATT
1 TAATATTTAATAAAAAAA
19161 TAATATTTAATAAAAATAA
1 TAATATTTAATAAAAA-AA
*
19180 -AA-ATTTAATATTTAATAAA
1 TAATATTTAATA---AAAAAA
19199 TAATATTTAATAAAAAAA
1 TAATATTTAATAAAAAAA
19217 T
1 T
19218 TTGTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 8 0.17
18 24 0.51
19 2 0.04
20 5 0.11
21 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATTTAATAAAAAAA
Found at i:21387 original size:15 final size:15
Alignment explanation
Indices: 21367--21396 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21357 TTTTTTAGTG
21367 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
21382 AACGTGTCATTTTTT
1 AACGTGTCATTTTTT
21397 TTTTTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
AACGTGTCATTTTTT
Found at i:21999 original size:14 final size:14
Alignment explanation
Indices: 21982--22012 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
21972 GATGGATATA
21982 TATCGTATAATTCT
1 TATCGTATAATTCT
21996 TATCGTATAATTCT
1 TATCGTATAATTCT
22010 TAT
1 TAT
22013 ATATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:23324 original size:18 final size:18
Alignment explanation
Indices: 23298--23338 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
23288 TAATGTTCAT
*
23298 ATATTATCATATAATAGA
1 ATATAATCATATAATAGA
23316 ATATAATCATATAATAGA
1 ATATAATCATATAATAGA
23334 ATATA
1 ATATA
23339 CAACAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
ATATAATCATATAATAGA
Found at i:23518 original size:10 final size:10
Alignment explanation
Indices: 23503--23554 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
23493 TTCAAAAATC
23503 ATCATATAAT
1 ATCATATAAT
23513 ATCATATAAT
1 ATCATATAAT
*
23523 AATGA-ATAAT
1 -ATCATATAAT
23533 CAT-ATAATAAT
1 -ATCAT-ATAAT
23544 ATCATATAAT
1 ATCATATAAT
23554 A
1 A
23555 AGGAGTATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 1 0.03
10 25 0.69
11 10 0.28
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (10 bp):
ATCATATAAT
Found at i:23524 original size:13 final size:14
Alignment explanation
Indices: 23503--23555 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
23493 TTCAAAAATC
*
23503 ATCATATAAT-ATC
1 ATCATATAATAATA
23516 AT-ATAATAATGAATA
1 ATCAT-ATAAT-AATA
23531 ATCATATAATAAT-
1 ATCATATAATAATA
23544 ATCATATAATAA
1 ATCATATAATAA
23556 GGAGTATTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 2 0.06
13 19 0.54
14 3 0.09
15 9 0.26
16 2 0.06
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (14 bp):
ATCATATAATAATA
Found at i:24157 original size:179 final size:180
Alignment explanation
Indices: 23534--24275 Score: 1407
Period size: 180 Copynumber: 4.1 Consensus size: 180
23524 ATGAATAATC
*
23534 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCAATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
23599 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
23664 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
131 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
23714 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
23779 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
23844 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
131 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
23894 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
23959 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
24024 AATCAAAGACGC-AAAAAAAAAACTATATTGACAAAATGAATAATCATAT
131 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
24073 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
*
24138 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATCAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
*
24203 AATCAAAGACGCAAAAAAAAAAAAACTATATTGACAAAATGAATAATCAGAT
131 AATCAAAGACGC--AAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
* *
24255 -GAGAATAATATCATATAATAA
1 ATATAATAATATCATATAATAA
24276 TGAATAATCC
Statistics
Matches: 554, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
179 178 0.32
180 321 0.58
181 19 0.03
182 36 0.06
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (180 bp):
ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATAT
Found at i:24194 original size:359 final size:361
Alignment explanation
Indices: 23534--24275 Score: 1409
Period size: 359 Copynumber: 2.1 Consensus size: 361
23524 ATGAATAATC
23534 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCAATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCAATTCGCCGGTATGTAGAAATTG
23599 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
23664 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATATATATAATAATATCAT
131 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATATATATAATAATATCAT
23729 ATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTGATGGACAATTTATTC
196 ATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTGATGGACAATTTATTC
*
23794 TATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATTAATCAAAGACGC-AA
261 TATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATCAAATTAATCAAAGACGCAAA
*
23858 AAAAAAAAACTATATTGACAAAATGAATAATCATAT
326 AAAAAAAAACTATATTGACAAAATGAATAATCAGAT
*
23894 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTG
1 ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCAATTCGCCGGTATGTAGAAATTG
23959 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
66 ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
24024 AATCAAAGACGC-AAAAAAAAAACTATATTGACAAAATGAATAATCATATATATAATAATATCAT
131 AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATATATATAATAATATCAT
24088 ATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTGATGGACAATTTATTC
196 ATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTGATGGACAATTTATTC
24153 TATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATCAAATTAATCAAAGACGCAAA
261 TATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATCAAATTAATCAAAGACGC-AA
24218 AAAAAAAAAACTATATTGACAAAATGAATAATCAGAT
325 AAAAAAAAAACTATATTGACAAAATGAATAATCAGAT
* *
24255 -GAGAATAATATCATATAATAA
1 ATATAATAATATCATATAATAA
24276 TGAATAATCC
Statistics
Matches: 375, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
359 178 0.47
360 160 0.43
361 37 0.10
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (361 bp):
ATATAATAATATCATATAATAAGGAGTATTGATTATCGAACCAATTCGCCGGTATGTAGAAATTG
ATGGACAATTTATTCTATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATGAAATT
AATCAAAGACGCAAAAAAAAAAACTATATTGACAAAATGAATAATCATATATATAATAATATCAT
ATAATAAGGAGTATTGATTATCGAACCGATTCGCCGGTATGTAGAAATTGATGGACAATTTATTC
TATATCAAACTATAAGTATTTCATTGGTTCATAAAAATAAACATCAAATTAATCAAAGACGCAAA
AAAAAAAAACTATATTGACAAAATGAATAATCAGAT
Found at i:24306 original size:13 final size:13
Alignment explanation
Indices: 24288--24312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24278 AATAATCCAG
24288 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
24301 AAAAAAAAAAAA
1 AAAAAAAAAAAA
24313 ATTAGGGGGT
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:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:24951 original size:48 final size:48
Alignment explanation
Indices: 24895--24991 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
24885 AATTGGTCAT
* *
24895 ATTTTATTAATGAAATGGGTTGGATTGGTATTAGTCTGGATACAAAAA
1 ATTTTATTAATGAAATGGGTTGGAGTGGTATTAGCCTGGATACAAAAA
24943 ATTTTATTAATGAAATGGGTTGGAGTGGTATTAGCCTGGATACAAAAA
1 ATTTTATTAATGAAATGGGTTGGAGTGGTATTAGCCTGGATACAAAAA
24991 A
1 A
24992 GGACTTTTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (48 bp):
ATTTTATTAATGAAATGGGTTGGAGTGGTATTAGCCTGGATACAAAAA
Found at i:25192 original size:9 final size:9
Alignment explanation
Indices: 25178--25209 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
25168 AGAAAAGGGC
25178 AGGAATTGG
1 AGGAATTGG
*
25187 AGGAATTGA
1 AGGAATTGG
25196 AGGAATTGG
1 AGGAATTGG
25205 AGGAA
1 AGGAA
25210 AGGGAGGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (9 bp):
AGGAATTGG
Found at i:25217 original size:18 final size:18
Alignment explanation
Indices: 25171--25218 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
25161 AAGCCGAAGA
25171 AAAGGGCAGGAATTGGAGG
1 AAAGGG-AGGAATTGGAGG
** *
25190 AATTGAAGGAATTGGAGG
1 AAAGGGAGGAATTGGAGG
25208 AAAGGGAGGAA
1 AAAGGGAGGAA
25219 GAAACAAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.42, C:0.02, G:0.44, T:0.12
Consensus pattern (18 bp):
AAAGGGAGGAATTGGAGG
Found at i:25761 original size:15 final size:15
Alignment explanation
Indices: 25741--25774 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
25731 AAAGAGAGTC
25741 GAATATTTAGATAAG
1 GAATATTTAGATAAG
*
25756 GAATATTTATATAAG
1 GAATATTTAGATAAG
25771 GAAT
1 GAAT
25775 CTTTTGATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (15 bp):
GAATATTTAGATAAG
Found at i:25837 original size:12 final size:12
Alignment explanation
Indices: 25814--26126 Score: 364
Period size: 12 Copynumber: 26.3 Consensus size: 12
25804 ACTCGATTTT
*
25814 CTAATTATGAAA
1 CTAATAATGAAA
25826 CTAATGAA-GAAA
1 CTAAT-AATGAAA
25838 CTAATAATGAAA
1 CTAATAATGAAA
25850 CTAATAATGAAA
1 CTAATAATGAAA
25862 CTAATAATGAAA
1 CTAATAATGAAA
25874 CTAATAATGAAGAAA
1 CTAATAAT---GAAA
* *
25889 CTACTACTGAAA
1 CTAATAATGAAA
25901 CTAATAATGAAA
1 CTAATAATGAAA
25913 CTAATAATGAAA
1 CTAATAATGAAA
25925 CTAATAATGAAA
1 CTAATAATGAAA
25937 CTAATAATGAAA
1 CTAATAATGAAA
25949 CTAATAATGAAA
1 CTAATAATGAAA
25961 CTAA-AA-GAAA
1 CTAATAATGAAA
*
25971 -TAATGAAATTAAAA
1 CTAAT--AA-TGAAA
**
25985 GAAATAATGAAA
1 CTAATAATGAAA
25997 CTAATAATGAAA
1 CTAATAATGAAA
26009 CTAATAATGAAA
1 CTAATAATGAAA
26021 CTAATAATGAAA
1 CTAATAATGAAA
26033 CTAA-AA-G--A
1 CTAATAATGAAA
26041 --AATAATGAAA
1 CTAATAATGAAA
26051 CTAA-AA-GAAA
1 CTAATAATGAAA
*
26061 -TAATGAAACTAAAA
1 CTAAT--AA-TGAAA
**
26075 GAAATAATGAAA
1 CTAATAATGAAA
26087 CTAATAATGAAA
1 CTAATAATGAAA
26099 CTAATAATGAAA
1 CTAATAATGAAA
26111 CTAATAATGAAA
1 CTAATAATGAAA
26123 CTAA
1 CTAA
26127 AATAAAATAC
Statistics
Matches: 263, Mismatches: 15, Indels: 46
0.81 0.05 0.14
Matches are distributed among these distances:
6 2 0.01
7 2 0.01
8 2 0.01
9 6 0.02
10 10 0.04
11 8 0.03
12 206 0.78
13 5 0.02
14 6 0.02
15 16 0.06
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.23
Consensus pattern (12 bp):
CTAATAATGAAA
Found at i:25974 original size:18 final size:18
Alignment explanation
Indices: 25951--26128 Score: 197
Period size: 18 Copynumber: 9.9 Consensus size: 18
25941 TAATGAAACT
25951 AATAATGAAACTAAAAGA
1 AATAATGAAACTAAAAGA
*
25969 AATAATGAAATTAAAAGA
1 AATAATGAAACTAAAAGA
25987 AATAATGAAACTAATAATGA
1 AATAATGAAACTAA-AA-GA
* **
26007 AACTAAT--AA-TGAAACT
1 AA-TAATGAAACTAAAAGA
26023 AATAATGAAACTAAAAGA
1 AATAATGAAACTAAAAGA
26041 AATAATGAAACTAAAAGA
1 AATAATGAAACTAAAAGA
26059 AATAATGAAACTAAAAGA
1 AATAATGAAACTAAAAGA
26077 AATAATGAAACTAATAATGA
1 AATAATGAAACTAA-AA-GA
* **
26097 AACTAAT--AA-TGAAACT
1 AA-TAATGAAACTAAAAGA
26113 AATAATGAAACTAAAA
1 AATAATGAAACTAAAA
26129 TAAAATACTT
Statistics
Matches: 136, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.06
16 4 0.03
17 8 0.06
18 92 0.68
19 8 0.06
20 8 0.06
21 8 0.06
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (18 bp):
AATAATGAAACTAAAAGA
Found at i:26403 original size:72 final size:72
Alignment explanation
Indices: 26286--26724 Score: 878
Period size: 72 Copynumber: 6.1 Consensus size: 72
26276 ATTACGAATT
26286 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
1 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
26351 CAGAAGA
66 CAGAAGA
26358 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
1 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
26423 CAGAAGA
66 CAGAAGA
26430 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
1 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
26495 CAGAAGA
66 CAGAAGA
26502 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
1 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
26567 CAGAAGA
66 CAGAAGA
26574 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
1 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
26639 CAGAAGA
66 CAGAAGA
26646 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
1 TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
26711 CAGAAGA
66 CAGAAGA
26718 TGAACAG
1 TGAACAG
26725 GGAAATATCG
Statistics
Matches: 367, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 367 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (72 bp):
TGAACAGACAATAGATACACTCAAATCATTATCAACAGAAAAAGAACTTTCTTTATTGACAGAAA
CAGAAGA
Found at i:26846 original size:21 final size:21
Alignment explanation
Indices: 26820--26864 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
26810 TAAAAAAATC
26820 TAATGGAATAAAAGAAATAAG
1 TAATGGAATAAAAGAAATAAG
26841 TAATGGAATAAAAGAAATAAG
1 TAATGGAATAAAAGAAATAAG
26862 TAA
1 TAA
26865 AGAAGTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (21 bp):
TAATGGAATAAAAGAAATAAG
Found at i:27394 original size:51 final size:52
Alignment explanation
Indices: 27339--27447 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 52
27329 ACGAAGAGAT
*
27339 AAGAGAAAGCATAGAAAAGATACAAGAAA-GAGAC-AAAGAGGAAGAAAAAAG
1 AAGAGAAAGCATAGAAAAGATACAA-AAAGGAGACAAAAGAGAAAGAAAAAAG
*
27390 AAGAGAAAGCATAGAAGAGATACAAAAAGGAGACAAAAAAGAGAAAGAAAAAAG
1 AAGAGAAAGCATAGAAAAGATACAAAAAGGAGAC--AAAAGAGAAAGAAAAAAG
27444 AAGA
1 AAGA
27448 CAAGAGTCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
50 3 0.06
51 29 0.56
54 20 0.38
ACGTcount: A:0.66, C:0.06, G:0.25, T:0.04
Consensus pattern (52 bp):
AAGAGAAAGCATAGAAAAGATACAAAAAGGAGACAAAAGAGAAAGAAAAAAG
Found at i:27428 original size:40 final size:37
Alignment explanation
Indices: 27363--27436 Score: 87
Period size: 40 Copynumber: 1.9 Consensus size: 37
27353 AAAAGATACA
*
27363 AGAAAGAGACAAAGAGGAAGAAAAAAGAAGAGAAAGCAT
1 AGAAAGAGACAAAAAGGAAG-AAAAA-AAGAGAAAGCAT
*
27402 AGAAGAGATACAAAAAGG-AGACAAAAAAGAGAAAG
1 AGAA-AGAGACAAAAAGGAAGA-AAAAAAGAGAAAG
27437 AAAAAAGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 10 0.32
39 10 0.32
40 11 0.35
ACGTcount: A:0.65, C:0.05, G:0.27, T:0.03
Consensus pattern (37 bp):
AGAAAGAGACAAAAAGGAAGAAAAAAAGAGAAAGCAT
Found at i:27440 original size:24 final size:25
Alignment explanation
Indices: 27404--27450 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
27394 GAAAGCATAG
* *
27404 AAGAGATAC-AAAAAGGAGACAAAA
1 AAGAGAAACAAAAAAGAAGACAAAA
*
27428 AAGAGAAAGAAAAAAGAAGACAA
1 AAGAGAAACAAAAAAGAAGACAA
27451 GAGTCAGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.02
Consensus pattern (25 bp):
AAGAGAAACAAAAAAGAAGACAAAA
Found at i:27832 original size:24 final size:24
Alignment explanation
Indices: 27805--27876 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
27795 GAAACCCTCT
27805 CATAAAGATCCAATGAAAAAAAAG
1 CATAAAGATCCAATGAAAAAAAAG
27829 CATAAAGATCCAATGAAAAAAAAG
1 CATAAAGATCCAATGAAAAAAAAG
27853 CATAAAGATCCAATGAAAAAAAAG
1 CATAAAGATCCAATGAAAAAAAAG
27877 AAAGTTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (24 bp):
CATAAAGATCCAATGAAAAAAAAG
Found at i:28176 original size:21 final size:21
Alignment explanation
Indices: 28130--28177 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
28120 GAGTTGAGAG
*
28130 AAGAATTGGGCGAAACTAAAA
1 AAGATTTGGGCGAAACTAAAA
28151 AAGATTTGGGCGAAACTAAAA
1 AAGATTTGGGCGAAACTAAAA
28172 AAGATT
1 AAGATT
28178 CGATAATCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.19
Consensus pattern (21 bp):
AAGATTTGGGCGAAACTAAAA
Done.