Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 13 of 147
Found at i:2812838 original size:2 final size:2
Alignment explanation
Indices: 2812833--2812869 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2812823 ATATATATAT
2812833 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2812870 ACCCGACTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2816022 original size:24 final size:23
Alignment explanation
Indices: 2815990--2816071 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
2815980 TTAAACATTT
2815990 TTATAATTTTTGTTATAATTTTAAA
1 TTAT-ATTTTTGTTAT-ATTTTAAA
**
2816015 TTATATTTTATTGTTATA-TTTACG
1 TTATA-TTT-TTGTTATATTTTAAA
*
2816039 TTATGTTATTATGTTATATTTTAAA
1 TTATATT-TT-TGTTATATTTTAAA
2816064 TTAT-TTTT
1 TTATATTTT
2816072 ATTAATTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
23 5 0.11
24 19 0.40
25 16 0.34
26 7 0.15
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.63
Consensus pattern (23 bp):
TTATATTTTTGTTATATTTTAAA
Found at i:2816031 original size:13 final size:12
Alignment explanation
Indices: 2815990--2816061 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
2815980 TTAAACATTT
2815990 TTATAATTTT-TG
1 TTAT-ATTTTATG
**
2816002 TTATAATTTTAAA
1 TTAT-ATTTTATG
2816015 TTATATTTTATTG
1 TTATATTTTA-TG
*
2816028 TTATA-TTTACG
1 TTATATTTTATG
*
2816039 TTATGTTATTATG
1 TTATATT-TTATG
2816052 TTATATTTTA
1 TTATATTTTA
2816062 AATTATTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
11 5 0.10
12 24 0.50
13 19 0.40
ACGTcount: A:0.29, C:0.01, G:0.07, T:0.62
Consensus pattern (12 bp):
TTATATTTTATG
Found at i:2819407 original size:24 final size:24
Alignment explanation
Indices: 2819374--2819422 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2819364 TGAATATTAT
2819374 TCATTCACTATGTGAATTAAAAAC
1 TCATTCACTATGTGAATTAAAAAC
*
2819398 TCATTTACTATGTGAATTAAAAAC
1 TCATTCACTATGTGAATTAAAAAC
2819422 T
1 T
2819423 TACTTCCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (24 bp):
TCATTCACTATGTGAATTAAAAAC
Found at i:2819476 original size:14 final size:16
Alignment explanation
Indices: 2819447--2819479 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2819437 ATTATAATAA
2819447 ATTATAATTATTTTAT
1 ATTATAATTATTTTAT
2819463 ATTATAA-T-TTTTAT
1 ATTATAATTATTTTAT
2819477 ATT
1 ATT
2819480 TTCAAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATAATTATTTTAT
Found at i:2833182 original size:3 final size:3
Alignment explanation
Indices: 2833174--2833217 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2833164 CACAAGTGTA
2833174 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2833218 GGTTTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2836931 original size:23 final size:25
Alignment explanation
Indices: 2836903--2836952 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2836893 TACTTAATTA
*
2836903 TTTAAA-TA-ACATAAGTGATTTTT
1 TTTAAATTATACATAAGTGATCTTT
*
2836926 TTTAAATTATATATAAGTGATCTTT
1 TTTAAATTATACATAAGTGATCTTT
2836951 TT
1 TT
2836953 ATTTAACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 2 0.09
25 15 0.65
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (25 bp):
TTTAAATTATACATAAGTGATCTTT
Found at i:2843542 original size:7 final size:7
Alignment explanation
Indices: 2843530--2843566 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
2843520 AGTAACAATG
2843530 TAAAATA
1 TAAAATA
2843537 TAAAATA
1 TAAAATA
2843544 TAAAATA
1 TAAAATA
2843551 TAAAATA
1 TAAAATA
2843558 TAAAATA
1 TAAAATA
2843565 TA
1 TA
2843567 TATTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAATA
Found at i:2844188 original size:21 final size:22
Alignment explanation
Indices: 2844145--2844195 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2844135 AGGAAAAGAA
*
2844145 TTTT-AAAAATAAATATGATAT
1 TTTTAAAAAATAAATATGAAAT
*
2844166 TTTTAAAAAATAAGTAT-AAAT
1 TTTTAAAAAATAAATATGAAAT
2844187 TTTATAAAA
1 TTT-TAAAA
2844196 TAATTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTTAAAAAATAAATATGAAAT
Found at i:2844189 original size:20 final size:22
Alignment explanation
Indices: 2844143--2844198 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
2844133 GAAGGAAAAG
2844143 AATTTT-AAAAATAAATATGAT
1 AATTTTAAAAAATAAATATGAT
* *
2844164 ATTTTTAAAAAATAAGTAT-A-
1 AATTTTAAAAAATAAATATGAT
*
2844184 AATTTTATAAAATAA
1 AATTTTAAAAAATAA
2844199 TTTTATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 13 0.43
21 6 0.20
22 11 0.37
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (22 bp):
AATTTTAAAAAATAAATATGAT
Found at i:2844237 original size:15 final size:16
Alignment explanation
Indices: 2844206--2844239 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2844196 TAATTTTATC
2844206 TTTTAAAAATAATAAT
1 TTTTAAAAATAATAAT
*
2844222 TTTTTAAAATAA-AAT
1 TTTTAAAAATAATAAT
2844237 TTT
1 TTT
2844240 ATTTTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAAAAATAATAAT
Found at i:2845570 original size:24 final size:25
Alignment explanation
Indices: 2845537--2845591 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
2845527 GAGTAATACC
*
2845537 ATATAAAAATAATAC-AAAAAAATT
1 ATATATAAATAATACAAAAAAAATT
2845561 ATATATAAATAATACAAAAAAAATT
1 ATATATAAATAATACAAAAAAAATT
2845586 ATATAT
1 ATATAT
2845592 GTGTTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
ATATATAAATAATACAAAAAAAATT
Found at i:2845885 original size:30 final size:30
Alignment explanation
Indices: 2845832--2845898 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2845822 AATTAGTTAT
2845832 TTAAT-ATTATATAAAAATTATTTTAAATA
1 TTAATAATTATATAAAAATTATTTTAAATA
* **
2845861 TTAATAATTAGTAT-AAATTTATTTTTTATA
1 TTAATAATTA-TATAAAAATTATTTTAAATA
2845891 TTAATAAT
1 TTAATAAT
2845899 ATAAATACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 25 0.76
31 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
TTAATAATTATATAAAAATTATTTTAAATA
Found at i:2846032 original size:27 final size:27
Alignment explanation
Indices: 2845988--2846040 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2845978 TTTGATATTA
2845988 AAAATTAATATAGTTATA-ATATAAATT
1 AAAATTAATATAGTTATATAT-TAAATT
*
2846015 AAAATTTATATA-TATATATATTAAAT
1 AAAATTAATATAGT-TATATATTAAAT
2846041 ACATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 20 0.87
28 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
AAAATTAATATAGTTATATATTAAATT
Found at i:2846247 original size:29 final size:29
Alignment explanation
Indices: 2846166--2846239 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
2846156 TCTTATTTTT
*
2846166 GTATATATTTGTGTTAACCATGTTTATTC
1 GTATATATTTGTGTTAATCATGTTTATTC
* * *
2846195 ATTTATATTTGTATTAATCATGTTTATTC
1 GTATATATTTGTGTTAATCATGTTTATTC
*
2846224 GTATATATTCGTGTTA
1 GTATATATTTGTGTTA
2846240 TTTATGTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.54
Consensus pattern (29 bp):
GTATATATTTGTGTTAATCATGTTTATTC
Found at i:2847232 original size:22 final size:22
Alignment explanation
Indices: 2847180--2847232 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2847170 ATCCGATTCG
2847180 AAATTAATAAAATATTATTTTTT
1 AAATT-ATAAAATATTATTTTTT
*
2847203 AAAATATAAAATATTATTTTTT
1 AAATTATAAAATATTATTTTTT
*
2847225 TAATTATA
1 AAATTATA
2847233 TAATTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTATAAAATATTATTTTTT
Found at i:2847282 original size:14 final size:13
Alignment explanation
Indices: 2847255--2847279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2847245 TAAAAAAATT
2847255 AAAAATAATTTTA
1 AAAAATAATTTTA
2847268 AAAAATAATTTT
1 AAAAATAATTTT
2847280 TAATATAATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:2848132 original size:10 final size:10
Alignment explanation
Indices: 2848117--2848141 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2848107 ATTTAAAACC
2848117 AATCCAGCAA
1 AATCCAGCAA
2848127 AATCCAGCAA
1 AATCCAGCAA
2848137 AATCC
1 AATCC
2848142 GGCCCTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.32, G:0.08, T:0.12
Consensus pattern (10 bp):
AATCCAGCAA
Found at i:2857394 original size:21 final size:21
Alignment explanation
Indices: 2857338--2857394 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
2857328 AAATCAACCG
2857338 ATCTATTTTGTAAATAGATCA
1 ATCTATTTTGTAAATAGATCA
* * *
2857359 AT-T-TTTTTTAAAAATGAATTA
1 ATCTATTTTGTAAATA-G-ATCA
2857380 ATCTATTTTGTAAAT
1 ATCTATTTTGTAAAT
2857395 TACCTCTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 7 0.26
22 1 0.04
23 8 0.30
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (21 bp):
ATCTATTTTGTAAATAGATCA
Found at i:2858456 original size:3 final size:3
Alignment explanation
Indices: 2858448--2858482 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2858438 ATTCATTAGT
2858448 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2858483 TAGAAATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2865905 original size:48 final size:48
Alignment explanation
Indices: 2865814--2865906 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
2865804 CTTGAAGTTG
* * *
2865814 AAAAAACGACCTAATTGTTCGACTCCTTGTCGTGAAGTTTATAAACTA
1 AAAAAACGACCTAATCGTTCGAATCCTTGTCGTGAAGTATATAAACTA
* *
2865862 AAAAAATGACCTAATCGTTCGAATCTTTGTCGTAGAA-TATATAAA
1 AAAAAACGACCTAATCGTTCGAATCCTTGTCGT-GAAGTATATAAA
2865907 TTATACGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 36 0.92
49 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (48 bp):
AAAAAACGACCTAATCGTTCGAATCCTTGTCGTGAAGTATATAAACTA
Found at i:2867693 original size:2 final size:2
Alignment explanation
Indices: 2867686--2867724 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2867676 ACACCCACCA
2867686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2867725 CACACACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2874529 original size:14 final size:14
Alignment explanation
Indices: 2874510--2874547 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2874500 CAAATCTACT
2874510 ATTTATAATATAAA
1 ATTTATAATATAAA
* *
2874524 ATTTATAAT-TTAT
1 ATTTATAATATAAA
2874537 ATTTATAATAT
1 ATTTATAATAT
2874548 CATTGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATAATATAAA
Found at i:2874847 original size:16 final size:16
Alignment explanation
Indices: 2874828--2874886 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
2874818 AATTTTATTT
*
2874828 TAATTTAAACTTAAAA
1 TAATTTAAATTTAAAA
2874844 TAATTT-AATTTAAAAA
1 TAATTTAAATTT-AAAA
*
2874860 TTATTTAAATTTTAAAA
1 TAATTTAAA-TTTAAAA
*
2874877 AAATTTAAAT
1 TAATTTAAAT
2874887 ACAATATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 4 0.11
16 16 0.44
17 13 0.36
18 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:2874876 original size:17 final size:17
Alignment explanation
Indices: 2874828--2874886 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
2874818 AATTTTATTT
*
2874828 TAATTTAAA-CTTAAAA
1 TAATTTAAATTTTAAAA
*
2874844 TAATTT-AATTTAAAAA
1 TAATTTAAATTTTAAAA
*
2874860 TTATTTAAATTTTAAAA
1 TAATTTAAATTTTAAAA
*
2874877 AAATTTAAAT
1 TAATTTAAAT
2874887 ACAATATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 2 0.06
16 16 0.46
17 17 0.49
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTAAATTTTAAAA
Found at i:2879833 original size:27 final size:27
Alignment explanation
Indices: 2879802--2879868 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
2879792 TTTTTTTTAG
2879802 TATGTATAAAATTTTTTTACTAAAATA
1 TATGTATAAAATTTTTTTACTAAAATA
* *
2879829 TATGTATAAAAGTTTTTTACTAAAATT
1 TATGTATAAAATTTTTTTACTAAAATA
2879856 TCATGTATAAAAT
1 T-ATGTATAAAAT
2879869 ATATGTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 26 0.72
28 10 0.28
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (27 bp):
TATGTATAAAATTTTTTTACTAAAATA
Found at i:2880367 original size:26 final size:25
Alignment explanation
Indices: 2880322--2880392 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 25
2880312 GCAATTAAAT
*
2880322 AAATATAATAATTTAAAATACGATTCAA
1 AAATATAA-AATTTAAAATA--ATACAA
*
2880350 TAATATAAAA-TTAAAATAATACAA
1 AAATATAAAATTTAAAATAATACAA
2880374 AAATATTAAAATTTAAAAT
1 AAATA-TAAAATTTAAAAT
2880393 TTTAATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
24 9 0.24
25 5 0.13
26 15 0.39
27 2 0.05
28 7 0.18
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (25 bp):
AAATATAAAATTTAAAATAATACAA
Found at i:2881168 original size:2 final size:2
Alignment explanation
Indices: 2881161--2881186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2881151 GGAAGTTTAA
2881161 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2881187 GAATAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2888992 original size:8 final size:8
Alignment explanation
Indices: 2888979--2889003 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2888969 TTACAGCTGG
2888979 TTGTAATC
1 TTGTAATC
2888987 TTGTAATC
1 TTGTAATC
2888995 TTGTAATC
1 TTGTAATC
2889003 T
1 T
2889004 ATATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTAATC
Found at i:2891104 original size:36 final size:36
Alignment explanation
Indices: 2891064--2891144 Score: 83
Period size: 37 Copynumber: 2.2 Consensus size: 36
2891054 CAATTCAATG
*
2891064 CAAAAGCAAAGTTTTCAAA-CAAAACGCAATTCAGCA
1 CAAAAGCAAAGTTTTCAAATCAAAA-GCAATCCAGCA
* * * * *
2891100 CAAAAAGAAAATTTTTTAAATTAAAATCAATCCAGCA
1 C-AAAAGCAAAGTTTTCAAATCAAAAGCAATCCAGCA
2891137 CAAAAGCA
1 CAAAAGCA
2891145 CGACTTTCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
36 7 0.19
37 25 0.69
38 4 0.11
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.20
Consensus pattern (36 bp):
CAAAAGCAAAGTTTTCAAATCAAAAGCAATCCAGCA
Found at i:2891191 original size:24 final size:25
Alignment explanation
Indices: 2891163--2891216 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2891153 AAGTTAGACA
* *
2891163 CAATTCAATTAAAAAGTAAAA-TTT
1 CAATTCAATGAAAAAGCAAAACTTT
*
2891187 CAATT-AATGCAAAAGCAAAACTTT
1 CAATTCAATGAAAAAGCAAAACTTT
2891211 CAATTC
1 CAATTC
2891217 CAACTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.30
Consensus pattern (25 bp):
CAATTCAATGAAAAAGCAAAACTTT
Found at i:2891282 original size:35 final size:35
Alignment explanation
Indices: 2891197--2891341 Score: 132
Period size: 35 Copynumber: 4.1 Consensus size: 35
2891187 CAATTAATGC
* * * *
2891197 AAAAGCAAAACTTTC-AATTCCAACTCAACTCAGTA
1 AAAATCAAAACTTTCAAATT-AAACCCAATTCAGTA
* * * * *
2891232 GAAAAGCAACACTTTCAAATTAACCCCAATTTAGCA
1 -AAAATCAAAACTTTCAAATTAAACCCAATTCAGTA
* * *
2891268 AAAA-GAAAAGCTTTCAAATCAAACCCAATTCAATA
1 AAAATCAAAA-CTTTCAAATTAAACCCAATTCAGTA
*
2891303 AAAATCAAAACTTTCAATTTAAACCCAATTCAGTA
1 AAAATCAAAACTTTCAAATTAAACCCAATTCAGTA
2891338 AAAA
1 AAAA
2891342 ATAATAATAA
Statistics
Matches: 88, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
34 3 0.03
35 54 0.61
36 27 0.31
37 4 0.05
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.23
Consensus pattern (35 bp):
AAAATCAAAACTTTCAAATTAAACCCAATTCAGTA
Found at i:2891341 original size:70 final size:71
Alignment explanation
Indices: 2891197--2891341 Score: 168
Period size: 70 Copynumber: 2.1 Consensus size: 71
2891187 CAATTAATGC
* * * * * *
2891197 AAAAGCAAAACTTTCAATTCCAACTCAACTCAGTAGAAAAGCAACACTTTCAAATTAACCCCAAT
1 AAAAGCAAAACTTTCAAATCAAACCCAACTCAATAGAAAAGCAAAACTTTCAAATTAAACCCAAT
*
2891262 TTAGCA
66 TCAGCA
* * *
2891268 AAAAG-AAAAGCTTTCAAATCAAACCCAATTCAATA-AAAATCAAAACTTTCAATTTAAACCCAA
1 AAAAGCAAAA-CTTTCAAATCAAACCCAACTCAATAGAAAAGCAAAACTTTCAAATTAAACCCAA
*
2891331 TTCAGTA
65 TTCAGCA
2891338 AAAA
1 AAAA
2891342 ATAATAATAA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
70 37 0.60
71 25 0.40
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.23
Consensus pattern (71 bp):
AAAAGCAAAACTTTCAAATCAAACCCAACTCAATAGAAAAGCAAAACTTTCAAATTAAACCCAAT
TCAGCA
Found at i:2891966 original size:22 final size:23
Alignment explanation
Indices: 2891918--2891969 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2891908 TTAATTTAAA
*
2891918 ATTTATTATAGTTTACTTTATCT
1 ATTTATTATAGTTTACTTTAACT
*
2891941 ATTTATTAT-GTTTA-TTTAAGT
1 ATTTATTATAGTTTACTTTAACT
2891962 GATTTATT
1 -ATTTATT
2891970 TGCAAAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.19
22 12 0.46
23 9 0.35
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.62
Consensus pattern (23 bp):
ATTTATTATAGTTTACTTTAACT
Found at i:2892082 original size:16 final size:17
Alignment explanation
Indices: 2892049--2892091 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
2892039 GTTGCCAATT
2892049 TTATTTATAAATTTAAAA
1 TTATTT-TAAATTTAAAA
2892067 TTATTTTAAA-TTAAAA
1 TTATTTTAAATTTAAAA
2892083 TTATCTTTA
1 TTAT-TTTA
2892092 TTACGTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTTAAATTTAAAA
Found at i:2894453 original size:16 final size:16
Alignment explanation
Indices: 2894432--2894463 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2894422 TTATTTGAAA
*
2894432 TTAATTTTTTTATAAT
1 TTAATTATTTTATAAT
2894448 TTAATTATTTTATAAT
1 TTAATTATTTTATAAT
2894464 ATTATTGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTAATTATTTTATAAT
Found at i:2896805 original size:30 final size:29
Alignment explanation
Indices: 2896731--2896806 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
2896721 GACCTAAAAT
* *
2896731 TAATAAAATATT-ATTTTTTAAATATAAA
1 TAATAAAATATTAATTATATAAATATAAA
* * * *
2896759 TATTTAAATTTATAATTATATAAATATATA
1 TAATAAAATAT-TAATTATATAAATATAAA
2896789 TAAATAAAATATTAATTA
1 T-AATAAAATATTAATTA
2896807 AAAAAATTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
28 8 0.22
29 1 0.03
30 20 0.56
31 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAATAAAATATTAATTATATAAATATAAA
Found at i:2909532 original size:29 final size:29
Alignment explanation
Indices: 2909485--2909544 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
2909475 CACCAAAAGT
2909485 ATCACTGAGCTCGGACTTGGTTCGATCAA
1 ATCACTGAGCTCGGACTTGGTTCGATCAA
2909514 ATCACTGAGCTCAGG-CTTGGTTCGATCAA
1 ATCACTGAGCTC-GGACTTGGTTCGATCAA
2909543 AT
1 AT
2909545 TAGACCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (29 bp):
ATCACTGAGCTCGGACTTGGTTCGATCAA
Found at i:2910699 original size:52 final size:52
Alignment explanation
Indices: 2910599--2910708 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
2910589 AGCACTCCTG
* ** * * *
2910599 CTAAATGCAGCTGTCACAGTCTCTAGACTTGGAATGCATAGATTCCAAGTCC
1 CTAAATGCAGCTGTCAAAGTCTCTAGACTTAAAAGGCATAAATCCCAAGTCC
*
2910651 CTAAATGCAGCTGTCAAAGTCTCTAGACTTAAAAGGTATAAATCCCAAGTCC
1 CTAAATGCAGCTGTCAAAGTCTCTAGACTTAAAAGGCATAAATCCCAAGTCC
2910703 CATAAA
1 C-TAAA
2910709 ATAAGAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 46 0.92
53 4 0.08
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (52 bp):
CTAAATGCAGCTGTCAAAGTCTCTAGACTTAAAAGGCATAAATCCCAAGTCC
Found at i:2911956 original size:16 final size:18
Alignment explanation
Indices: 2911927--2911966 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
2911917 AACTACAAAA
2911927 AAATAA-AATAAAATAAT
1 AAATAATAATAAAATAAT
2911944 -AATAATAAT-AAATAAT
1 AAATAATAATAAAATAAT
2911960 AAATAAT
1 AAATAAT
2911967 TCATCAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAATAATAAAATAAT
Found at i:2914024 original size:6 final size:6
Alignment explanation
Indices: 2914015--2914079 Score: 67
Period size: 6 Copynumber: 10.3 Consensus size: 6
2914005 TAGAGGTGGA
* * *
2914015 GGAGGT GGAGGT GGAGGT GGTGAT GGAGATGAT GGAGGT GGAGGT GGAGGC
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAG--G-T GGAGGT GGAGGT GGAGGT
*
2914066 GGAAGT GGAGGT GG
1 GGAGGT GGAGGT GG
2914080 TGAAGGTGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 42 0.88
7 1 0.02
9 5 0.10
ACGTcount: A:0.20, C:0.02, G:0.62, T:0.17
Consensus pattern (6 bp):
GGAGGT
Found at i:2914087 original size:33 final size:33
Alignment explanation
Indices: 2914007--2914088 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
2913997 AGCGTTGGTA
* * *
2914007 GAGGTGGAGGAGGTGGAGGTGGAGGTGGTGATG
1 GAGGTGGTGGAGGTGGAGGTGGAGGCGGAGATG
* *
2914040 GAGATGATGGAGGTGGAGGTGGAGGCGGA-AGTG
1 GAGGTGGTGGAGGTGGAGGTGGAGGCGGAGA-TG
*
2914073 GAGGTGGTGAAGGTGG
1 GAGGTGGTGGAGGTGG
2914089 CAAAGGTGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.21, C:0.01, G:0.61, T:0.17
Consensus pattern (33 bp):
GAGGTGGTGGAGGTGGAGGTGGAGGCGGAGATG
Found at i:2915785 original size:101 final size:101
Alignment explanation
Indices: 2915610--2915812 Score: 336
Period size: 101 Copynumber: 2.0 Consensus size: 101
2915600 CACCAAATAA
* *
2915610 ATTCAGTATTTGAGAGTAATTGAATACATTCAAAATCAAGATAGCAGAACCAACCTTTATGATTA
1 ATTCAGTATTTGAAAGTAATTGAACACATTCAAAATCAAGATAGCAGAACCAACCTTTATGATTA
2915675 TGTGAACACTGGGTTATTGAACCAACAAGAAAGAAC
66 TGTGAACACTGGGTTATTGAACCAACAAGAAAGAAC
* * *
2915711 ATTCAGTATTTGAAAGTAACTT-AGCACATTCAAAATCAAGATCGCAGAACCAACCTTTCTGATT
1 ATTCAGTATTTGAAAGTAA-TTGAACACATTCAAAATCAAGATAGCAGAACCAACCTTTATGATT
*
2915775 ATGTGAACACTGGGTTATTGAATCAACAAGAAAGAAC
65 ATGTGAACACTGGGTTATTGAACCAACAAGAAAGAAC
2915812 A
1 A
2915813 GGTCAACTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 93 0.98
102 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (101 bp):
ATTCAGTATTTGAAAGTAATTGAACACATTCAAAATCAAGATAGCAGAACCAACCTTTATGATTA
TGTGAACACTGGGTTATTGAACCAACAAGAAAGAAC
Found at i:2916684 original size:3 final size:3
Alignment explanation
Indices: 2916676--2916705 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2916666 ATATATTAAC
2916676 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2916706 GATAATGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2919735 original size:21 final size:21
Alignment explanation
Indices: 2919706--2919746 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2919696 TGTTATCAGC
*
2919706 CAAACATAAAAGTTCCATTGTA
1 CAAACAT-AAAGATCCATTGTA
2919728 CAAA-ATAAAGATCCATTGT
1 CAAACATAAAGATCCATTGT
2919747 TGTAACCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 2 0.11
22 4 0.22
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (21 bp):
CAAACATAAAGATCCATTGTA
Found at i:2921277 original size:26 final size:26
Alignment explanation
Indices: 2921248--2921299 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2921238 GGGAAAAAAA
2921248 AAGACTTCAATTAGCAAAGTAAAGAC
1 AAGACTTCAATTAGCAAAGTAAAGAC
2921274 AAGACTTCAATTAGCAAAGTAAAGAC
1 AAGACTTCAATTAGCAAAGTAAAGAC
2921300 CACATCAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (26 bp):
AAGACTTCAATTAGCAAAGTAAAGAC
Found at i:2933373 original size:21 final size:21
Alignment explanation
Indices: 2933347--2933390 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2933337 TCCCTTTCAA
2933347 ATTGGGTTGTGAGTGTTAATC
1 ATTGGGTTGTGAGTGTTAATC
2933368 ATTGGGTTGTGAGTGTTAATC
1 ATTGGGTTGTGAGTGTTAATC
2933389 AT
1 AT
2933391 ACTTGGCTTG
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:0.20, C:0.05, G:0.32, T:0.43
Consensus pattern (21 bp):
ATTGGGTTGTGAGTGTTAATC
Found at i:2934010 original size:217 final size:215
Alignment explanation
Indices: 2933622--2934025 Score: 587
Period size: 217 Copynumber: 1.9 Consensus size: 215
2933612 TAAACTTTTA
* * *
2933622 ATTCTTCAAGTAACCTCATCAACCAAATTCTTCACAAATACCATAATGTATTGCTCTAAACTCAG
1 ATTCTCCAAGTAACCTCATCAACCAAATTCTTCACAAATACCATAA-GCATTACTCTAAACTCAG
* * * * *
2933687 CCTTAGTACTGTTCCTAGCTACAACAGCTTGCCTTTTATGTCGCCAATACATAAGTGCATTATCC
65 CCTTAGCACTGTTCATAGCTACAACAACTTGCCTTTTATGTCACCAATACATAAGTGCAATATCC
* * * * * *
2933752 TGTAGTGGACTTTTTATCTATTACTGATCTAGCCCAGTTAGCATCCATGTACACCTTAACTACCA
130 TATAGTGAACCTTTTATCTATTACTGATCCAACACAGTTAGCATCCATGTACACCTTAACTACCA
2933817 TGTCCGTTTACTTCTTAAAGT
195 TGTCCGTTTACTTCTTAAAGT
* *
2933838 ATTCTCCAAGTAACTTCATCAACCAAATTCCTTCACAAATACTATGGAA-CATTACTCTAAACTC
1 ATTCTCCAAGTAACCTCATCAACCAAATT-CTTCACAAATACCAT--AAGCATTACTCTAAACTC
*
2933902 AGCCTTAGCACTGTTCATAGCTACAACAACTTGCTTTTTACT-TCACCAATACATAAGTGCAATA
63 AGCCTTAGCACTGTTCATAGCTACAACAACTTGCCTTTTA-TGTCACCAATACATAAGTGCAATA
*
2933966 TCCTATAGTGAACCTTTTATCTATTACTGATCCAACATAGTTAGCATCCATGTACACCTT
127 TCCTATAGTGAACCTTTTATCTATTACTGATCCAACACAGTTAGCATCCATGTACACCTT
2934026 GATTGCCCTG
Statistics
Matches: 166, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
216 27 0.16
217 136 0.82
218 1 0.01
219 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (215 bp):
ATTCTCCAAGTAACCTCATCAACCAAATTCTTCACAAATACCATAAGCATTACTCTAAACTCAGC
CTTAGCACTGTTCATAGCTACAACAACTTGCCTTTTATGTCACCAATACATAAGTGCAATATCCT
ATAGTGAACCTTTTATCTATTACTGATCCAACACAGTTAGCATCCATGTACACCTTAACTACCAT
GTCCGTTTACTTCTTAAAGT
Found at i:2934141 original size:3 final size:3
Alignment explanation
Indices: 2934135--2934162 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2934125 TTTTAGTTTT
2934135 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2934163 GGTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2935244 original size:3 final size:3
Alignment explanation
Indices: 2935197--2935232 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
2935187 ATTGTTTTAC
*
2935197 AAT AAGT AAT AAT AAT AGT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2935233 CACCAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2935687 original size:31 final size:31
Alignment explanation
Indices: 2935649--2935759 Score: 168
Period size: 31 Copynumber: 3.6 Consensus size: 31
2935639 TAAAATCAAT
2935649 ACCCTAAACCCTTTAAACCTCAAACATTAAA
1 ACCCTAAACCCTTTAAACCTCAAACATTAAA
*
2935680 ACCCTAAACTCTTTAAACCTCAAACATTAAA
1 ACCCTAAACCCTTTAAACCTCAAACATTAAA
* * * *
2935711 ACTCTAAACTCTTTAAACCCCAAACACTAAA
1 ACCCTAAACCCTTTAAACCTCAAACATTAAA
*
2935742 ACCCTAAACCCTTCAAAC
1 ACCCTAAACCCTTTAAAC
2935760 ATTAAAATCA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (31 bp):
ACCCTAAACCCTTTAAACCTCAAACATTAAA
Found at i:2935704 original size:16 final size:15
Alignment explanation
Indices: 2935658--2935735 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
2935648 TACCCTAAAC
2935658 CCTTTAAACCTCAAA
1 CCTTTAAACCTCAAA
* *
2935673 CATTAAAACC-CTAAA
1 CCTTTAAACCTC-AAA
2935688 CTCTTTAAACCTCAAA
1 C-CTTTAAACCTCAAA
* *
2935704 -CATTAAAACTCTAAA
1 CCTTTAAACCTC-AAA
*
2935719 CTCTTTAAACCCCAAA
1 C-CTTTAAACCTCAAA
2935735 C
1 C
2935736 ACTAAAACCC
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.21
15 15 0.31
16 14 0.29
17 9 0.19
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (15 bp):
CCTTTAAACCTCAAA
Found at i:2935786 original size:28 final size:28
Alignment explanation
Indices: 2935739--2935807 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
2935729 CCCAAACACT
2935739 AAAACCCTAAACCCTTCAAACAT-TAAAATC
1 AAAACCCTAAA--CTTCAAAC-TCTAAAATC
*
2935769 AAAATCCTAAACTTCAAACTCTAAAATC
1 AAAACCCTAAACTTCAAACTCTAAAATC
2935797 AAAACCCTAAA
1 AAAACCCTAAA
2935808 AACCGAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 25 0.69
30 10 0.28
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (28 bp):
AAAACCCTAAACTTCAAACTCTAAAATC
Found at i:2942167 original size:29 final size:30
Alignment explanation
Indices: 2942119--2942182 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 30
2942109 AGATAAGACC
*
2942119 CACAAATTATATTCAAAAAAGAAAAAAAAA
1 CACAAATAATATTCAAAAAAGAAAAAAAAA
2942149 CACAAATAATATTC-AAAAAGAAAAAAAAA
1 CACAAATAATATTCAAAAAAGAAAAAAAAA
2942178 CACAA
1 CACAA
2942183 CTATAGCCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.70, C:0.12, G:0.03, T:0.14
Consensus pattern (30 bp):
CACAAATAATATTCAAAAAAGAAAAAAAAA
Found at i:2942195 original size:29 final size:29
Alignment explanation
Indices: 2942134--2942195 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
2942124 ATTATATTCA
**
2942134 AAAAAGAAAAAAAAACACAAATAATATTC
1 AAAAAGAAAAAAAAACACAAATAATAGCC
*
2942163 AAAAAGAAAAAAAAACACAACT-ATAGCC
1 AAAAAGAAAAAAAAACACAAATAATAGCC
*
2942191 TAAAA
1 AAAAA
2942196 TTACTCCTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.71, C:0.13, G:0.05, T:0.11
Consensus pattern (29 bp):
AAAAAGAAAAAAAAACACAAATAATAGCC
Found at i:2947135 original size:25 final size:26
Alignment explanation
Indices: 2947107--2947155 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2947097 ATATATTAAG
2947107 TTAAT-TAAAATTTAGTTTCGAAAAA
1 TTAATATAAAATTTAGTTTCGAAAAA
2947132 TTAATATAAAATTTAGTTTCGAAA
1 TTAATATAAAATTTAGTTTCGAAA
2947156 CTATAACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (26 bp):
TTAATATAAAATTTAGTTTCGAAAAA
Found at i:2955409 original size:18 final size:18
Alignment explanation
Indices: 2955380--2955424 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
2955370 TAATTATAAA
2955380 AATAATAAAATATAA-AGTT
1 AATAA-AAAATA-AATAGTT
*
2955399 AATAAAAAATAAATTGTT
1 AATAAAAAATAAATAGTT
2955417 AATAAAAA
1 AATAAAAA
2955425 TGATTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 17 0.71
19 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AATAAAAAATAAATAGTT
Found at i:2955423 original size:16 final size:16
Alignment explanation
Indices: 2955382--2955423 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
2955372 ATTATAAAAA
2955382 TAATAAAATATAAAGT
1 TAATAAAATATAAAGT
*
2955398 TAATAAAAAATAAATTGT
1 TAATAAAATATAAA--GT
2955416 TAATAAAA
1 TAATAAAA
2955424 ATGATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.57
18 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (16 bp):
TAATAAAATATAAAGT
Found at i:2957977 original size:32 final size:33
Alignment explanation
Indices: 2957941--2958002 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2957931 TGATCCCTCA
*
2957941 TTAAATTTAA-TTAATTTATAT-TTTTTAATTTT
1 TTAAAATTAATTTAATTT-TATGTTTTTAATTTT
*
2957973 TTAAAATTAATTTTATTTTATGTTTTTAAT
1 TTAAAATTAATTTAATTTTATGTTTTTAAT
2958003 AACAAACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (33 bp):
TTAAAATTAATTTAATTTTATGTTTTTAATTTT
Found at i:2958083 original size:29 final size:29
Alignment explanation
Indices: 2958050--2958106 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2958040 TTAAGTCTAA
*
2958050 TCATATAAATAATAATAAAAA-CCCTAGAG
1 TCATACAAATAATAA-AAAAAGCCCTAGAG
2958079 TCATACAAATAATAAAAAAAGCCCTAGA
1 TCATACAAATAATAAAAAAAGCCCTAGA
2958107 CTTGCAAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.21
Consensus pattern (29 bp):
TCATACAAATAATAAAAAAAGCCCTAGAG
Found at i:2970241 original size:48 final size:48
Alignment explanation
Indices: 2970170--2970267 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
2970160 GCTCTAAAAA
2970170 CAACTGTTTTCCAAAGGATGCTTTGGCTTGCATCCAAAGAAGCCTATG
1 CAACTGTTTTCCAAAGGATGCTTTGGCTTGCATCCAAAGAAGCCTATG
2970218 CAACTGTTTTCCAAAGGATGCTTTGGCTTGCATCCAAAGAAGCCTATG
1 CAACTGTTTTCCAAAGGATGCTTTGGCTTGCATCCAAAGAAGCCTATG
2970266 CA
1 CA
2970268 TATCTTCAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (48 bp):
CAACTGTTTTCCAAAGGATGCTTTGGCTTGCATCCAAAGAAGCCTATG
Found at i:2970256 original size:23 final size:23
Alignment explanation
Indices: 2970179--2970256 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
2970169 ACAACTGTTT
2970179 TCCAAAGGATGCTTTGGCTTGCA
1 TCCAAAGGATGCTTTGGCTTGCA
* * * **
2970202 TCCAAA-GAAGCCTAT-GCAACTGTTT
1 TCCAAAGGATG-CTTTGGC--TTG-CA
2970227 TCCAAAGGATGCTTTGGCTTGCA
1 TCCAAAGGATGCTTTGGCTTGCA
2970250 TCCAAAG
1 TCCAAAG
2970257 AAGCCTATGC
Statistics
Matches: 39, Mismatches: 10, Indels: 12
0.64 0.16 0.20
Matches are distributed among these distances:
22 5 0.13
23 16 0.41
24 4 0.10
25 9 0.23
26 5 0.13
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (23 bp):
TCCAAAGGATGCTTTGGCTTGCA
Found at i:2973027 original size:66 final size:66
Alignment explanation
Indices: 2972921--2973045 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
2972911 AGGTTGAAGG
* * * *
2972921 TAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTGTATTCTCCATACTAAG
1 TAATCCATCCAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTGCACTGTATTCTCCATACTAAG
2972986 C
66 C
* * *
2972987 TAATCCATCCAAGCAAAATCATCTGCCCCATATGCATTTTCCTTCACTGTATTCTCCAT
1 TAATCCATCCAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTGCACTGTATTCTCCAT
2973046 TACTTGCTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (66 bp):
TAATCCATCCAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTGCACTGTATTCTCCATACTAAG
C
Found at i:2973249 original size:56 final size:56
Alignment explanation
Indices: 2973168--2973280 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
2973158 TTGAAGGTAA
* * * *
2973168 TCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTGTATTCTCCAT
1 TCCATCCAAGCAAAATCATCTGTCCCAGAAGCATTTTCCTGCACTGTATTCTCCAT
*
2973224 TCCATCCAAGCAAAATCATCTGTCCCAGAAGCATTTTCCTTCACTGTATTCTCCAT
1 TCCATCCAAGCAAAATCATCTGTCCCAGAAGCATTTTCCTGCACTGTATTCTCCAT
2973280 T
1 T
2973281 ACTAGCTCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (56 bp):
TCCATCCAAGCAAAATCATCTGTCCCAGAAGCATTTTCCTGCACTGTATTCTCCAT
Found at i:2973504 original size:66 final size:66
Alignment explanation
Indices: 2973398--2973526 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
2973388 TCCCCGTTGA
* * * *
2973398 AGGTAATACATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGACTGTATTCTCCATTCT
1 AGGTAATACATCCAAGCAAAACCATCTGTCCCAGAGGCATTTTCCTGCACTATATTCTCCATTCT
2973463 G
66 G
* * * *
2973464 AGGTAATCCATCCTAGCAAAACCATCTG-CCTCAGATGCATTTTCCTTCACTATATTCTCCATT
1 AGGTAATACATCCAAGCAAAACCATCTGTCC-CAGAGGCATTTTCCTGCACTATATTCTCCATT
2973527 ACTTGCTCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
65 2 0.04
66 52 0.96
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (66 bp):
AGGTAATACATCCAAGCAAAACCATCTGTCCCAGAGGCATTTTCCTGCACTATATTCTCCATTCT
G
Found at i:2973587 original size:246 final size:246
Alignment explanation
Indices: 2972721--2973948 Score: 1729
Period size: 242 Copynumber: 5.1 Consensus size: 246
2972711 GTTGAAGGAG
* *
2972721 TGTACTCTCCATTCCAAGGTAAAT-CATCCAAGCAAAACCATCTGCCCCAGATGCATTTTCCTTC
1 TGTATTCTCCATTCCAAGGT-AATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTC
* *
2972785 ACTGTATTCTCCATTACTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCTGTGAAGCAGA
65 ACTGTATTCTCCATTACTTGCTCATTCTGAGACTCTGCGACATCTAAGAGATTCAGTGAAGCAGA
* * *
2972850 ACTGCTTTCATTGGCCTCAGAGCTTGGGCCAACAGCACCTGATATTTGAATAAATGAGTCCAGGT
130 ACTGATTTCATTGGCCTCAGTGCTTGGGCCAACAGCACCTGATA-TTGAATAAATGATTCCAGGT
*
2972915 TGAAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAG
194 TGAAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAC
* * * *
2972968 TGTATTCTCCATACTAAGCTAATCCATCCAAGCAAAATCATCTGCCCCATATGCATTTTCCTTCA
1 TGTATTCTCCATTCCAAGGTAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCA
** * *
2973033 CTGTATTCTCCATTACTTGCTCATTCTGACTCTCTGTGACATCTAAGAGA-TAATGTGAAGCAGA
66 CTGTATTCTCCATTACTTGCTCATTCTGAGACTCTGCGACATCTAAGAGATTCA-GTGAAGCAGA
*
2973097 ACTGATTTCATTGGCCTCAGTGATTGAGG-CAACAG--CCTGATATTGAATAAATGATTCCAGGT
130 ACTGATTTCATTGGCCTCAGTGCTTG-GGCCAACAGCACCTGATATTGAATAAATGATTCCAGGT
*
2973159 TGAAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAG
194 TGAAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAC
* *
2973212 TGTA-T-T-C--TCC-A--T--TCCATCCAAGCAAAATCATCTGTCCCAGAAGCATTTTCCTTCA
1 TGTATTCTCCATTCCAAGGTAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCA
* ** * * * *
2973267 CTGTATTCTCCATTACTAGCTCATTCTGACTCTCAGTGACATCTGAGAGATTCAATGAAGCAGAA
66 CTGTATTCTCCATTACTTGCTCATTCTGAGACTCTGCGACATCTAAGAGATTCAGTGAAGCAGAA
* ** * **
2973332 CTGATTTCATTGGCCTCAGTGCTTGGGTCAACAGCACCTTCTATAGAATAAATGATTCCCCGTTG
131 CTGATTTCATTGGCCTCAGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCAGGTTG
*
2973397 AAGGTAATACATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAC
196 AAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAC
** * * *
2973448 TGTATTCTCCATTCTGAGGTAATCCATCCTAGCAAAACCATCTGCCTCAGATGCATTTTCCTTCA
1 TGTATTCTCCATTCCAAGGTAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCA
* * *
2973513 CTATATTCTCCATTACTTGCTCATTTTGAGACTCAGCGACATCTAAGAGATTCAGTGAAGCAGAA
66 CTGTATTCTCCATTACTTGCTCATTCTGAGACTCTGCGACATCTAAGAGATTCAGTGAAGCAGAA
* * * * * *
2973578 CTAATTTCATTGGTCTCAATGCTTAGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTAG
131 CTGATTTCATTGGCCTCAGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCAGGTTG
*
2973643 AAGATAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGA-
196 AAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAC
2973693 -GT-TT-TCCATTCCAAGGTAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCA
1 TGTATTCTCCATTCCAAGGTAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCA
* * * *
2973755 CTATGTTCACCATTACTTGTTCATTCTGAGACTCTGCGACATCTAAGAGATTCAGTGAAGCAGAA
66 CTGTATTCTCCATTACTTGCTCATTCTGAGACTCTGCGACATCTAAGAGATTCAGTGAAGCAGAA
* * **
2973820 CTGATTTCATTGGCCTCAGTGCTTGGGCCAACAGCACCTGATGTTGAATAAATGGTTCTTGGTTG
131 CTGATTTCATTGGCCTCAGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCAGGTTG
* * **
2973885 AAGGTAATCCATCCAAGTCAAATCATCTGTCCCAGATGCATTTTCCTTCAC
196 AAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAC
*
2973936 TGTATTCTTCATT
1 TGTATTCTCCATT
2973949 ACTTGCTCAT
Statistics
Matches: 875, Mismatches: 85, Indels: 43
0.87 0.08 0.04
Matches are distributed among these distances:
233 2 0.00
234 127 0.15
235 2 0.00
236 78 0.09
237 1 0.00
238 2 0.00
239 2 0.00
241 3 0.00
242 217 0.25
243 3 0.00
244 81 0.09
245 9 0.01
246 206 0.24
247 140 0.16
248 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (246 bp):
TGTATTCTCCATTCCAAGGTAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCA
CTGTATTCTCCATTACTTGCTCATTCTGAGACTCTGCGACATCTAAGAGATTCAGTGAAGCAGAA
CTGATTTCATTGGCCTCAGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCAGGTTG
AAGGTAATCCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAC
Found at i:2974013 original size:180 final size:180
Alignment explanation
Indices: 2973705--2974111 Score: 591
Period size: 180 Copynumber: 2.3 Consensus size: 180
2973695 TTTCCATTCC
* *
2973705 AAGGTAATCCATCCAAG-CAAAATCATCTGCCCCAGATGCATTTTCCTTCACTATGTTCACCATT
1 AAGGTAATCCATCCAAGTC-AAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCACCATT
* * * *
2973769 ACTTGTTCATTCTGAGACTCTGCGACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGC
65 ACTTGCTCATTCTGAGACTCTGCAACAGCTAAGAGATTCAGTGAAGCAGAACTGATTCCATTGGC
* * *
2973834 CTCAGTGCTTGGGCCAACAGCACCTGATGTTGAATAAATGGTTCTTGGTTG
130 CTCAGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTG
* **
2973885 AAGGTAATCCATCCAAGTCAAATCATCTGTCCCAGATGCATTTTCCTTCACTGTATTCTTCATTA
1 AAGGTAATCCATCCAAGTCAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCACCATTA
* * * *
2973950 CTTGCTCATTTTGAGACTCTTCAACAGCTAAGAGATTCAGTGAAGCTGACCTGATTCCATTGGCC
66 CTTGCTCATTCTGAGACTCTGCAACAGCTAAGAGATTCAGTGAAGCAGAACTGATTCCATTGGCC
* * * *
2974015 TCGGTGCTTTGGTCAACAGCACCTGGTATTGAATAAATGATTCCTGGTTG
131 TCAGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTG
* * *
2974065 AAGGTAATGCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCT
1 AAGGTAATCCATCCAAGTCAAATCATCTGTCCCAGATGCATTTTCCT
2974112 GGAGTATATT
Statistics
Matches: 203, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 202 1.00
181 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (180 bp):
AAGGTAATCCATCCAAGTCAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCACCATTA
CTTGCTCATTCTGAGACTCTGCAACAGCTAAGAGATTCAGTGAAGCAGAACTGATTCCATTGGCC
TCAGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTG
Found at i:2974188 original size:66 final size:66
Alignment explanation
Indices: 2974065--2974194 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 66
2974055 TTCCTGGTTG
* * * * * *
2974065 AAGGTAATGCATCCAAGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTATATTCCCCATTC
1 AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTCGACTATATTCCCCATTC
2974130 C
66 C
* * *
2974131 AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCG-CTGTATTCTCCATT
1 AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGAGGCATTTTCC-TCGACTATATTCCCCATT
2974195 ACTTGCTCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 52 0.96
67 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (66 bp):
AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTCGACTATATTCCCCATTC
C
Found at i:2974297 original size:426 final size:424
Alignment explanation
Indices: 2973464--2974800 Score: 2036
Period size: 426 Copynumber: 3.1 Consensus size: 424
2973454 CTCCATTCTG
* *
2973464 AGGTAATCCATCCTAGCAAAACCATCTG-CCTCAGATGCATTTTCCTTCACTATATTCTCCATTA
1 AGGTAATCCATCCAAGCAAAATCATCTGTCC-CAGATGCATTTTCCTTCACTATATTCTCCATTA
* * * *
2973528 CTTGCTCATTTTGAGACTCAGCGACATCTAAGAGATTCAGTGAAGCAGAACTAATTTCATTGGTC
65 CTTGCTCATTTTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCC
** * * *
2973593 TCAATGCTTAGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTAGAAGATAATCCATCCA
130 TCGGTGCTTTGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCA
2973658 AGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTT-TT-CCATTCCAAGGTAATCCATCCAA
195 AGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTTATTCCCATTCCAAGGTAATCCATCCAA
* * *
2973721 GCAAAATCATCTGCCCCAGATGCATTTTCCTTCACTATGTTCACCATTACTTGTTCATTCTGAGA
260 GCAAAATCATCTGCCCCAGATGCATTTTCCTTCACTATATTCTCCATTACTTGCTCATTCTGAGA
* *
2973786 CTCTGCGACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCTCAGTGCTTGGGCCAA
325 CTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCTCGGTGCTTGGGCCAA
2973851 CAGCACCTGATGTTGAATAAATGGTTCTTGGTTGA
390 CAGCACCTGATGTTGAATAAATGGTTCTTGGTTGA
* *
2973886 AGGTAATCCATCCAAGTC-AAATCATCTGTCCCAGATGCATTTTCCTTCACTGTATTCTTCATTA
1 AGGTAATCCATCCAAG-CAAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCTCCATTA
* * * * *
2973950 CTTGCTCATTTTGAGACTCTTCAACAGCTAAGAGATTCAGTGAAGCTGACCTGATTCCATTGGCC
65 CTTGCTCATTTTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCC
* * *
2974015 TCGGTGCTTTGGTCAACAGCACCTGGTATTGAATAAATGATTCCTGGTTGAAGGTAATGCATCCA
130 TCGGTGCTTTGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCA
*
2974080 AGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTATATTCCCCATTCCAAGGCAATCCATCC
195 AGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGT-TATT-CCCATTCCAAGGTAATCCATCC
* *
2974145 AAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCGCTGTATTCTCCATTACTTGCTCATTCTGA
258 AAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCACTATATTCTCCATTACTTGCTCATTCTGA
* *
2974210 GACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCTTGGTGCTTGCGCC
323 GACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCTCGGTGCTTGGGCC
* * ** *
2974275 AACAGCATCTGATGTAGAATAAATGACTCCTGGTTGA
388 AACAGCACCTGATGTTGAATAAATGGTTCTTGGTTGA
* **
2974312 AGGTAATCCATCCAAGCAAAATCATCTGGCCCAGATGCATTTTCCTTTGCTATATTCTCCATTAC
1 AGGTAATCCATCCAAGCAAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCTCCATTAC
* *
2974377 TTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCAGTGGCCT
66 TTGCTCATTTTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCT
* * * *
2974442 TGGTG-TTTGGGCCAACAACACCTGATGTTGAATAAATGATTCCTGGTTGAAGGCAATCCATCCA
131 CGGTGCTTT-GGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCA
* * *
2974506 AGTAAAATCATCTGTTCCAGAGGAATTTTCCTGGAGTGTATTCTCCATTCCTAGGTAATCCATCC
195 AGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGT-TATTC-CCATTCCAAGGTAATCCATCC
* * *
2974571 AAGCAAAATCATCTGCCCTAGGTGCATTTTCCTTCACTATATTCTCCATTACTTGCTCGTTCTGA
258 AAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCACTATATTCTCCATTACTTGCTCATTCTGA
* * *
2974636 GACTCTGCAATATCTAAGAGATTCAGTAAATCAGAACTGATTTCATTGGCCTCGGTGCTTGGGCC
323 GACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCTCGGTGCTTGGGCC
2974701 AACAGCACCTGATGTTGAATAAATGGTTCTTGGTTGA
388 AACAGCACCTGATGTTGAATAAATGGTTCTTGGTTGA
* * * ** *
2974738 AGGTAATCCATCCAAGTAAAATCATCAGTCCCAGAGGCATTTTCCTGGACTGTATTCTCCATT
1 AGGTAATCCATCCAAGCAAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCTCCATT
2974801 CCGAGGTAAT
Statistics
Matches: 823, Mismatches: 83, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
422 205 0.25
423 4 0.00
424 2 0.00
425 5 0.01
426 607 0.74
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (424 bp):
AGGTAATCCATCCAAGCAAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCTCCATTAC
TTGCTCATTTTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCT
CGGTGCTTTGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCAA
GTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTTATTCCCATTCCAAGGTAATCCATCCAAG
CAAAATCATCTGCCCCAGATGCATTTTCCTTCACTATATTCTCCATTACTTGCTCATTCTGAGAC
TCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCTCGGTGCTTGGGCCAAC
AGCACCTGATGTTGAATAAATGGTTCTTGGTTGA
Found at i:2974326 original size:246 final size:246
Alignment explanation
Indices: 2973885--2974357 Score: 725
Period size: 246 Copynumber: 1.9 Consensus size: 246
2973875 TTCTTGGTTG
* * *
2973885 AAGGTAATCCATCCAAGTCAAATCATCTGTCCCAGATGCATTTTCCTTCACTGTATTCTTCATTA
1 AAGGCAATCCATCCAAGTCAAATCATCTGCCCCAGATGCATTTTCCTTCACTGTATTCTCCATTA
* * * *
2973950 CTTGCTCATTTTGAGACTCTTCAACAGCTAAGAGATTCAGTGAAGCTGACCTGATTCCATTGGCC
66 CTTGCTCATTCTGAGACTCTGCAACAGCTAAGAGATTCAGTGAAGCAGAACTGATTCCATTGGCC
* * * * *
2974015 TCGGTGCTTTGGTCAACAGCACCTGGTATTGAATAAATGATTCCTGGTTGAAGGTAATGCATCCA
131 TCGGTGCTTTGGCCAACAGCACCTGATATAGAATAAATGACTCCTGGTTGAAGGTAATCCATCCA
* *
2974080 AGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTATATTCCCCATTCC
196 AGCAAAATCATCTGGCCCAGAGGCATTTTCCTGGAGTATATTCCCCATTCC
*
2974131 AAGGCAATCCATCCAAG-CAAAATCATCTGCCCCAGATGCATTTTCCTTCGCTGTATTCTCCATT
1 AAGGCAATCCATCCAAGTC-AAATCATCTGCCCCAGATGCATTTTCCTTCACTGTATTCTCCATT
* *
2974195 ACTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGC
65 ACTTGCTCATTCTGAGACTCTGCAACAGCTAAGAGATTCAGTGAAGCAGAACTGATTCCATTGGC
* * *
2974260 CTTGGTGC-TTGCGCCAACAGCATCTGATGTAGAATAAATGACTCCTGGTTGAAGGTAATCCATC
130 CTCGGTGCTTTG-GCCAACAGCACCTGATATAGAATAAATGACTCCTGGTTGAAGGTAATCCATC
*
2974324 CAAGCAAAATCATCTGGCCCAGATGCATTTTCCT
194 CAAGCAAAATCATCTGGCCCAGAGGCATTTTCCT
2974358 TTGCTATATT
Statistics
Matches: 204, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
245 4 0.02
246 200 0.98
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (246 bp):
AAGGCAATCCATCCAAGTCAAATCATCTGCCCCAGATGCATTTTCCTTCACTGTATTCTCCATTA
CTTGCTCATTCTGAGACTCTGCAACAGCTAAGAGATTCAGTGAAGCAGAACTGATTCCATTGGCC
TCGGTGCTTTGGCCAACAGCACCTGATATAGAATAAATGACTCCTGGTTGAAGGTAATCCATCCA
AGCAAAATCATCTGGCCCAGAGGCATTTTCCTGGAGTATATTCCCCATTCC
Found at i:2974550 original size:180 final size:180
Alignment explanation
Indices: 2974131--2974554 Score: 670
Period size: 180 Copynumber: 2.4 Consensus size: 180
2974121 TCCCCATTCC
2974131 AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCGCTGTATTCTCCATTA
1 AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCGCTGTATTCTCCATTA
*
2974196 CTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCC
66 CTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCAGTGGCC
* *
2974261 TTGGTGCTTGCGCCAACAGCATCTGATGTAGAATAAATGACTCCTGGTTG
131 TTGGTGCTTGCGCCAACAACACCTGATGTAGAATAAATGACTCCTGGTTG
* * * *
2974311 AAGGTAATCCATCCAAGCAAAATCATCTGGCCCAGATGCATTTTCCTTTGCTATATTCTCCATTA
1 AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCGCTGTATTCTCCATTA
2974376 CTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCAGTGGCC
66 CTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCAGTGGCC
* * * *
2974441 TTGGTGTTTGGGCCAACAACACCTGATGTTGAATAAATGATTCCTGGTTG
131 TTGGTGCTTGCGCCAACAACACCTGATGTAGAATAAATGACTCCTGGTTG
* ** * * * *
2974491 AAGGCAATCCATCCAAGTAAAATCATCTGTTCCAGAGGAATTTTCC-TGGAGTGTATTCTCCATT
1 AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCG-CTGTATTCTCCATT
2974555 CCTAGGTAAT
Statistics
Matches: 223, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
179 2 0.01
180 221 0.99
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (180 bp):
AAGGCAATCCATCCAAGCAAAATCATCTGCCCCAGATGCATTTTCCTTCGCTGTATTCTCCATTA
CTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCAGTGGCC
TTGGTGCTTGCGCCAACAACACCTGATGTAGAATAAATGACTCCTGGTTG
Found at i:2974614 original size:66 final size:66
Alignment explanation
Indices: 2974496--2974620 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 66
2974486 GGTTGAAGGC
* * * * *
2974496 AATCCATCCAAGTAAAATCATCTGTTCCAGAGGAATTTTCCTGGAGTGTATTCTCCATTCCTAGG
1 AATCCATCCAAGCAAAATCATCTGTCCCAGAGGAATTTTCCTGCACTATATTCTCCATTCCTAGG
2974561 T
66 T
* *
2974562 AATCCATCCAAGCAAAATCATCTG-CCCTAG-GTGCATTTTCCTTCACTATATTCTCCATT
1 AATCCATCCAAGCAAAATCATCTGTCCC-AGAG-GAATTTTCCTGCACTATATTCTCCATT
2974621 ACTTGCTCGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
65 3 0.06
66 47 0.94
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (66 bp):
AATCCATCCAAGCAAAATCATCTGTCCCAGAGGAATTTTCCTGCACTATATTCTCCATTCCTAGG
T
Found at i:2974748 original size:246 final size:245
Alignment explanation
Indices: 2974312--2975214 Score: 1418
Period size: 246 Copynumber: 3.7 Consensus size: 245
2974302 TCCTGGTTGA
**
2974312 AGGTAATCCATCCAAGCAAAATCATCTGGCCCAGATGCATTTTCCTTTGCTATATTCTCCATTAC
1 AGGTAATCCATCCAAGCAAAATCATCT-GCCCAGATGCATTTTCCTTCACTATATTCTCCATTAC
*
2974377 TTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCAGTGGCCT
65 TTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCT
* * * *
2974442 TGGTGTTTGGGCCAACAACACCTGATGTTGAATAAATGATTCCTGGTTGAAGGCAATCCATCCAA
130 CGGTGCTTGGGCCAACAGCACCTGATGTTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCAA
* *
2974507 GTAAAATCATCTGTTCCAGAGGAATTTTCCTGGAGTGTATTCTCCATTCCT
195 GTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTGTATTCTCCATTCCT
*
2974558 AGGTAATCCATCCAAGCAAAATCATCTGCCCTAGGTGCATTTTCCTTCACTATATTCTCCATTAC
1 AGGTAATCCATCCAAGCAAAATCATCTGCCC-AGATGCATTTTCCTTCACTATATTCTCCATTAC
* * * *
2974623 TTGCTCGTTCTGAGACTCTGCAATATCTAAGAGATTCAGTAAATCAGAACTGATTTCATTGGCCT
65 TTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCT
* *
2974688 CGGTGCTTGGGCCAACAGCACCTGATGTTGAATAAATGGTTCTTGGTTGAAGGTAATCCATCCAA
130 CGGTGCTTGGGCCAACAGCACCTGATGTTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCAA
* * *
2974753 GTAAAATCATCAGTCCCAGAGGCATTTTCCTGGACTGTATTCTCCATTCCG
195 GTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTGTATTCTCCATTCCT
2974804 AGGTAATCCATCCAAGCAAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCTCCATTAC
1 AGGTAATCCATCCAAGCAAAATCATCTG-CCCAGATGCATTTTCCTTCACTATATTCTCCATTAC
* * * *
2974869 TTGCTCATTTTGAGACTCTGCGACATCTGAGAGATTCAGTGAAGC-GAAATTGATTTCATTGGCC
65 TTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAG-AACTGATTTCATTGGCC
*
2974933 TCGGTGCTTGGGCCAACAGCACCTGATATTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCA
129 TCGGTGCTTGGGCCAACAGCACCTGATGTTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCA
*
2974998 AGTAAAATCATCTGTCCCAGGGGCATTTTCCTGGAGTGTATTCTCCATT-CT
194 AGTAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTGTATTCTCCATTCCT
* * *
2975049 GAGGTAATCCATACAAGCAAAATCATCTGCCCCAGATGCGTTTTCCTTCACTGTATTCTCCAGTT
1 -AGGTAATCCATCCAAGCAAAATCATCTG-CCCAGATGCATTTTCCTTCACTATATTCTCCA-TT
* * * *
2975114 -CTTGCTCTTTCTGAGACTCCGCAATATCTAAGAGATTCTGTGAAGCAGAACTGATTTCATTGGC
63 ACTTGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGC
2975178 CTCGGTGCTTGGGCCAACAGCACCTGATAG-TGAATAA
128 CTCGGTGCTTGGGCCAACAGCACCTGAT-GTTGAATAA
2975215 TCACTAGAAG
Statistics
Matches: 602, Mismatches: 48, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
245 6 0.01
246 590 0.98
247 6 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (245 bp):
AGGTAATCCATCCAAGCAAAATCATCTGCCCAGATGCATTTTCCTTCACTATATTCTCCATTACT
TGCTCATTCTGAGACTCTGCAACATCTAAGAGATTCAGTGAAGCAGAACTGATTTCATTGGCCTC
GGTGCTTGGGCCAACAGCACCTGATGTTGAATAAATGATTCCTGGTTGAAGGTAATCCATCCAAG
TAAAATCATCTGTCCCAGAGGCATTTTCCTGGAGTGTATTCTCCATTCCT
Found at i:2974844 original size:66 final size:66
Alignment explanation
Indices: 2974738--2974866 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 66
2974728 TCTTGGTTGA
* * *
2974738 AGGTAATCCATCCAAGTAAAATCATCAGTCCCAGAGGCATTTTCCTGGACTGTATTCTCCATTCC
1 AGGTAATCCATCCAAGCAAAATCATCAGTCCCAGAGGCATTTTCCTGCACTATATTCTCCATTCC
2974803 G
66 G
* * *
2974804 AGGTAATCCATCCAAGCAAAATCATCTGTCCCAGATGCATTTTCCTTCACTATATTCTCCATT
1 AGGTAATCCATCCAAGCAAAATCATCAGTCCCAGAGGCATTTTCCTGCACTATATTCTCCATT
2974867 ACTTGCTCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (66 bp):
AGGTAATCCATCCAAGCAAAATCATCAGTCCCAGAGGCATTTTCCTGCACTATATTCTCCATTCC
G
Found at i:2975093 original size:66 final size:67
Alignment explanation
Indices: 2974984--2975115 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 67
2974974 TCCTGGTTGA
* * * * * *
2974984 AGGTAATCCATCCAAGTAAAATCATCTGTCCCAGGGGCATTTTCCTGGAGTGTATTCTCCA-TTC
1 AGGTAATCCATACAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTGCACTGTATTCTCCAGTTC
2975048 TG
66 TG
* * *
2975050 AGGTAATCCATACAAGCAAAATCATCTGCCCCAGATGCGTTTTCCTTCACTGTATTCTCCAGTTC
1 AGGTAATCCATACAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTGCACTGTATTCTCCAGTTC
2975115 T
66 T
2975116 TGCTCTTTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 52 0.93
67 4 0.07
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.32
Consensus pattern (67 bp):
AGGTAATCCATACAAGCAAAATCATCTGCCCCAGAGGCATTTTCCTGCACTGTATTCTCCAGTTC
TG
Found at i:2977349 original size:21 final size:20
Alignment explanation
Indices: 2977311--2977354 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2977301 ATTAATTTAA
*
2977311 AAATAAAATAATATTAAATT
1 AAATAAAATAATAATAAATT
*
2977331 AAATAAAAATCATAATAAATT
1 AAAT-AAAATAATAATAAATT
2977352 AAA
1 AAA
2977355 AAATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAAAATAATAATAAATT
Found at i:2977354 original size:26 final size:25
Alignment explanation
Indices: 2977277--2977354 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 25
2977267 TTTATTTTCA
2977277 TAAA-AAAAATTATAAATATAATT-AAT
1 TAAATAAAAA-TAT-AATA-AATTAAAT
* *
2977303 TAATTTAAAAATAAAATAATATTAAAT
1 TAA-ATAAAAATATAATAA-ATTAAAT
2977330 TAAATAAAAATCATAATAAATTAAA
1 TAAATAAAAAT-ATAATAAATTAAA
2977355 AAATATTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
25 1 0.02
26 23 0.53
27 14 0.33
28 5 0.12
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAATAAAAATATAATAAATTAAAT
Found at i:2977942 original size:22 final size:22
Alignment explanation
Indices: 2977919--2977985 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
2977909 TGAAATTATA
2977919 ATATTTAATTAAATATTATAT-
1 ATATTTAATTAAATATTATATC
2977940 A-A--TAA-TAAATATTATATC
1 ATATTTAATTAAATATTATATC
* *
2977958 CTATTTAATTAAATATTATTTC
1 ATATTTAATTAAATATTATATC
2977980 ATATTT
1 ATATTT
2977986 CATATTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 12 0.32
18 3 0.08
19 1 0.03
20 1 0.03
21 4 0.11
22 17 0.45
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTAATTAAATATTATATC
Found at i:2977972 original size:29 final size:29
Alignment explanation
Indices: 2977940--2978020 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
2977930 AATATTATAT
* *
2977940 AATAATAAATATTATATCCTATTTAATTA
1 AATATTAAATATTATATCATATTTAATTA
** *
2977969 AATATTATTTCA-TATTTCATATTTAATTA
1 AATATTAAAT-ATTATATCATATTTAATTA
* *
2977998 AATATTTAATATTATATAATATT
1 AATATTAAATATTATATCATATT
2978021 AAATATTAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
28 1 0.03
29 38 0.95
30 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (29 bp):
AATATTAAATATTATATCATATTTAATTA
Found at i:2978021 original size:24 final size:22
Alignment explanation
Indices: 2977994--2978042 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
2977984 TTCATATTTA
*
2977994 ATTAAATATTTAATATTATATAAT
1 ATTAAATA-TTAAGA-TATATAAT
2978018 ATTAAATATTAAGATATATAAT
1 ATTAAATATTAAGATATATAAT
2978040 ATT
1 ATT
2978043 CCTAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.46
23 5 0.21
24 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTAAATATTAAGATATATAAT
Found at i:2978169 original size:10 final size:10
Alignment explanation
Indices: 2978075--2978301 Score: 113
Period size: 10 Copynumber: 23.1 Consensus size: 10
2978065 TGTGATTAAG
2978075 TATTAAATAT
1 TATTAAATAT
*
2978085 TATACTAAATTT
1 TAT--TAAATAT
2978097 TATT-AA-A-
1 TATTAAATAT
2978104 TATTAAATAT
1 TATTAAATAT
*
2978114 GTGATTAAGTAT
1 -T-ATTAAATAT
* * *
2978126 TATGAAAAAG
1 TATTAAATAT
2978136 TATTAAATA-
1 TATTAAATAT
*
2978145 TA--ATAT-T
1 TATTAAATAT
2978152 TAATTAAATAT
1 T-ATTAAATAT
2978163 TATT-AA-A-
1 TATTAAATAT
*
2978170 TATCAAATAT
1 TATTAAATAT
2978180 T-TATATAATAT
1 TAT-TA-AATAT
*
2978191 TAATTTAATAT
1 T-ATTAAATAT
* *
2978202 TTTTAATTAT
1 TATTAAATAT
*
2978212 TATTAAATAC
1 TATTAAATAT
*
2978222 TATT-ATTAT
1 TATTAAATAT
* *
2978231 TTTTAGATAT
1 TATTAAATAT
*
2978241 TATTAAATAC
1 TATTAAATAT
2978251 TATTAAA-AT
1 TATTAAATAT
2978260 TATTAAATATT
1 TATTAAATA-T
*
2978271 TAATAAAATAT
1 T-ATTAAATAT
*
2978282 TATTAAATGT
1 TATTAAATAT
2978292 TA-TAAATAT
1 TATTAAATAT
2978301 T
1 T
2978302 TAACAAAATG
Statistics
Matches: 161, Mismatches: 33, Indels: 47
0.67 0.14 0.20
Matches are distributed among these distances:
7 11 0.07
8 6 0.04
9 30 0.19
10 68 0.42
11 20 0.12
12 25 0.16
13 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (10 bp):
TATTAAATAT
Found at i:2978286 original size:31 final size:30
Alignment explanation
Indices: 2978146--2978303 Score: 101
Period size: 29 Copynumber: 5.3 Consensus size: 30
2978136 TATTAAATAT
* *
2978146 AATATTTAATTAAATATTATT-AAA-TATCA
1 AATATTT-ATAAAATATTATTAAAATTATTA
* * *
2978175 AATATTTATATAATATTAATTTAATATTTTTA
1 AATATTTATAAAATATT-A-TTAAAATTATTA
* * * ** *
2978207 ATTA-TTATTAAATACTATTATTATTTTTA
1 AATATTTATAAAATATTATTAAAATTATTA
* * *
2978236 GATA-TTATTAAATACTATTAAAATTATTA
1 AATATTTATAAAATATTATTAAAATTATTA
*
2978265 AATATTTAATAAAATATTATTAAATGTTA-TA
1 AATATTT-ATAAAATATTATTAAA-ATTATTA
2978296 AATATTTA
1 AATATTTA
2978304 ACAAAATGTT
Statistics
Matches: 103, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
28 8 0.08
29 46 0.45
30 6 0.06
31 34 0.33
32 9 0.09
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (30 bp):
AATATTTATAAAATATTATTAAAATTATTA
Found at i:2978298 original size:19 final size:19
Alignment explanation
Indices: 2978075--2978301 Score: 85
Period size: 19 Copynumber: 11.6 Consensus size: 19
2978065 TGTGATTAAG
*
2978075 TATTAAATATTATACTAAATTT
1 TATTAAATA-T-TA-TAAATAT
2978097 TATTAAATA-T-TAAATAT
1 TATTAAATATTATAAATAT
* * *
2978114 GTGATTAAGTATTATGAAAAAG
1 -T-ATTAAATATTAT-AAATAT
*
2978136 TATTAAATA-TA-ATAT-T
1 TATTAAATATTATAAATAT
*
2978152 TAATTAAATATTATTAA-A-
1 T-ATTAAATATTATAAATAT
*
2978170 TATCAAATATTTATATAATAT
1 TATTAAATA-TTATA-AATAT
* * *
2978191 TAATTTAATATTTTTAATTAT
1 T-ATTAAATA-TTATAAATAT
* * *
2978212 TATTAAATACTATTATTAT
1 TATTAAATATTATAAATAT
* * *
2978231 TTTTAGATATTATTAAATAC
1 TATTAAATATTA-TAAATAT
2978251 TATTAAA-ATTATTAAATATT
1 TATTAAATATTA-TAAATA-T
* *
2978271 TAATAAAATATTATTAAATGT
1 T-ATTAAATATTA-TAAATAT
2978292 TA-TAAATATT
1 TATTAAATATT
2978302 TAACAAAATG
Statistics
Matches: 155, Mismatches: 32, Indels: 39
0.69 0.14 0.17
Matches are distributed among these distances:
16 1 0.01
17 23 0.15
18 8 0.05
19 47 0.30
20 27 0.17
21 15 0.10
22 34 0.22
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (19 bp):
TATTAAATATTATAAATAT
Found at i:2978304 original size:31 final size:32
Alignment explanation
Indices: 2978245--2978333 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
2978235 AGATATTATT
* * *
2978245 AAATACTATTAAA-ATTATTAAATATTTAATA
1 AAATATTATTAAATATTACTAAATATTTAACA
*
2978276 AAATATTATTAAATGTTA-TAAATATTTAACA
1 AAATATTATTAAATATTACTAAATATTTAACA
* * *
2978307 AAATGTTGTTATATATTACTAAATATT
1 AAATATTATTAAATATTACTAAATATT
2978334 CGATATTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 38 0.78
32 11 0.22
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (32 bp):
AAATATTATTAAATATTACTAAATATTTAACA
Found at i:2978447 original size:37 final size:37
Alignment explanation
Indices: 2978381--2978466 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
2978371 ATCAATAACC
*
2978381 AATAT-ATATTTATATAATATTAATTAAATAAC-ATTA
1 AATATAATATTTATATAATATTAATGAAAT-ACTATTA
* *
2978417 AATATAATATTTATTTAAATATT-GTGAAATACTATTA
1 AATATAATATTTATAT-AATATTAATGAAATACTATTA
2978454 AATATAATATTTA
1 AATATAATATTTA
2978467 GGTAAATACT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
36 7 0.16
37 31 0.70
38 6 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (37 bp):
AATATAATATTTATATAATATTAATGAAATACTATTA
Found at i:2978483 original size:19 final size:19
Alignment explanation
Indices: 2978459--2978512 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2978449 TATTAAATAT
2978459 AATATTTAGGTAAATA-CTA
1 AATATTTAGGTAAATATC-A
2978478 AATATTT--GTATAATATCA
1 AATATTTAGGTA-AATATCA
*
2978496 AATATTTAGTTAAATAT
1 AATATTTAGGTAAATAT
2978513 TATATAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 13 0.43
20 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (19 bp):
AATATTTAGGTAAATATCA
Found at i:2978645 original size:24 final size:24
Alignment explanation
Indices: 2978618--2978699 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
2978608 ATAATTATAG
*
2978618 TTATTTATTTATATAATTAATATT
1 TTATTTAATTATATAATTAATATT
*
2978642 TTA-TAAATTA-ATTGAATTAATA--
1 TTATTTAATTATA-T-AATTAATATT
*
2978664 TT-TTTAATTATATTATTTAAT-TT
1 TTATTTAATTATA-TAATTAATATT
2978687 TTATTTAATTATA
1 TTATTTAATTATA
2978700 ATATTATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
22 15 0.32
23 11 0.23
24 21 0.45
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (24 bp):
TTATTTAATTATATAATTAATATT
Found at i:2978692 original size:11 final size:13
Alignment explanation
Indices: 2978656--2978704 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2978646 AAATTAATTG
2978656 AATTAATATT-TTT
1 AATT-ATATTATTT
2978669 AATTATATTATTT
1 AATTATATTATTT
2978682 AATT-T-TTATTT
1 AATTATATTATTT
*
2978693 AATTATAATATT
1 AATTATATTATT
2978705 ATTTAAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.31
12 7 0.22
13 15 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTATATTATTT
Found at i:2978938 original size:19 final size:18
Alignment explanation
Indices: 2978910--2978951 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2978900 TAATTTGGGT
2978910 GTTTTAAATTTATCATTAA
1 GTTTTAAATTTAT-ATTAA
*
2978929 GTTTTTAATTTATATTAA
1 GTTTTAAATTTATATTAA
2978947 -TTTTA
1 GTTTTA
2978952 TCATTATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
GTTTTAAATTTATATTAA
Found at i:2979840 original size:14 final size:15
Alignment explanation
Indices: 2979806--2979839 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2979796 AAAAAATTAG
* *
2979806 AAAAATTTACAATCA
1 AAAAATTGAAAATCA
2979821 AAAAATTGAAAATCA
1 AAAAATTGAAAATCA
2979836 AAAA
1 AAAA
2979840 TAAAAATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAATTGAAAATCA
Found at i:2983149 original size:32 final size:32
Alignment explanation
Indices: 2983113--2983190 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
2983103 TTTATAACCA
* *
2983113 ATGATGTTTTAAGTTATTTTACTTAATTTTGG
1 ATGATGTTTTAAGTTATTTTACATAACTTTGG
* *
2983145 ATGATGTTTTAATTTATTTTGCATAACTTTGG
1 ATGATGTTTTAAGTTATTTTACATAACTTTGG
*
2983177 ATGATGTTTGAAGT
1 ATGATGTTTTAAGT
2983191 ATGGATGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.53
Consensus pattern (32 bp):
ATGATGTTTTAAGTTATTTTACATAACTTTGG
Found at i:2983255 original size:167 final size:167
Alignment explanation
Indices: 2982976--2983283 Score: 370
Period size: 167 Copynumber: 1.8 Consensus size: 167
2982966 TTGGAACTTG
* * ** *
2982976 GGATGATATTTTAAATTATTTTGCTTAACTCTGATTAATATTTGAAGTTTGTTTGATGTTTGTGT
1 GGATGATATTTTAAATTATTTTGCATAACTCTGATTAATATTTGAAGTATGGATGATATTTGTGT
* * ** * *
2983041 CAAGAATAGTGTTAGCAAGGATTTATTGTGTTGTACCTATACAATATTAAATTCTATTTATGTTT
66 CAAGAATAGTATTAGCAAGGATATATTGTCATGTACCTATACAATATTAAATTCTATTGATGTCT
2983106 ATAACCAATGATGTTTTAAGTTATTTTACTTAATTTT
131 ATAACCAATGATGTTTTAAGTTATTTTACTTAATTTT
* * * * *
2983143 GGATGATGTTTTAATTTATTTTGCATAACTTTGGA-TGATGTTTGAAGTATGGATGATATTTGTG
1 GGATGATATTTTAAATTATTTTGCATAACTCT-GATTAATATTTGAAGTATGGATGATATTTGTG
* * * * *
2983207 TCAAGAATATTATTTGCAAGGATATATTGTACAT-TACCT-TAGCAATATTACATTTTGTTGATG
65 TCAAGAATAGTATTAGCAAGGATATATTGT-CATGTACCTATA-CAATATTAAATTCTATTGATG
*
2983270 TCTATAAGCAATGA
128 TCTATAACCAATGA
2983284 CAATGAATTA
Statistics
Matches: 116, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
166 2 0.02
167 111 0.96
168 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (167 bp):
GGATGATATTTTAAATTATTTTGCATAACTCTGATTAATATTTGAAGTATGGATGATATTTGTGT
CAAGAATAGTATTAGCAAGGATATATTGTCATGTACCTATACAATATTAAATTCTATTGATGTCT
ATAACCAATGATGTTTTAAGTTATTTTACTTAATTTT
Found at i:2984607 original size:21 final size:20
Alignment explanation
Indices: 2984583--2984678 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 20
2984573 GATTTCCTCA
*
2984583 AAATTCAACTCCAAAACCTAG
1 AAATTCAA-ACCAAAACCTAG
* *
2984604 AAATTCAAACCTAAACTTA-
1 AAATTCAAACCAAAACCTAG
*
2984623 AAACTTCAAACCTAAACCTAG
1 AAA-TTCAAACCAAAACCTAG
*
2984644 AAAATTCAAACCCCAAATCCTAG
1 -AAATTCAAA--CCAAAACCTAG
2984667 AAACTTCAAACC
1 AAA-TTCAAACC
2984679 TAGAAATTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.05
20 23 0.37
21 16 0.25
22 6 0.10
23 15 0.24
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATTCAAACCAAAACCTAG
Found at i:2985033 original size:3 final size:3
Alignment explanation
Indices: 2985025--2985070 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
2985015 GATAAAAATA
2985025 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
2985070 A
1 A
2985071 GTTGACCCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2995576 original size:17 final size:17
Alignment explanation
Indices: 2995554--2995591 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2995544 TGTCTACTAG
2995554 GTTTTTCAGGTCATTTT
1 GTTTTTCAGGTCATTTT
2995571 GTTTTTCAGGTCATTTT
1 GTTTTTCAGGTCATTTT
2995588 GTTT
1 GTTT
2995592 AATAAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.61
Consensus pattern (17 bp):
GTTTTTCAGGTCATTTT
Found at i:2997255 original size:12 final size:11
Alignment explanation
Indices: 2997216--2997263 Score: 60
Period size: 12 Copynumber: 4.1 Consensus size: 11
2997206 CAAAATTTGT
2997216 AAAATAATAATGA
1 AAAATAA-AAT-A
*
2997229 TAAATAAAATA
1 AAAATAAAATA
2997240 AAAATAAAAGTA
1 AAAATAAAA-TA
2997252 AAAATAAAATA
1 AAAATAAAATA
2997263 A
1 A
2997264 GAAAAAGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 12 0.38
12 14 0.44
13 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:2997300 original size:15 final size:16
Alignment explanation
Indices: 2997273--2997315 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
2997263 AGAAAAAGCT
2997273 TAAAAAATGAAAATTG
1 TAAAAAATGAAAATTG
2997289 TAAAAAAT-AAAA-T-
1 TAAAAAATGAAAATTG
*
2997302 TAGAAAATGAAAAT
1 TAAAAAATGAAAAT
2997316 AAAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
15 4 0.17
16 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (16 bp):
TAAAAAATGAAAATTG
Found at i:2997329 original size:29 final size:29
Alignment explanation
Indices: 2997252--2997329 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
2997242 AATAAAAGTA
**
2997252 AAAATAAAATAAGAAAAAGCTTAAAAAATG
1 AAAATAAAA-AAGAAAAAAATTAAAAAATG
** * *
2997282 AAAATTGTAAAA-AATAAAATTAGAAAATG
1 AAAA-TAAAAAAGAAAAAAATTAAAAAATG
2997311 AAAATAAAAAAGAAAAAAA
1 AAAATAAAAAAGAAAAAAA
2997330 ATTTACGATA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
28 5 0.14
29 23 0.62
30 6 0.16
31 3 0.08
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (29 bp):
AAAATAAAAAAGAAAAAAATTAAAAAATG
Found at i:2998618 original size:2 final size:2
Alignment explanation
Indices: 2998613--2998637 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2998603 TCAGAGAGCA
2998613 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2998638 CACACACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3004193 original size:23 final size:24
Alignment explanation
Indices: 3004159--3004207 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
3004149 CTAACTCAAT
3004159 ATAAGGGGTTTTTACATTAGGATC
1 ATAAGGGGTTTTTACATTAGGATC
*
3004183 ATAA-GGGTTTTTGCATTAGGATC
1 ATAAGGGGTTTTTACATTAGGATC
3004206 AT
1 AT
3004208 GCACTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (24 bp):
ATAAGGGGTTTTTACATTAGGATC
Found at i:3006459 original size:28 final size:28
Alignment explanation
Indices: 3006399--3006459 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
3006389 AAAAGCCCAA
*
3006399 AATTTTAATTTAATTTTGACTTTGATTT
1 AATTTTAATTTAATTTTGACTTTGATCT
* * **
3006427 TATTTTAATTTGATTTTGTTTTTGATCT
1 AATTTTAATTTAATTTTGACTTTGATCT
3006455 AATTT
1 AATTT
3006460 GGTCAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (28 bp):
AATTTTAATTTAATTTTGACTTTGATCT
Found at i:3007479 original size:12 final size:13
Alignment explanation
Indices: 3007465--3007537 Score: 78
Period size: 14 Copynumber: 5.5 Consensus size: 13
3007455 TTGTTTGATT
3007465 TTTATTTTTTAT-
1 TTTATTTTTTATA
3007477 TTTATTTTTCTAT-
1 TTTATTTTT-TATA
*
3007490 TTTGTTTTTTATA
1 TTTATTTTTTATA
*
3007503 TATATTTTTTTATA
1 TTTA-TTTTTTATA
*
3007517 TTTGTATTTTTATA
1 TTTAT-TTTTTATA
3007531 TTTATTT
1 TTTATTT
3007538 AATTGTATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
12 12 0.24
13 16 0.31
14 23 0.45
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTATTTTTTATA
Found at i:3007526 original size:28 final size:26
Alignment explanation
Indices: 3007464--3007537 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 26
3007454 TTTGTTTGAT
*
3007464 TTTTATTTTTTAT-TTTATTTTTCTA
1 TTTTGTTTTTTATATTTATTTTTCTA
* *
3007489 TTTTGTTTTTTATATATATTTTTTTA
1 TTTTGTTTTTTATATTTATTTTTCTA
3007515 TATTTGTATTTTTATATTTATTT
1 T-TTTGT-TTTTTATATTTATTT
3007538 AATTGTATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 12 0.29
26 11 0.26
27 5 0.12
28 14 0.33
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (26 bp):
TTTTGTTTTTTATATTTATTTTTCTA
Found at i:3007700 original size:14 final size:13
Alignment explanation
Indices: 3007648--3007700 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
3007638 TTAATAATTA
3007648 ATATTATTGCATG
1 ATATTATTGCATG
3007661 ATA-TATT--AT-
1 ATATTATTGCATG
*
3007670 ATTATTATTGTATG
1 A-TATTATTGCATG
3007684 ATATTATTTGCATG
1 ATATTA-TTGCATG
3007698 ATA
1 ATA
3007701 ATTTTTGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
9 1 0.03
10 4 0.12
11 4 0.12
12 4 0.12
13 10 0.30
14 10 0.30
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (13 bp):
ATATTATTGCATG
Found at i:3024415 original size:6 final size:6
Alignment explanation
Indices: 3024299--3024456 Score: 60
Period size: 7 Copynumber: 25.5 Consensus size: 6
3024289 GGTTAGTTCA
* * * * *
3024299 GTTTA- GTTTAGG GTTTGG GATT-G GTTTAG GGTTAG GTTTTAG ATTTTGG
1 GTTTAG GTTTA-G GTTTAG GTTTAG GTTTAG GTTTAG G-TTTAG -GTTTAG
* * *
3024348 GTTTTGG GTCTT-G GTTTAAG GTTTATG G-CTAG GTTTAAG GTTTAAA
1 G-TTTAG GT-TTAG GTTT-AG GTTTA-G GTTTAG GTTT-AG GTTT-AG
* *
3024394 GTTTAGG GTTTTG GTTTAG GTTTA- GTTTAAG G-TTAA GTTTAGG GTTTAG
1 GTTTA-G GTTTAG GTTTAG GTTTAG GTTT-AG GTTTAG GTTTA-G GTTTAG
*
3024443 GTTT-G GTTTGG GTT
1 GTTTAG GTTTAG GTT
3024457 AGGATGGTGG
Statistics
Matches: 119, Mismatches: 16, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
5 24 0.20
6 46 0.39
7 49 0.41
ACGTcount: A:0.16, C:0.01, G:0.34, T:0.49
Consensus pattern (6 bp):
GTTTAG
Found at i:3024426 original size:12 final size:12
Alignment explanation
Indices: 3024380--3024442 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
3024370 TTATGGCTAG
3024380 GTTTAAGGTTTAAA
1 GTTTAAGGTTT--A
* *
3024394 GTTTAGGGTTTTG
1 GTTTAAGG-TTTA
3024407 GTTT-AGGTTTA
1 GTTTAAGGTTTA
*
3024418 GTTTAAGGTTAA
1 GTTTAAGGTTTA
*
3024430 GTTTAGGGTTTA
1 GTTTAAGGTTTA
3024442 G
1 G
3024443 GTTTGGTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 7 0.17
12 19 0.47
13 4 0.10
14 7 0.17
15 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (12 bp):
GTTTAAGGTTTA
Found at i:3025505 original size:25 final size:25
Alignment explanation
Indices: 3025459--3025511 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
3025449 TTTTTTTTCA
3025459 TTTATTTATTTTAAAAACTAAATTT
1 TTTATTTATTTTAAAAACTAAATTT
3025484 TTTATTT-TTTTAAGTAAA-TAAATTT
1 TTTATTTATTTTAA--AAACTAAATTT
3025509 TTT
1 TTT
3025512 TTGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 6 0.23
25 17 0.65
26 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTATTTATTTTAAAAACTAAATTT
Found at i:3026054 original size:19 final size:19
Alignment explanation
Indices: 3026032--3026181 Score: 60
Period size: 19 Copynumber: 7.8 Consensus size: 19
3026022 GAAGTCTAGG
3026032 TTAGGGTTTGAGGTTTGGT
1 TTAGGGTTTGAGGTTTGGT
** * *
3026051 TTAGATTTTAAGGTTAAGGTT
1 TTAGGGTTTGAGGTT-TGG-T
* *
3026072 TTATGGTTT-TGGTTTACGG-
1 TTAGGGTTTGAGGTTT--GGT
* * *
3026091 TTACGATTTGAGATCTTGG-
1 TTAGGGTTTGAGGT-TTGGT
* *
3026110 TTAGGATTTG-GATTTGGT
1 TTAGGGTTTGAGGTTTGGT
*
3026128 TTAGGGTTT-AAGTTGTGGT
1 TTAGGGTTTGAGGTT-TGGT
* *
3026147 TTAGGGATT-AGGTTAGGGT
1 TTAGGGTTTGAGGTT-TGGT
*
3026166 TTAGGGTTTGGGGTTT
1 TTAGGGTTTGAGGTTT
3026182 ATGATTTGGG
Statistics
Matches: 97, Mismatches: 24, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
17 4 0.04
18 13 0.13
19 57 0.59
20 12 0.12
21 11 0.11
ACGTcount: A:0.17, C:0.02, G:0.35, T:0.47
Consensus pattern (19 bp):
TTAGGGTTTGAGGTTTGGT
Found at i:3026137 original size:7 final size:7
Alignment explanation
Indices: 3026125--3026256 Score: 75
Period size: 7 Copynumber: 20.0 Consensus size: 7
3026115 ATTTGGATTT
3026125 GGTTTAG
1 GGTTTAG
3026132 GGTTTA-
1 GGTTTAG
*
3026138 AGTTGT-G
1 GGTT-TAG
3026145 -GTTTAG
1 GGTTTAG
*
3026151 GGATTA-
1 GGTTTAG
3026157 GG-TTAG
1 GGTTTAG
3026163 GGTTTAG
1 GGTTTAG
*
3026170 GGTTTGG
1 GGTTTAG
*
3026177 GGTTTAT
1 GGTTTAG
*
3026184 GATTT-G
1 GGTTTAG
* *
3026190 GGGTTAT
1 GGTTTAG
3026197 GGTTT-G
1 GGTTTAG
*
3026203 GTTTTAG
1 GGTTTAG
3026210 GGTTTA-
1 GGTTTAG
*
3026216 GGCTTAG
1 GGTTTAG
3026223 GGTTTAG
1 GGTTTAG
**
3026230 TATTT-G
1 GGTTTAG
*
3026236 GTTTTAG
1 GGTTTAG
*
3026243 GATTTAG
1 GGTTTAG
3026250 GGTTTAG
1 GGTTTAG
3026257 TATTTAGGAT
Statistics
Matches: 93, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
5 4 0.04
6 27 0.29
7 62 0.67
ACGTcount: A:0.15, C:0.01, G:0.38, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:3026173 original size:13 final size:14
Alignment explanation
Indices: 3026144--3026256 Score: 76
Period size: 13 Copynumber: 8.5 Consensus size: 14
3026134 TTTAAGTTGT
*
3026144 GGTTTAGGGATTA-
1 GGTTTAGGGTTTAG
3026157 GG-TTAGGGTTTAG
1 GGTTTAGGGTTTAG
* *
3026170 GGTTTGGGGTTTAT
1 GGTTTAGGGTTTAG
* * *
3026184 GATTT-GGGGTTAT
1 GGTTTAGGGTTTAG
*
3026197 GGTTT-GGTTTTAG
1 GGTTTAGGGTTTAG
*
3026210 GGTTTA-GGCTTAG
1 GGTTTAGGGTTTAG
**
3026223 GGTTTAGTATTT-G
1 GGTTTAGGGTTTAG
* *
3026236 GTTTTAGGATTTAG
1 GGTTTAGGGTTTAG
3026250 GGTTTAG
1 GGTTTAG
3026257 TATTTAGGAT
Statistics
Matches: 78, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
12 9 0.12
13 47 0.60
14 22 0.28
ACGTcount: A:0.15, C:0.01, G:0.38, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAG
Found at i:3026262 original size:7 final size:7
Alignment explanation
Indices: 3026205--3026268 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
3026195 ATGGTTTGGT
*
3026205 TTTAGGG
1 TTTAGGA
3026212 TTTAGG-
1 TTTAGGA
* *
3026218 CTTAGGG
1 TTTAGGA
*
3026225 TTTAGTA
1 TTTAGGA
*
3026232 TTT-GGT
1 TTTAGGA
3026238 TTTAGGA
1 TTTAGGA
*
3026245 TTTAGGG
1 TTTAGGA
*
3026252 TTTAGTA
1 TTTAGGA
3026259 TTTAGGA
1 TTTAGGA
3026266 TTT
1 TTT
3026269 TGGTTTGGAT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
6 9 0.20
7 35 0.80
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.50
Consensus pattern (7 bp):
TTTAGGA
Found at i:3035634 original size:12 final size:12
Alignment explanation
Indices: 3035619--3035652 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3035609 TAAAAAGATT
3035619 AATAATATTATA
1 AATAATATTATA
3035631 AATAATTATTATA
1 AATAA-TATTATA
*
3035644 AATATTATT
1 AATAATATT
3035653 TACAATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATAATATTATA
Found at i:3035700 original size:29 final size:27
Alignment explanation
Indices: 3035628--3035701 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
3035618 TAATAATATT
*
3035628 ATAAATAATTATTATAAATATTATTTACA
1 ATAAA-AATT-TTATCAATATTATTTACA
* * *
3035657 ATCAAAATTTAATCAATACTTATTTAGTA
1 ATAAAAATTTTATCAATA-TTATTTA-CA
3035686 ATAAAAATTTTATCAA
1 ATAAAAATTTTATCAA
3035702 AAATTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
27 7 0.19
28 11 0.30
29 19 0.51
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (27 bp):
ATAAAAATTTTATCAATATTATTTACA
Found at i:3035715 original size:11 final size:12
Alignment explanation
Indices: 3035688--3035717 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3035678 ATTTAGTAAT
3035688 AAAAATTTTATC
1 AAAAATTTTATC
*
3035700 AAAAATTTTATT
1 AAAAATTTTATC
3035712 AAAAAT
1 AAAAAT
3035718 ACAATCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATTTTATC
Found at i:3045791 original size:67 final size:67
Alignment explanation
Indices: 3045683--3045813 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
3045673 AGTGATACTC
* *
3045683 TCTATCAATGAGCCTACTAGTCAGAGCAGTAATAGCAGTTACTTGTTAAAAGTCATTCACTTAAC
1 TCTATCAATGAGCCCACTAGTCAGAGCAATAATAGCAGTTACTTGTTAAAAGTCATTCACTTAAC
3045748 TT
66 TT
**
3045750 TCTATCAATGAGCCCACTAGTCAGAGCAATAATAGCAGTTACTTGTTCCAAGTCATTCACTTAA
1 TCTATCAATGAGCCCACTAGTCAGAGCAATAATAGCAGTTACTTGTTAAAAGTCATTCACTTAA
3045814 AGGGCTTTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (67 bp):
TCTATCAATGAGCCCACTAGTCAGAGCAATAATAGCAGTTACTTGTTAAAAGTCATTCACTTAAC
TT
Found at i:3056160 original size:24 final size:24
Alignment explanation
Indices: 3056133--3056179 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3056123 TTACTCAAAA
* *
3056133 TTAAAAATTTAATGATAAATTTAT
1 TTAAAAATATAATAATAAATTTAT
3056157 TTAAAAATATAATAATAAATTTA
1 TTAAAAATATAATAATAAATTTA
3056180 AATCATAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAAAATATAATAATAAATTTAT
Found at i:3058327 original size:2 final size:2
Alignment explanation
Indices: 3058320--3058354 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3058310 AGGTTTAATC
3058320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3058355 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3058359 original size:2 final size:2
Alignment explanation
Indices: 3058354--3058390 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3058344 ATATATATAT
3058354 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3058391 AATCAACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3059210 original size:3 final size:3
Alignment explanation
Indices: 3059196--3059239 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
3059186 AATTAGGTTT
* *
3059196 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3059240 TGTTTCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3060019 original size:20 final size:20
Alignment explanation
Indices: 3059991--3060030 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3059981 TTGGTAAGTC
* *
3059991 AAGATCCGCGCGTTGACCTG
1 AAGACCCGCGCGCTGACCTG
3060011 AAGACCCGCGCGCTGACCTG
1 AAGACCCGCGCGCTGACCTG
3060031 CATCTTGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (20 bp):
AAGACCCGCGCGCTGACCTG
Done.