Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
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: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 1 of 11
Found at i:2040 original size:33 final size:32
Alignment explanation
Indices: 1999--2074 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
1989 GATATAAAAA
* * *
1999 ATAATATAAATTTAAGAATGTCTTAAATTTTAT
1 ATAATATAAA-TTAAGAATATATCAAATTTTAT
**
2032 ATAATATAAATTATTAATATATCAAATTTTAT
1 ATAATATAAATTAAGAATATATCAAATTTTAT
2064 ATAAATATAAA
1 AT-AATATAAA
2075 ATATTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 19 0.51
33 18 0.49
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (32 bp):
ATAATATAAATTAAGAATATATCAAATTTTAT
Found at i:2043 original size:16 final size:16
Alignment explanation
Indices: 2022--2074 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
2012 AAGAATGTCT
2022 TAAATTTTATATAATA
1 TAAATTTTATATAATA
2038 TAAATTATTA-AT-ATA
1 TAAATT-TTATATAATA
2053 TCAAATTTTATATAAATA
1 T-AAATTTTATAT-AATA
2071 TAAA
1 TAAA
2075 ATATTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.22
16 15 0.47
17 6 0.19
18 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:2063 original size:18 final size:18
Alignment explanation
Indices: 2023--2076 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2013 AGAATGTCTT
2023 AAATTTTATAT-AATAT-
1 AAATTTTATATAAATATA
*
2039 AAA--TTAT-TAATATATC
1 AAATTTTATATAA-ATATA
2055 AAATTTTATATAAATATA
1 AAATTTTATATAAATATA
2073 AAAT
1 AAAT
2077 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 4 0.13
16 6 0.19
18 12 0.39
19 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTTATATAAATATA
Found at i:2085 original size:27 final size:27
Alignment explanation
Indices: 2002--2085 Score: 62
Period size: 32 Copynumber: 2.9 Consensus size: 27
1992 ATAAAAAATA
* * *
2002 ATATAAATTTAAGAATGTCTTAAATTTT
1 ATATAAATATAA-AATATTTTAAATTTT
*
2030 ATAT-AATATAAATTATTAATATATCAAATTTT
1 ATATAAATATAAA--A-T-AT-T-TTAAATTTT
2062 ATATAAATATAAAATATTTTAAAT
1 ATATAAATATAAAATATTTTAAAT
2086 ACAATTATGA
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
26 1 0.02
27 11 0.25
28 6 0.14
29 3 0.07
30 2 0.05
31 1 0.02
32 12 0.27
33 8 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATAAATATAAAATATTTTAAATTTT
Found at i:3254 original size:13 final size:13
Alignment explanation
Indices: 3236--3260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3226 TTTATTAAAA
3236 AATTTAAAAAATT
1 AATTTAAAAAATT
3249 AATTTAAAAAAT
1 AATTTAAAAAAT
3261 ATATGATAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTTAAAAAATT
Found at i:4983 original size:38 final size:36
Alignment explanation
Indices: 4902--5035 Score: 164
Period size: 38 Copynumber: 3.7 Consensus size: 36
4892 ATTAGTTGAT
*
4902 GGTTAGAGAATTTAATTTGAAATTAGT-TGAC-GAC
1 GGTTAGAGAATTCAATTTGAAATTAGTGTGACTGAC
4936 GGTTAGAGAATTCAATTTGAAATTAGCTGGTGACTGAC
1 GGTTAGAGAATTCAATTTGAAATTAG-T-GTGACTGAC
* *
4974 GGTTAGAGAATTCAATTTGAAATTGGTCGACGACTGAC
1 GGTTAGAGAATTCAATTTGAAATTAGT-G-TGACTGAC
** *
5012 GACTAAAGAATTCAATTTGAAATT
1 GGTTAGAGAATTCAATTTGAAATT
5036 GACCGGTGGC
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
34 25 0.28
35 1 0.01
37 6 0.07
38 56 0.64
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (36 bp):
GGTTAGAGAATTCAATTTGAAATTAGTGTGACTGAC
Found at i:5057 original size:76 final size:72
Alignment explanation
Indices: 4905--5061 Score: 172
Period size: 76 Copynumber: 2.1 Consensus size: 72
4895 AGTTGATGGT
* * * * *
4905 TAGAGAATTTAATTTGAAATTAGTTGACGACGGTTAGAGAATTCAATTTGAAATTAGCTGGTGAC
1 TAGAGAATTCAATTTGAAATTAGTCGACGACGGCTAAAGAATTCAATTTGAAATTAGCCGGTGAC
*
4970 TGACGGT
66 TGACGGC
*
4977 TAGAGAATTCAATTTGAAATTGGTCGACGACTGACGACTAAAGAATTCAATTTGAAATT-GACCG
1 TAGAGAATTCAATTTGAAATTAGTCGACGAC-G--G-CTAAAGAATTCAATTTGAAATTAG-CCG
* **
5041 GTGGCTGGTGGC
61 GTGACTGACGGC
5053 TAGAGAATT
1 TAGAGAATT
5062 TCAAATTAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
72 28 0.40
73 1 0.01
75 2 0.03
76 39 0.56
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (72 bp):
TAGAGAATTCAATTTGAAATTAGTCGACGACGGCTAAAGAATTCAATTTGAAATTAGCCGGTGAC
TGACGGC
Found at i:5060 original size:38 final size:38
Alignment explanation
Indices: 4905--5061 Score: 144
Period size: 38 Copynumber: 4.2 Consensus size: 38
4895 AGTTGATGGT
* * *
4905 TAGAGAATTTAATTTGAAATT-A--GTTGAC-GACGGT
1 TAGAGAATTCAATTTGAAATTGACCGGTGACTGACGGC
* *
4939 TAGAGAATTCAATTTGAAATT-AGCTGGTGACTGACGGT
1 TAGAGAATTCAATTTGAAATTGA-CCGGTGACTGACGGC
** ** *
4977 TAGAGAATTCAATTTGAAATTGGTCGACGACTGACGAC
1 TAGAGAATTCAATTTGAAATTGACCGGTGACTGACGGC
* * **
5015 TAAAGAATTCAATTTGAAATTGACCGGTGGCTGGTGGC
1 TAGAGAATTCAATTTGAAATTGACCGGTGACTGACGGC
5053 TAGAGAATT
1 TAGAGAATT
5062 TCAAATTAAA
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
34 21 0.21
37 5 0.05
38 73 0.74
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (38 bp):
TAGAGAATTCAATTTGAAATTGACCGGTGACTGACGGC
Found at i:10802 original size:21 final size:21
Alignment explanation
Indices: 10776--10819 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
10766 CTCACTGTCC
10776 TTCCTCTATTTTCAATAAAGG
1 TTCCTCTATTTTCAATAAAGG
10797 TTCCTCTATTTTCAATAAAGG
1 TTCCTCTATTTTCAATAAAGG
10818 TT
1 TT
10820 ACAGGTTAAC
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:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (21 bp):
TTCCTCTATTTTCAATAAAGG
Found at i:11761 original size:2 final size:2
Alignment explanation
Indices: 11754--11781 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11744 TTATATCAAC
11754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11782 TACGGTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11855 original size:2 final size:2
Alignment explanation
Indices: 11848--11878 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11838 AAGTTTTGTT
11848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11879 GTTCAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12221 original size:3 final size:3
Alignment explanation
Indices: 12215--12246 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12205 TCGGTTTTTT
*
12215 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12247 TGTTTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12663 original size:16 final size:16
Alignment explanation
Indices: 12642--12673 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12632 ATATATTATA
12642 TATGTATATTATAATT
1 TATGTATATTATAATT
*
12658 TATGTATATTTTAATT
1 TATGTATATTATAATT
12674 ATTTTTCTCC
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:0.06, T:0.59
Consensus pattern (16 bp):
TATGTATATTATAATT
Found at i:12881 original size:22 final size:21
Alignment explanation
Indices: 12856--12900 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
12846 AATTCATATC
12856 ATATAAATTTTAATCATAATTT
1 ATATAAATTTTAATCAT-ATTT
** *
12878 ATATTTATTTTAATTATATTT
1 ATATAAATTTTAATCATATTT
12899 AT
1 AT
12901 TTCAAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATAAATTTTAATCATATTT
Found at i:14063 original size:2 final size:2
Alignment explanation
Indices: 14058--14091 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
14048 CATTCTTGTT
14058 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14092 GATGTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:14925 original size:17 final size:15
Alignment explanation
Indices: 14889--14921 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
14879 TTTGAATTTC
*
14889 TATTTTTTTCATGAT
1 TATTTTTTTCATAAT
14904 TATTTTTTTCATAAT
1 TATTTTTTTCATAAT
14919 TAT
1 TAT
14922 ATTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (15 bp):
TATTTTTTTCATAAT
Found at i:15172 original size:37 final size:37
Alignment explanation
Indices: 15105--15178 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
15095 TTTAGATGTG
*
15105 TATATAATATATATTTTATTAAAGAGTTTGAAAATATT
1 TATATAATATATATATTA-TAAAGAGTTTGAAAATATT
15143 TATATATATATATATATTA-AAAGTA-TTTGAAAATAT
1 TATATA-ATATATATATTATAAAG-AGTTTGAAAATAT
15179 CGGTAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 15 0.45
38 7 0.21
39 11 0.33
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (37 bp):
TATATAATATATATATTATAAAGAGTTTGAAAATATT
Found at i:15552 original size:23 final size:22
Alignment explanation
Indices: 15521--15564 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
15511 TATTTTATTG
15521 TTTAAAAATTATTT-TATATTAAA
1 TTTAAAAA-TATTTATA-ATTAAA
*
15544 TTTATAAATATTTATAATTAA
1 TTTAAAAATATTTATAATTAA
15565 TGTTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAAAATATTTATAATTAAA
Found at i:15720 original size:2 final size:2
Alignment explanation
Indices: 15713--15737 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15703 ATTTGATGTG
15713 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15738 TTCCCACAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16049 original size:3 final size:3
Alignment explanation
Indices: 16041--16078 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16031 GGGTATCCTA
16041 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 AA
16079 GATTGTTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19622 original size:26 final size:26
Alignment explanation
Indices: 19593--19661 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
19583 TATATGAACT
* *
19593 GACTAAATAAAATTTTAAATTTTACC
1 GACTAAATTAAATTTTAAACTTTACC
*
19619 GACTAAATTAAATTTTAAGCTTTACC
1 GACTAAATTAAATTTTAAACTTTACC
*
19645 AACTAAATTAAATTTTA
1 GACTAAATTAAATTTTA
19662 GATTATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (26 bp):
GACTAAATTAAATTTTAAACTTTACC
Found at i:20334 original size:28 final size:28
Alignment explanation
Indices: 20276--20342 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
20266 TTCATATAAG
*
20276 ATAAAT-TATTAATATATTAACATTTTAT
1 ATAAATATA-TAATATATTAACATATTAT
*
20304 ATAAATATATAATATTTTAA-ATATTAT
1 ATAAATATATAATATATTAACATATTAT
20331 -TATAATATATAA
1 ATA-AATATATAA
20343 AAATATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 15 0.43
28 16 0.46
29 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (28 bp):
ATAAATATATAATATATTAACATATTAT
Found at i:20592 original size:16 final size:16
Alignment explanation
Indices: 20552--20601 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
20542 GATTGTAACA
*
20552 TTTTATTTAAA-AATT
1 TTTTATTTAAATAAAT
*
20567 TTAATTATTTAATTAAAT
1 TT--TTATTTAAATAAAT
20585 TTTTATTTAAATAAAT
1 TTTTATTTAAATAAAT
20601 T
1 T
20602 GTGTATCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 2 0.07
16 14 0.48
17 8 0.28
18 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATTTAAATAAAT
Found at i:21302 original size:22 final size:19
Alignment explanation
Indices: 21272--21313 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
21262 TATTTTTATT
21272 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
21293 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
21313 T
1 T
21314 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:22614 original size:2 final size:2
Alignment explanation
Indices: 22607--22636 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22597 TATTTGTTTC
*
22607 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22637 TATTATAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22988 original size:13 final size:13
Alignment explanation
Indices: 22961--22999 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
22951 TATTTATTTA
22961 TTTATATTATA--
1 TTTATATTATATT
22972 TTTATATTATATT
1 TTTATATTATATT
*
22985 TTTATAATATATT
1 TTTATATTATATT
22998 TT
1 TT
23000 AATAGTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.44
13 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:22994 original size:11 final size:11
Alignment explanation
Indices: 22955--22985 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
22945 TAGATGTATT
22955 TATT-TATTTA
1 TATTATATTTA
22965 TATTATATTTA
1 TATTATATTTA
22976 TATTATATTT
1 TATTATATTT
22986 TTATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATATTTA
Found at i:25378 original size:33 final size:30
Alignment explanation
Indices: 25341--25419 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 30
25331 TTTTTATGTT
25341 ATTTTTATATTTAAGATATTAAATATTATATAA
1 ATTTTTATATTTAAGA-ATT--ATATTATATAA
* * *
25374 ATTTTGATATGTTAATAATTATTTTATATAA
1 ATTTTTATAT-TTAAGAATTATATTATATAA
25405 ATTTTAATATATTTA
1 ATTTT--TATATTTA
25420 TATACTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 15 0.38
32 3 0.08
33 16 0.41
34 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (30 bp):
ATTTTTATATTTAAGAATTATATTATATAA
Found at i:25430 original size:31 final size:31
Alignment explanation
Indices: 25366--25431 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
25356 ATATTAAATA
* * *
25366 TTATATAAATTTTGATATGTTAATAATTATT
1 TTATATAAATTTTAATATATTAATAACTATT
*
25397 TTATATAAATTTTAATATATTTATATACT-TT
1 TTATATAAATTTTAATATATTAATA-ACTATT
25428 TTAT
1 TTAT
25432 TTTACTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (31 bp):
TTATATAAATTTTAATATATTAATAACTATT
Found at i:25628 original size:21 final size:21
Alignment explanation
Indices: 25586--25628 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
25576 TATTTTTATT
**
25586 TAAATTTAATTATAAATTTTA
1 TAAATTTAATTATAAAAATTA
25607 TAAATATTAA-TATAAAAATTA
1 TAAAT-TTAATTATAAAAATTA
25628 T
1 T
25629 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATTTAATTATAAAAATTA
Found at i:25651 original size:21 final size:23
Alignment explanation
Indices: 25626--25667 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
25616 ATATAAAAAT
25626 TATTTTTTAAA-AAT-ATTTTAA
1 TATTTTTTAAATAATAATTTTAA
25647 TATTTTTTAAATAATAATTTT
1 TATTTTTTAAATAATAATTTT
25668 GATCTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTTTTAAATAATAATTTTAA
Found at i:25865 original size:2 final size:2
Alignment explanation
Indices: 25858--25882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25848 GATCTCAAGC
25858 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
25883 GCTGTCTGCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:26139 original size:22 final size:22
Alignment explanation
Indices: 26114--26166 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
26104 AAAGAATGGC
*
26114 ATTTAAAATAATTTA-AAATTTA
1 ATTT-AAATAATTTATAAAATTA
*
26136 ATTTAATTAATTTATAAAATTA
1 ATTTAAATAATTTATAAAATTA
26158 ATTTTAAAT
1 A-TTTAAAT
26167 TTTAACATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.35
22 11 0.42
23 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAAATAATTTATAAAATTA
Found at i:26570 original size:22 final size:21
Alignment explanation
Indices: 26544--26588 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
26534 TATATTTATA
26544 TTAAAAAATAATATTAATAAAT
1 TTAAAAAATAATATTAA-AAAT
** *
26566 TTAAAATTTAATATTTAAAAT
1 TTAAAAAATAATATTAAAAAT
26587 TT
1 TT
26589 TTTTATCCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAAAATAATATTAAAAAT
Found at i:28206 original size:17 final size:19
Alignment explanation
Indices: 28176--28213 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28166 GAATAATATA
*
28176 TTTTAATAGTATTATA-AT
1 TTTTAAGAGTATTATAGAT
28194 TTTTAAGAG-ATTATAGAT
1 TTTTAAGAGTATTATAGAT
28212 TT
1 TT
28214 AAATCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTAAGAGTATTATAGAT
Found at i:28855 original size:17 final size:18
Alignment explanation
Indices: 28826--28872 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
28816 TTTTTAAAAA
28826 AAAT-TATGTTTAATGTT
1 AAATATATGTTTAATGTT
28843 AAATATATG-TTAATGTT
1 AAATATATGTTTAATGTT
*
28860 AAATATATATTTA
1 AAATATATGTTTA
28873 TATATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
AAATATATGTTTAATGTT
Found at i:31397 original size:20 final size:20
Alignment explanation
Indices: 31368--31412 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31358 GGATCAGCTC
*
31368 TATTAGAATTATTATTGAAA
1 TATTAAAATTATTATTGAAA
* *
31388 TATTAAAATTTTTATTTAAA
1 TATTAAAATTATTATTGAAA
31408 T-TTAA
1 TATTAA
31413 TTATAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TATTAAAATTATTATTGAAA
Found at i:31437 original size:24 final size:23
Alignment explanation
Indices: 31385--31438 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
31375 ATTATTATTG
* *
31385 AAAT-ATTAAAATTTTTATTTAA
1 AAATAATTAAAATATTAATTTAA
**
31407 ATTTAATTATAAATATTAATTTAA
1 AAATAATTA-AAATATTAATTTAA
31431 AAATAATT
1 AAATAATT
31439 TTTATATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 2 0.08
23 4 0.17
24 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATAATTAAAATATTAATTTAA
Found at i:31570 original size:24 final size:25
Alignment explanation
Indices: 31542--31590 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
31532 GTTTAAATTA
31542 TTATTTAAA-TAATAATAAATATTT
1 TTATTTAAATTAATAATAAATATTT
*
31566 TTATTTAAATTTAATTATAAATATT
1 TTATTTAAA-TTAATAATAAATATT
31591 AATATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
26 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATTTAAATTAATAATAAATATTT
Found at i:32083 original size:5 final size:5
Alignment explanation
Indices: 32056--32128 Score: 55
Period size: 5 Copynumber: 15.0 Consensus size: 5
32046 CATTTATTCG
* * **
32056 TATTT TATT- TATT- TATTT TATTA TATTA TAATTA TATT- TAAAA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA TATTA TATTA TATTA
*
32104 TA-TA TATATA TATTT TATTA TATTA
1 TATTA TAT-TA TATTA TATTA TATTA
32129 ATAATATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
4 14 0.25
5 32 0.57
6 10 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:32124 original size:40 final size:40
Alignment explanation
Indices: 32074--32169 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
32064 TTATTTATTT
*
32074 TATTATATTATAATT-AT-ATTTAAAATATTATATATATATA
1 TATTATATTAT-ATTAATAATAT-AAATATTATATATATATA
* * * *
32114 TATTTTATTATATTAATAATATAAATATTTTATATATTTT
1 TATTATATTATATTAATAATATAAATATTATATATATATA
*
32154 TATTAGATTTATATTA
1 TATTATA-TTATATTA
32170 TTTTTTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
39 3 0.07
40 32 0.70
41 11 0.24
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (40 bp):
TATTATATTATATTAATAATATAAATATTATATATATATA
Found at i:32146 original size:25 final size:23
Alignment explanation
Indices: 32069--32151 Score: 84
Period size: 25 Copynumber: 3.6 Consensus size: 23
32059 TTTATTTATT
32069 TATTTTATTATATTATAAT-T-A
1 TATTTTATTATATTATAATATAA
**
32090 TA-TTTAAAATATTATATATATATA
1 TATTTTATTATATTATA-ATATA-A
32114 TATTTTATTATATTAATAATATAAA
1 TATTTTATTATATT-ATAATAT-AA
32139 TATTTTA-TATATT
1 TATTTTATTATATT
32152 TTTATTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 12 0.24
21 4 0.08
22 1 0.02
24 9 0.18
25 21 0.41
26 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTTATTATATTATAATATAA
Found at i:32186 original size:22 final size:20
Alignment explanation
Indices: 32141--32189 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
32131 AATATAAATA
32141 TTTTATA-TATTTTTATTAG
1 TTTTATATTATTTTTATTAG
* *
32160 ATTTATATTATTTTTTAATTAT
1 TTTTATATTA-TTTTT-ATTAG
32182 TTTTATAT
1 TTTTATAT
32190 CGTATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 5 0.21
22 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTATATTATTTTTATTAG
Found at i:34120 original size:20 final size:20
Alignment explanation
Indices: 34095--34132 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34085 TAATAATTAT
34095 ATTATTTATTAT-ATTTTTAA
1 ATTA-TTATTATAATTTTTAA
34115 ATTATTATTATAATTTTT
1 ATTATTATTATAATTTTT
34133 TTTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTATTATTATAATTTTTAA
Found at i:34139 original size:21 final size:21
Alignment explanation
Indices: 34091--34156 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
34081 AGGATAATAA
34091 TTATATTATTTATTAT-A-TTT
1 TTATATTA-TTATTATAATTTT
*
34111 TTAAATTATTATTATAATTTT
1 TTATATTATTATTATAATTTT
* * *
34132 TTTTATTATTAATAAAATTTAT
1 TTATATTATTATTATAATTT-T
34154 TTA
1 TTA
34157 ATTTATAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 19 0.51
22 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATTATTATTATAATTTT
Found at i:34455 original size:16 final size:16
Alignment explanation
Indices: 34434--34464 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34424 AATTATACAT
34434 GTTAATATAAATTTAA
1 GTTAATATAAATTTAA
34450 GTTAATATAAATTTA
1 GTTAATATAAATTTA
34465 TCAGTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
GTTAATATAAATTTAA
Found at i:34561 original size:2 final size:2
Alignment explanation
Indices: 34554--34587 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34544 ATAACAAATA
*
34554 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34588 GAAGAACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34742 original size:23 final size:24
Alignment explanation
Indices: 34698--34742 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
34688 TAAAATTTCT
34698 ATTTATAATTGATTTATTAAAAAA
1 ATTTATAATTGATTTATTAAAAAA
*
34722 ATTT-TAATT-ATTTTTTAAAAA
1 ATTTATAATTGATTTATTAAAAA
34743 GGTGATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTATAATTGATTTATTAAAAAA
Found at i:35221 original size:16 final size:15
Alignment explanation
Indices: 35201--35231 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35191 AAAAAAACTT
*
35201 ATTTTTTTAATTTTA
1 ATTTTTTTTATTTTA
35216 ATTTTTTTTATTTTA
1 ATTTTTTTTATTTTA
35231 A
1 A
35232 ATATTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTTTATTTTA
Found at i:36685 original size:15 final size:16
Alignment explanation
Indices: 36665--36694 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
36655 ATTTTATTTG
36665 AATATTTAT-TTTAAA
1 AATATTTATATTTAAA
36680 AATATTTATATTTAA
1 AATATTTATATTTAA
36695 TATTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATTTATATTTAAA
Found at i:36890 original size:18 final size:17
Alignment explanation
Indices: 36867--36901 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
36857 AAATTTTAAA
36867 ATAATTAAATATATATTT
1 ATAATT-AATATATATTT
*
36885 ATAATTAATATTTATTT
1 ATAATTAATATATATTT
36902 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATTAATATATATTT
Found at i:38961 original size:2 final size:2
Alignment explanation
Indices: 38954--38983 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38944 TTTCTTTTTA
38954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38984 TGAAAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39572 original size:25 final size:28
Alignment explanation
Indices: 39544--39599 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 28
39534 AATATTTTTA
39544 TTTAAAT-TTAATATAAA-AATAA-ATT
1 TTTAAATATTAATATAAATAATAATATT
* *
39569 TTT-AATATTATTTTAAATAATAATATT
1 TTTAAATATTAATATAAATAATAATATT
39596 TTTA
1 TTTA
39600 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 3 0.12
25 11 0.44
26 5 0.20
27 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTAAATATTAATATAAATAATAATATT
Found at i:40725 original size:16 final size:16
Alignment explanation
Indices: 40704--40734 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40694 AATTATACAT
*
40704 GTTAATATAAATTTAA
1 GTTAATAAAAATTTAA
40720 GTTAATAAAAATTTA
1 GTTAATAAAAATTTA
40735 TCAGTTCTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
GTTAATAAAAATTTAA
Found at i:43399 original size:31 final size:30
Alignment explanation
Indices: 43364--43427 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
43354 TTTATTGAAC
** *
43364 TTATTCAATTAAGTCCTCCTTATTTAACATT
1 TTATTCAATTAAGTCCAACTTAATTAAC-TT
*
43395 TTATTTAATTAAGTCCAACTTAATTAACTT
1 TTATTCAATTAAGTCCAACTTAATTAACTT
43425 TTA
1 TTA
43428 AGTGTAATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (30 bp):
TTATTCAATTAAGTCCAACTTAATTAACTT
Found at i:43710 original size:17 final size:15
Alignment explanation
Indices: 43690--43723 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
43680 TTTTTTATTT
43690 TATTATCATATTTAATA
1 TATTAT-ATATTT-ATA
43707 TATTATATATTTATA
1 TATTATATATTTATA
43722 TA
1 TA
43724 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATATATTTATA
Found at i:43815 original size:17 final size:19
Alignment explanation
Indices: 43777--43817 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
43767 AATTTTTTTA
*
43777 AAAAATAAAATCTTATATT
1 AAAAATAAAATCTGATATT
43796 AAAAATAAAAT-TGA-ATT
1 AAAAATAAAATCTGATATT
43813 AAAAA
1 AAAAA
43818 ATCGAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATAAAATCTGATATT
Found at i:46210 original size:14 final size:14
Alignment explanation
Indices: 46191--46218 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46181 TTAATTATAA
46191 AATATATAAATATT
1 AATATATAAATATT
46205 AATATATAAATATT
1 AATATATAAATATT
46219 TTTAATTTTT
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):
AATATATAAATATT
Found at i:46210 original size:21 final size:21
Alignment explanation
Indices: 46161--46214 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
46151 TTTTATTTAA
* *
46161 TAATTAAAAAATATTTAAATT
1 TAATTATAAAATATATAAATT
46182 TAATTATAAAATATATAAATAT
1 TAATTATAAAATATATAAAT-T
46204 TAATATATAAA
1 TAAT-TATAAA
46215 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.62
22 5 0.17
23 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATTATAAAATATATAAATT
Found at i:46233 original size:27 final size:28
Alignment explanation
Indices: 46201--46260 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
46191 AATATATAAA
**
46201 TATTAATATATAAAT-ATTTTTAATTTT
1 TATTAATATATAAATAATAATTAATTTT
* *
46228 TATTAATTTATTAATAATAATTAATTTT
1 TATTAATATATAAATAATAATTAATTTT
46256 T-TTAA
1 TATTAA
46261 AACTAACGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTAATATATAAATAATAATTAATTTT
Found at i:46896 original size:20 final size:22
Alignment explanation
Indices: 46863--46914 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
46853 ATAATATAAT
*
46863 TTTATAATTATTATT-TTAAAA
1 TTTATAATTTTTATTATTAAAA
*
46884 TTT-TAATTTTTATTATTAATA
1 TTTATAATTTTTATTATTAAAA
46905 TTTATAATTT
1 TTTATAATTT
46915 ATGATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 11 0.41
22 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATAATTTTTATTATTAAAA
Found at i:46901 original size:29 final size:30
Alignment explanation
Indices: 46857--46935 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
46847 ATAATTATAA
46857 TATAA-TTTTATAATTATTATTTTAAAATT
1 TATAATTTTTATAATTATTATTTTAAAATT
* * *
46886 T-TAATTTTTATTATTAATA-TTTATAATT
1 TATAATTTTTATAATTATTATTTTAAAATT
*
46914 TATGATTTTTATAATTAATTAT
1 TATAATTTTTATAATT-ATTAT
46936 AATAATATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 12 0.30
29 25 0.62
30 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (30 bp):
TATAATTTTTATAATTATTATTTTAAAATT
Found at i:46940 original size:29 final size:29
Alignment explanation
Indices: 46857--46967 Score: 79
Period size: 29 Copynumber: 3.8 Consensus size: 29
46847 ATAATTATAA
*
46857 TATAA-TTTTATAATTATTATTTTAA-AATT
1 TATAATTTTTATAATTA--ATTATAATAATT
* *
46886 T-TAATTTTTATTATTAA-TATTTATAATT
1 TATAATTTTTATAATTAATTA-TAATAATT
*
46914 TATGATTTTTATAATTAATTATAATAATAT
1 TATAATTTTTATAATTAATTATAATAAT-T
* * *
46944 TAATTATATTTATAA-TAATAATAA
1 T-ATAATTTTTATAATTAATTATAA
46968 ATATAATGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.02
27 3 0.05
28 8 0.12
29 31 0.47
30 12 0.18
31 11 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TATAATTTTTATAATTAATTATAATAATT
Found at i:46958 original size:21 final size:20
Alignment explanation
Indices: 46924--46972 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
46914 TATGATTTTT
46924 ATAATTA-ATTATAATAATA
1 ATAATTATATTATAATAATA
*
46943 TTAATTATATTTATAATAATA
1 ATAATTATA-TTATAATAATA
*
46964 ATAAATATA
1 ATAATTATA
46973 ATGATATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 18 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATTATATTATAATAATA
Found at i:46962 original size:15 final size:16
Alignment explanation
Indices: 46863--46959 Score: 66
Period size: 16 Copynumber: 6.5 Consensus size: 16
46853 ATAATATAAT
46863 TTTATAATT-ATTAT-
1 TTTATAATTAATTATA
*
46877 TTTAAAATT--TTA-A
1 TTTATAATTAATTATA
*
46890 TTT-TTATT-ATTAATA
1 TTTATAATTAATT-ATA
* * *
46905 TTTATAATTTATGATT
1 TTTATAATTAATTATA
46921 TTTATAATTAATTATA
1 TTTATAATTAATTATA
* *
46937 ATAAT-ATTAATTATA
1 TTTATAATTAATTATA
46952 TTTATAAT
1 TTTATAAT
46960 AATAATAAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
12 3 0.05
13 8 0.13
14 9 0.14
15 17 0.27
16 24 0.38
17 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
TTTATAATTAATTATA
Found at i:48000 original size:19 final size:19
Alignment explanation
Indices: 47978--48028 Score: 50
Period size: 23 Copynumber: 2.5 Consensus size: 19
47968 ATATTTTTTA
47978 AATAATTAT-AAATTTAATT
1 AATAATTATCAAA-TTAATT
47997 AATAAATTTTCATCAAATTAATT
1 AAT-AA--TT-ATCAAATTAATT
48020 AATAATTAT
1 AATAATTAT
48029 TTAATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
22 4 0.15
23 11 0.41
24 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAATTATCAAATTAATT
Found at i:48034 original size:19 final size:18
Alignment explanation
Indices: 47962--48035 Score: 53
Period size: 19 Copynumber: 4.1 Consensus size: 18
47952 TATTAGATAA
* *
47962 TAATTAATATTTTTTAAA
1 TAATTAATATTATTTAAT
*
47980 TAATT-ATA-AATTTAAT
1 TAATTAATATTATTTAAT
* * **
47996 TAATAAATTTTCATCAAAT
1 TAATTAATATT-ATTTAAT
48015 TAATTAATAATTATTTAAT
1 TAATTAAT-ATTATTTAAT
48034 TA
1 TA
48036 TAATTTTTTA
Statistics
Matches: 40, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
16 9 0.22
17 5 0.12
18 5 0.12
19 19 0.47
20 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAATATTATTTAAT
Found at i:48040 original size:14 final size:15
Alignment explanation
Indices: 48014--48046 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
48004 TTTCATCAAA
48014 TTAATTAATAATTAT
1 TTAATTAATAATTAT
*
48029 TTAATT-ATAATTTT
1 TTAATTAATAATTAT
48043 TTAA
1 TTAA
48047 AATTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAATAATTAT
Found at i:48323 original size:19 final size:19
Alignment explanation
Indices: 48294--48348 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
48284 ATATTAATTT
48294 AATTAAAAATATTATAAAAA
1 AATT-AAAATATTATAAAAA
*
48314 AATTAAAATATTA-AATAA
1 AATTAAAATATTATAAAAA
*
48332 AAGT-AAATAGTTATAAA
1 AATTAAAATA-TTATAAA
48349 GATATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 5 0.17
18 10 0.33
19 11 0.37
20 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
AATTAAAATATTATAAAAA
Found at i:50644 original size:37 final size:36
Alignment explanation
Indices: 50582--50661 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
50572 TAAAATTTTT
* * * *
50582 TTAATATTTATAATATTATTAAAATATTATTTTAATA
1 TTAATTTTTATAATATTATTAAAATAATA-ATTAAAA
*
50619 TTAATTTTTATAAT-TTAATTTAAATAATAATTAAAA
1 TTAATTTTTATAATATT-ATTAAAATAATAATTAAAA
50655 TTAATTT
1 TTAATTT
50662 AAATTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 14 0.38
37 23 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
TTAATTTTTATAATATTATTAAAATAATAATTAAAA
Found at i:52825 original size:17 final size:17
Alignment explanation
Indices: 52792--52825 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52782 TTACTTTTAT
* *
52792 TTTTATTTATTTTTTTG
1 TTTTATTTAATTGTTTG
52809 TTTTATTTAATTGTTTG
1 TTTTATTTAATTGTTTG
52826 GTTATCTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTTATTTAATTGTTTG
Found at i:54752 original size:16 final size:16
Alignment explanation
Indices: 54731--54765 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54721 AGCAAAAAAA
54731 TTTTAAAAATAAA-TAT
1 TTTTAAAAA-AAATTAT
54747 TTTTAAAAAAAATTAT
1 TTTTAAAAAAAATTAT
54763 TTT
1 TTT
54766 ATTTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTAAAAAAAATTAT
Found at i:55603 original size:23 final size:23
Alignment explanation
Indices: 55567--55614 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
55557 ATTTTTATTT
**
55567 AATTTTAATTTTTTAAAAATTAA
1 AATTTTAACGTTTTAAAAATTAA
* *
55590 AATTTTAACGTTTTGATAATTAA
1 AATTTTAACGTTTTAAAAATTAA
55613 AA
1 AA
55615 AGATACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTTTAACGTTTTAAAAATTAA
Found at i:59125 original size:83 final size:82
Alignment explanation
Indices: 59027--59182 Score: 179
Period size: 82 Copynumber: 1.9 Consensus size: 82
59017 CAGGTTGTTC
* * * * * *
59027 ATATAACTATATTTAATAAG-TAGTATCTAATTGAGTCTAAAGTTCAAACTCGAGTATCTATAAC
1 ATATAACTATATTTAA-AAGATAGCACCTAAAT-AGTCTAAAGTTCAAACTCAAGCATCTAAAAC
59091 TTTTTATTTTAATTTATTT
64 TTTTTATTTTAATTTATTT
* * * * *
59110 ATATAATTATTTTTAAAAGATAGCACCTAAATAGTTTAGAGTTCAAATTCAAGCATCTAAAACTT
1 ATATAACTATATTTAAAAGATAGCACCTAAATAGTCTAAAGTTCAAACTCAAGCATCTAAAACTT
*
59175 TTTTTTTT
66 TTTATTTT
59183 TTGTTTTAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
82 37 0.62
83 23 0.38
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (82 bp):
ATATAACTATATTTAAAAGATAGCACCTAAATAGTCTAAAGTTCAAACTCAAGCATCTAAAACTT
TTTATTTTAATTTATTT
Found at i:60180 original size:113 final size:112
Alignment explanation
Indices: 59934--60249 Score: 420
Period size: 113 Copynumber: 2.8 Consensus size: 112
59924 ATTTATGTTA
* * * * *
59934 ACTAGTTTT-AACTTGTTCTATGCATGGATAAACAATTCAA-TATAATGTTCAATACATTTATAT
1 ACTAGTTTTAAACATGTGCTATGCATGGATAAACAAATCAATTATAATTTTCATTACATTTATAT
* * *
59997 AACATTATTTAAAAATTAAATATATTTTATTTTGAAAATAATAATAT
66 AATATTATTTAAAAATTAAATATATTTTATATTAAAAATAATAATAT
* * * *
60044 ATTAGTTTCAAACATGTGCTATGCATAGATAAACAAATCAATTACAATTTTCATTACATTTATAT
1 ACTAGTTTTAAACATGTGCTATGCATGGATAAACAAATCAATTATAATTTTCATTACATTTATAT
* * *
60109 AATATTAATTAAAAATTGAATATATTTTTATATTAAAAATAATAATTT
66 AATATTATTTAAAAATTAAATATA-TTTTATATTAAAAATAATAATAT
* * * *
60157 ACTAATTTTAAACATGTGCTATGCACGGATAAACAAAGCAATGATAATTTTCATTACATTTATAT
1 ACTAGTTTTAAACATGTGCTATGCATGGATAAACAAATCAATTATAATTTTCATTACATTTATAT
* *
60222 AATATTATTTAAAAATTAATTTTATTTT
66 AATATTATTTAAAAATTAAATATATTTT
60250 GAAAATAACA
Statistics
Matches: 176, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
110 7 0.04
111 27 0.15
112 45 0.26
113 97 0.55
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (112 bp):
ACTAGTTTTAAACATGTGCTATGCATGGATAAACAAATCAATTATAATTTTCATTACATTTATAT
AATATTATTTAAAAATTAAATATATTTTATATTAAAAATAATAATAT
Found at i:63112 original size:25 final size:24
Alignment explanation
Indices: 63065--63113 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
63055 TTAAAAATTA
*
63065 ATTTTTAAATAAAATAATTTTATT
1 ATTTTTAAATAAAATAATATTATT
63089 ATTTTTAATATATAAAT-ATATTATT
1 ATTTTTAA-ATA-AAATAATATTATT
63114 TAAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTAAATAAAATAATATTATT
Found at i:64392 original size:17 final size:17
Alignment explanation
Indices: 64370--64411 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
64360 AAATATATAA
64370 ATATATATATATTAAAT
1 ATATATATATATTAAAT
* *
64387 ATATATTTATATTTAAT
1 ATATATATATATTAAAT
*
64404 ATTTATAT
1 ATATATAT
64412 TTAAATTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATATATATTAAAT
Found at i:64405 original size:13 final size:13
Alignment explanation
Indices: 64389--64419 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
64379 TATTAAATAT
64389 ATATTTATATTTA
1 ATATTTATATTTA
64402 ATATTTATATTTA
1 ATATTTATATTTA
64415 A-ATTT
1 ATATTT
64420 GAATAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:64429 original size:19 final size:19
Alignment explanation
Indices: 64381--64429 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
64371 TATATATATA
*
64381 TTAA-ATATATATTTATAT
1 TTAATATATATATTTAAAT
*
64399 TTAATATTTATATTTAAAT
1 TTAATATATATATTTAAAT
64418 TTGAATA-ATATA
1 TT-AATATATATA
64430 AATGTACGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAATATATATATTTAAAT
Found at i:66436 original size:13 final size:13
Alignment explanation
Indices: 66417--66447 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
66407 ATTTTAATAT
66417 ATATTAAATATAA
1 ATATTAAATATAA
*
66430 GTATTAAATATAA
1 ATATTAAATATAA
66443 ATATT
1 ATATT
66448 TTAAAGATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
ATATTAAATATAA
Found at i:68813 original size:24 final size:23
Alignment explanation
Indices: 68773--68820 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
68763 TAAATATAAT
68773 TATAATATATAAAAATAATACGAA
1 TATAATATATAAAAAT-ATACGAA
**
68797 TATAATATATATGAATATACGAA
1 TATAATATATAAAAATATACGAA
68820 T
1 T
68821 TATCAAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (23 bp):
TATAATATATAAAAATATACGAA
Found at i:69370 original size:16 final size:15
Alignment explanation
Indices: 69315--69373 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
69305 AAATTTTCAA
69315 GTCATTTTCGGGTTCG
1 GTCATTTT-GGGTTCG
* *
69331 AGTTATTTTGAGTTCG
1 -GTCATTTTGGGTTCG
*
69347 GATAATTTTGGGTTCAG
1 G-TCATTTTGGGTTC-G
69364 GTCATTTTGG
1 GTCATTTTGG
69374 ATTTGGGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 25 0.71
17 9 0.26
ACGTcount: A:0.15, C:0.10, G:0.29, T:0.46
Consensus pattern (15 bp):
GTCATTTTGGGTTCG
Found at i:71399 original size:16 final size:15
Alignment explanation
Indices: 71380--71461 Score: 67
Period size: 16 Copynumber: 5.2 Consensus size: 15
71370 AGTTCGAATC
71380 ATTTTAGATTTAAATT
1 ATTTTA-ATTTAAATT
*
71396 ATTTTAAATTT-GATT
1 ATTTT-AATTTAAATT
* *
71411 CATTTTAAATTACATT
1 -ATTTTAATTTAAATT
*
71427 ATTTTAAATTTTAATT
1 ATTTT-AATTTAAATT
*
71443 ATTTTTAATTCAAATT
1 A-TTTTAATTTAAATT
71459 ATT
1 ATT
71462 ATATTTTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 14 0.26
16 34 0.64
17 5 0.09
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTTTAATTTAAATT
Found at i:71402 original size:32 final size:31
Alignment explanation
Indices: 71366--71461 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
71356 CTTGAATCAA
* *
71366 TTTAAGTTCGAATCATTTTAGATTTAAATTAT
1 TTTAAATTCGAATCATTTTA-AATTAAATTAT
* * *
71398 TTTAAATTTGATTCATTTTAAATTACATTAT
1 TTTAAATTCGAATCATTTTAAATTAAATTAT
** * *
71429 TTTAAATTTTAATTATTTTTAATTCAAATTAT
1 TTTAAATTCGAATCATTTTAAATT-AAATTAT
71461 T
1 T
71462 ATATTTTATA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 29 0.55
32 24 0.45
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.55
Consensus pattern (31 bp):
TTTAAATTCGAATCATTTTAAATTAAATTAT
Found at i:71431 original size:31 final size:32
Alignment explanation
Indices: 71378--71437 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
71368 TAAGTTCGAA
*
71378 TCATTTTAGATTTAAATTATTTTAAATTTGAT
1 TCATTTTAGAATTAAATTATTTTAAATTTGAT
*
71410 TCATTTTA-AATTACATTATTTTAAATTT
1 TCATTTTAGAATTAAATTATTTTAAATTT
71438 TAATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (32 bp):
TCATTTTAGAATTAAATTATTTTAAATTTGAT
Found at i:71432 original size:15 final size:15
Alignment explanation
Indices: 71393--71436 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
71383 TTAGATTTAA
**
71393 ATTATTTTAAATTTG
1 ATTATTTTAAATTAC
71408 ATTCATTTTAAATTAC
1 ATT-ATTTTAAATTAC
71424 ATTATTTTAAATT
1 ATTATTTTAAATT
71437 TTAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTATTTTAAATTAC
Found at i:71447 original size:31 final size:32
Alignment explanation
Indices: 71378--71461 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
71368 TAAGTTCGAA
* * *
71378 TCATTTTAGATTTAAATTATTTTAAATTTGAT
1 TCATTTTAAATTCAAATTATTTTAAATTTAAT
*
71410 TCATTTTAAATT-ACATTATTTTAAATTTTAAT
1 TCATTTTAAATTCAAATTATTTTAAA-TTTAAT
*
71442 T-ATTTTTAATTCAAATTATT
1 TCATTTTAAATTCAAATTATT
71462 ATATTTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (32 bp):
TCATTTTAAATTCAAATTATTTTAAATTTAAT
Found at i:71504 original size:152 final size:152
Alignment explanation
Indices: 71322--71628 Score: 587
Period size: 152 Copynumber: 2.0 Consensus size: 152
71312 ACACTCAAAT
71322 TTATCAAATTGTTTAAATTGTTTTGAGTTAATTACTTGAATCAATTTAAGTTCGAATCATTTTAG
1 TTATCAAATTGTTTAAATTGTTTTGAGTTAATTACTTGAATCAATTTAAGTTCGAATCATTTTAG
71387 ATTTAAATTATTTTAAATTTGATTCATTTTAAATTACATTATTTTAAATTTTAATTATTTTTAAT
66 ATTTAAATTATTTTAAATTTGATTCATTTTAAATTACATTATTTTAAATTTTAATTATTTTTAAT
71452 TCAAATTATTATATTTTATATC
131 TCAAATTATTATATTTTATATC
* *
71474 TTATCAAATTGTTTAAATTGTTTTGTGTTAATTACTTGAATCAATTTAAGTTCGCATCATTTTAG
1 TTATCAAATTGTTTAAATTGTTTTGAGTTAATTACTTGAATCAATTTAAGTTCGAATCATTTTAG
*
71539 ATTTAAATTATTTTAAATTTGATTCATTTTAAATTACATTATTTTAAATTTTAATTTTTTTTAAT
66 ATTTAAATTATTTTAAATTTGATTCATTTTAAATTACATTATTTTAAATTTTAATTATTTTTAAT
71604 TCAAATTATTATATTTTATATC
131 TCAAATTATTATATTTTATATC
71626 TTA
1 TTA
71629 AATTATAATT
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (152 bp):
TTATCAAATTGTTTAAATTGTTTTGAGTTAATTACTTGAATCAATTTAAGTTCGAATCATTTTAG
ATTTAAATTATTTTAAATTTGATTCATTTTAAATTACATTATTTTAAATTTTAATTATTTTTAAT
TCAAATTATTATATTTTATATC
Found at i:71551 original size:16 final size:15
Alignment explanation
Indices: 71532--71613 Score: 58
Period size: 16 Copynumber: 5.2 Consensus size: 15
71522 AGTTCGCATC
71532 ATTTTAGATTTAAATT
1 ATTTTA-ATTTAAATT
*
71548 ATTTTAAATTT-GATT
1 ATTTT-AATTTAAATT
* *
71563 CATTTTAAATTACATT
1 -ATTTTAATTTAAATT
*
71579 ATTTTAAATTTTAATTT
1 ATTTT-AA-TTTAAATT
* *
71596 TTTTTAATTCAAATT
1 ATTTTAATTTAAATT
71611 ATT
1 ATT
71614 ATATTTTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
15 20 0.39
16 21 0.41
17 10 0.20
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTTTAATTTAAATT
Found at i:71583 original size:31 final size:32
Alignment explanation
Indices: 71530--71589 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
71520 TAAGTTCGCA
*
71530 TCATTTTAGATTTAAATTATTTTAAATTTGAT
1 TCATTTTAGAATTAAATTATTTTAAATTTGAT
*
71562 TCATTTTA-AATTACATTATTTTAAATTT
1 TCATTTTAGAATTAAATTATTTTAAATTT
71590 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (32 bp):
TCATTTTAGAATTAAATTATTTTAAATTTGAT
Found at i:71584 original size:15 final size:15
Alignment explanation
Indices: 71545--71588 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
71535 TTAGATTTAA
**
71545 ATTATTTTAAATTTG
1 ATTATTTTAAATTAC
71560 ATTCATTTTAAATTAC
1 ATT-ATTTTAAATTAC
71576 ATTATTTTAAATT
1 ATTATTTTAAATT
71589 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTATTTTAAATTAC
Found at i:71598 original size:15 final size:15
Alignment explanation
Indices: 71532--71604 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
71522 AGTTCGCATC
*
71532 ATTTTAGATTTAAATT
1 ATTTTAAATTT-AATT
*
71548 ATTTTAAATTTGATT
1 ATTTTAAATTTAATT
71563 CATTTTAAA-TTACATT
1 -ATTTTAAATTTA-ATT
71579 ATTTTAAATTTTAATT
1 ATTTTAAA-TTTAATT
* *
71595 TTTTTTAATT
1 ATTTTAAATT
71605 CAAATTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 15 0.31
16 30 0.62
17 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTAAATTTAATT
Found at i:71612 original size:32 final size:31
Alignment explanation
Indices: 71541--71613 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
71531 CATTTTAGAT
* *
71541 TTAAATTATTTTAAATTTGATTCATTTTAAA
1 TTAAATTATTTTAAATTTAATTCATTTTTAA
* *
71572 TTACATTATTTTAAATTTTAATT-TTTTTTAA
1 TTAAATTATTTTAAA-TTTAATTCATTTTTAA
71603 TTCAAATTATT
1 TT-AAATTATT
71614 ATATTTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (31 bp):
TTAAATTATTTTAAATTTAATTCATTTTTAA
Found at i:71642 original size:22 final size:22
Alignment explanation
Indices: 71581--71657 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
71571 ATTACATTAT
* *
71581 TTTAAATTTTAATTTTTTTTAA
1 TTTAAATTATAATTTTTTATAA
* * *
71603 TTCAAATTATTATATTTTAT-A
1 TTTAAATTATAATTTTTTATAA
71624 TCTTAAATTATAATTTTTTTATAAA
1 T-TTAAATTATAA-TTTTTTAT-AA
*
71649 ATTAAATTA
1 TTTAAATTA
71658 AATCAAATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
21 2 0.05
22 24 0.57
23 7 0.17
24 8 0.19
25 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAATTATAATTTTTTATAA
Found at i:72248 original size:2 final size:2
Alignment explanation
Indices: 72235--72266 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
72225 AGGGTAATTT
*
72235 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72267 AAACTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73867 original size:19 final size:19
Alignment explanation
Indices: 73845--73881 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
73835 TAAAAAATCA
* *
73845 AATTCAGTTTGATTTATCG
1 AATTAAGTTTGAGTTATCG
73864 AATTAAGTTTGAGTTATC
1 AATTAAGTTTGAGTTATC
73882 ATATGAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (19 bp):
AATTAAGTTTGAGTTATCG
Found at i:74115 original size:17 final size:15
Alignment explanation
Indices: 74093--74164 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 15
74083 CGATTTTTAT
74093 TTTTAATTAAGCTTAAA
1 TTTTAATTAA--TTAAA
74110 TTTTAA--AATTAAA
1 TTTTAATTAATTAAA
*
74123 ATTTAATTAAATTCAAA
1 TTTTAATT-AATT-AAA
*
74140 TTTTAATT-TTTAAA
1 TTTTAATTAATTAAA
74154 TTTTAAATTAA
1 TTTT-AATTAA
74165 ATTTAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
13 10 0.22
14 7 0.16
15 8 0.18
16 4 0.09
17 16 0.36
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (15 bp):
TTTTAATTAATTAAA
Found at i:74140 original size:16 final size:17
Alignment explanation
Indices: 74115--74174 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 17
74105 TTAAATTTTA
74115 AAATTAAAA-TTTAATT
1 AAATTAAAATTTTAATT
*
74131 AAATTCAAATTTTAATT
1 AAATTAAAATTTTAATT
*
74148 ---TTTAAATTTTAAATT
1 AAATTAAAATTTT-AATT
74163 AAATTTAAAATT
1 AAA-TTAAAATT
74175 CTTACTACCG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 9 0.26
15 4 0.11
16 8 0.23
17 7 0.20
19 7 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATTAAAATTTTAATT
Found at i:76938 original size:24 final size:24
Alignment explanation
Indices: 76892--76939 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
76882 TTATTTTTAT
*
76892 AATTTATTAATGGGAAAAAATTAA
1 AATTTATTAATGAGAAAAAATTAA
* * *
76916 AATTTATTGATGAGCAAATATTAA
1 AATTTATTAATGAGAAAAAATTAA
76940 CTCATATTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.35
Consensus pattern (24 bp):
AATTTATTAATGAGAAAAAATTAA
Found at i:77434 original size:22 final size:23
Alignment explanation
Indices: 77387--77431 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
77377 ACACAACATT
*
77387 TAATTGATTTATTTTTTAAAAAA
1 TAATTGATTTATTTTATAAAAAA
77410 TAATTGATTTATTTTATAAAAA
1 TAATTGATTTATTTTATAAAAA
77432 TAACATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATTGATTTATTTTATAAAAAA
Found at i:78046 original size:274 final size:272
Alignment explanation
Indices: 77627--78451 Score: 682
Period size: 273 Copynumber: 3.0 Consensus size: 272
77617 TTTTAAATAT
* *
77627 AAAAAAAGGTAATTTTATCTTAAAGTTTTTTTTTTAACTTTCCAACTATATAGAAAAGTTACTTT
1 AAAAAAAGATAATTTTATCTTAAAG---TTTTTTTAACTTTCCAACTATATAGAAAAGTTAATTT
* * * * * *
77692 CTCATTTCTCCTCATAAAAATCACATTTTTATGATTATGGGAAAGTAATTCTCAAACAAAAATTA
63 CTCAATTATCCTCATAAAAATCACATTTCTATAATCATGAGAAAGTAATTCTCAAACAAAAATTA
* * * *
77757 TATTTACAGTAAAATCAACTACTTAATAACATA-CTAAACT-TAAGAATTTAATTGGTAAGAATT
128 CATTTACAATAAAATCAAC-ACTTAATAACATATC-AAA-TATAAGAATTTAATTAGTAAGAATC
* * *
77820 TGATTTTAAAAAAAGTGAAAAATTTTCA-TCAAACTAAACACTCTTAAAGTGCGAGATTATACAT
190 TGATTTTAAAAAAAGTGAAAAATTTCCATTCAAACTAAACAC-CTCAAAGTGCGAGATTACACAT
*
77884 ATCTTATAAGATAAGATATG
254 ATCTTATAAAATAAGATA-G
* * *
77904 TGAAGAAAGATAATTTTATCTTAAAGTTGTTTTAACTTTCCAA-TAATATAAGAAAA-TTAATTT
1 -AAAAAAAGATAATTTTATCTTAAAGTTTTTTTAACTTTCCAACT-ATAT-AGAAAAGTTAATTT
*** * *
77967 CTCAATTAT-CTCATCGGAATTACATTTCTATAATCGTGAGAAAGTAATTCAT-AAA-AGAAAAT
63 CTCAATTATCCTCATAAAAATCACATTTCTATAATCATGAGAAAGTAATTC-TCAAACA-AAAAT
* *
78029 TACATTTCCAATAAAATCAACACTTTATAACATATCAAATATAAGAATTTAATTAGTAAGAATCT
126 TACATTTACAATAAAATCAACACTTAATAACATATCAAATATAAGAATTTAATTAGTAAGAATCT
* * * * * * *
78094 GATTTTTAAGATAGTGCAAAATTTCCATTGAAGCTAAACACCTCAAATTGCGAGATTACACATAT
191 GATTTTAAAAAAAGTGAAAAATTTCCATTCAAACTAAACACCTCAAAGTGCGAGATTACACATAT
78159 CTTATAAAATAAGATAG
256 CTTATAAAATAAGATAG
* * * * * *
78176 AAAAAAAGTTAATATTT-TCTTAAAGTTTTTTTTTGGAGCTTTTCAATTATATTGAAAAGTTACT
1 AAAAAAAGATAAT-TTTATCTTAAAG--TTTTTTT--AACTTTCCAACTATATAGAAAAGTTAAT
* * * ** * * * *
78240 TTC-CTAATTCTCCTCATGAAAATC-CTATTT-TCATGATTGTGGGAAAGCAATTCCCAAA-TAA
61 TTCTC-AATTATCCTCATAAAAATCAC-ATTTCT-ATAATCATGAGAAAGTAATTCTCAAACAAA
* * * * * * * * *
78301 AATTATATTT-CAATAAAATCAATACTTTATAATATAACAAACATAAGAATTTACTT-G-ATGGG
123 AATTACATTTACAATAAAATCAACACTTAATAACATATCAAATATAAGAATTTAATTAGTA-AGA
* * * * * ** * **
78363 ATTTGATTTTCAAGAAAA-CGAGAAATTTTCA-TCAAA-TCAAATGTCATCAAAGTGTAAGATTA
187 ATCTGATTTT-AAAAAAAGTGAAAAATTTCCATTCAAACT-AAA-CACCTCAAAGTGCGAGATTA
78425 CACATATCTTATAAAATAAGATA-
249 CACATATCTTATAAAATAAGATAG
78448 AAAA
1 AAAA
78452 TTATCTTATT
Statistics
Matches: 447, Mismatches: 77, Indels: 52
0.78 0.13 0.09
Matches are distributed among these distances:
271 19 0.04
272 16 0.04
273 159 0.36
274 121 0.27
275 71 0.16
276 39 0.09
278 22 0.05
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (272 bp):
AAAAAAAGATAATTTTATCTTAAAGTTTTTTTAACTTTCCAACTATATAGAAAAGTTAATTTCTC
AATTATCCTCATAAAAATCACATTTCTATAATCATGAGAAAGTAATTCTCAAACAAAAATTACAT
TTACAATAAAATCAACACTTAATAACATATCAAATATAAGAATTTAATTAGTAAGAATCTGATTT
TAAAAAAAGTGAAAAATTTCCATTCAAACTAAACACCTCAAAGTGCGAGATTACACATATCTTAT
AAAATAAGATAG
Found at i:78633 original size:27 final size:26
Alignment explanation
Indices: 78591--78653 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
78581 GAATAACATG
*
78591 AAAAAATAATTAAAATATGATATAAT
1 AAAAAATAATTAAAATATGATACAAT
78617 ATAAAAATAATGT-AAATATGATACAAT
1 A-AAAAATAAT-TAAAATATGATACAAT
78644 AAACAAATAA
1 AAA-AAATAA
78654 ACATATCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 3 0.09
27 29 0.88
28 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (26 bp):
AAAAAATAATTAAAATATGATACAAT
Found at i:79824 original size:25 final size:24
Alignment explanation
Indices: 79775--79841 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 24
79765 TTTAAGATAA
*
79775 AATATATTTATTTAAAATTTAATTTATT
1 AATATATTTATTT---ATATAATTT-TT
79803 AATA-ATTTATATTATATAATTTTT
1 AATATATTTAT-TTATATAATTTTT
79827 AATATATTTATTTAT
1 AATATATTTATTTAT
79842 TTATATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 10 0.28
25 14 0.39
27 6 0.17
28 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATATATTTATTTATATAATTTTT
Found at i:79907 original size:28 final size:27
Alignment explanation
Indices: 79778--79910 Score: 96
Period size: 28 Copynumber: 4.8 Consensus size: 27
79768 AAGATAAAAT
79778 ATATTTATTTA-A-AATTTAATTTAT-TA
1 ATATTTATTTATATAATTT--TTTATATA
*
79804 ATAATTTATATTATATAATTTTTAATATA
1 AT-ATTTAT-TTATATAATTTTTTATATA
* * *
79833 TTTATTTATTTATATTA-TTTTTATATC
1 -ATATTTATTTATATAATTTTTTATATA
* *
79860 GTATTATATTT-TAATTATTTTTTATATA
1 ATATT-TATTTAT-ATAATTTTTTATATA
*
79888 ATATTTATGTCATATAATTTTTT
1 ATATTTAT-TTATATAATTTTTT
79911 TATCTCTAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
26 7 0.08
27 26 0.30
28 37 0.43
29 10 0.12
30 6 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
ATATTTATTTATATAATTTTTTATATA
Found at i:80080 original size:19 final size:18
Alignment explanation
Indices: 80052--80106 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
80042 TAAAATTATG
80052 TTAA-ATTATATTCATATA
1 TTAATATTATATT-ATATA
*
80070 TTAATATTATATTTATATTT
1 TTAATATTATA-TTATA-TA
*
80090 TTTATATTATATTATAT
1 TTAATATTATATTATAT
80107 TATTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.16
19 14 0.44
20 13 0.41
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATTATATTATATA
Found at i:80085 original size:25 final size:25
Alignment explanation
Indices: 80057--80107 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
80047 TTATGTTAAA
80057 TTATA-TTCATATATTAATATTATAT
1 TTATATTTCATATATT-ATATTATAT
**
80082 TTATATTTTTTATATTATATTATAT
1 TTATATTTCATATATTATATTATAT
80107 T
1 T
80108 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTATATTTCATATATTATATTATAT
Found at i:80098 original size:20 final size:20
Alignment explanation
Indices: 80046--80114 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
80036 ATGTATTAAA
* *
80046 ATTATGTTAAATTATATTCAT
1 ATTATTTTATATTATATT-AT
*
80067 A-TA-TTAATATTATATTTAT
1 ATTATTTTATATTATA-TTAT
80086 ATT-TTTTATATTATATTAT
1 ATTATTTTATATTATATTAT
80105 ATTATTTTAT
1 ATTATTTTAT
80115 TTTTTATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 18 0.45
20 21 0.52
21 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (20 bp):
ATTATTTTATATTATATTAT
Found at i:80117 original size:5 final size:5
Alignment explanation
Indices: 80066--80114 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
80056 ATTATATTCA
* *
80066 TATAT TAATAT TATATT TATAT T-TTT TATAT TATAT TATAT TATTT TAT
1 TATAT T-ATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TAT
80115 TTTTTATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
4 3 0.08
5 25 0.66
6 10 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:80123 original size:27 final size:25
Alignment explanation
Indices: 80066--80128 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 25
80056 ATTATATTCA
80066 TATATTAATATTATATTTATATTTTT
1 TATATT-ATATTATATTTATATTTTT
*
80092 TATATTATATTATATTATTTTATTTTT
1 TATATTATATTATA-T-TTATATTTTT
*
80119 TATATAATAT
1 TATATTATAT
80129 AACTGTGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 8 0.24
26 7 0.21
27 18 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATATTATATTATATTTATATTTTT
Found at i:80351 original size:2 final size:2
Alignment explanation
Indices: 80344--80385 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
80334 TCAAATACCT
80344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80386 CACACATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80639 original size:2 final size:2
Alignment explanation
Indices: 80632--80664 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
80622 TGCAACCCTA
80632 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
80665 GTGTTAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:86552 original size:2 final size:2
Alignment explanation
Indices: 86545--86583 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
86535 TCAAGTCCTT
86545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
86584 GCATACGATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89316 original size:54 final size:54
Alignment explanation
Indices: 89201--89319 Score: 220
Period size: 54 Copynumber: 2.2 Consensus size: 54
89191 GGGTTACTCC
*
89201 AATGGTCATGGAGGTCGAGGCAGTGGAAGGGGAGGTGGCGGTGGAGCCTACCAA
1 AATGGTCGTGGAGGTCGAGGCAGTGGAAGGGGAGGTGGCGGTGGAGCCTACCAA
*
89255 AATGGTCGTGGAGGTCGAGGCAGTGGAAGGGGAGGTGGCGGTGGAGCCTACCAG
1 AATGGTCGTGGAGGTCGAGGCAGTGGAAGGGGAGGTGGCGGTGGAGCCTACCAA
89309 AATGGTCGTGG
1 AATGGTCGTGG
89320 CCAATATTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.22, C:0.14, G:0.48, T:0.16
Consensus pattern (54 bp):
AATGGTCGTGGAGGTCGAGGCAGTGGAAGGGGAGGTGGCGGTGGAGCCTACCAA
Found at i:89866 original size:22 final size:21
Alignment explanation
Indices: 89823--89866 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
89813 ATTTTTTATT
*
89823 TAAATTTAATTAAATTATATA
1 TAAATTTAATTAAAATATATA
89844 TAAATATTAATATAAAATA-ATA
1 TAAAT-TTAAT-TAAAATATATA
89866 T
1 T
89867 GTTAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 9 0.45
23 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTAATTAAAATATATA
Found at i:90687 original size:27 final size:27
Alignment explanation
Indices: 90620--90675 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
90610 AAATATTATA
* *
90620 TATATAAATATTTAAATGTTTTAAAATT
1 TATATAAATA-TAAAATATTTTAAAATT
90648 TATATAAATATAAAATATTTT-AAATT
1 TATATAAATATAAAATATTTTAAAATT
90674 TA
1 TA
90676 ATTATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 7 0.27
27 9 0.35
28 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TATATAAATATAAAATATTTTAAAATT
Found at i:91040 original size:54 final size:51
Alignment explanation
Indices: 90975--91093 Score: 125
Period size: 52 Copynumber: 2.3 Consensus size: 51
90965 ATAATTAAAA
* *
90975 ATATGATATAAAATATGACATAATATTAAAATATATATAAATTTATTAAAATTT
1 ATATAATATAAAATATGA-AT-ATATTAAAATATATATAAATATA-TAAAATTT
* * * * *
91029 ATATAATATAAATTATTAATTTATTAAAATTTATATAAATATATAATATTT
1 ATATAATATAAAATATGAATATATTAAAATATATATAAATATATAAAATTT
91080 A-A-AATATAATAATA
1 ATATAATATAA-AATA
91094 ATATAAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
49 7 0.12
50 4 0.07
51 8 0.14
52 20 0.36
53 2 0.04
54 15 0.27
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (51 bp):
ATATAATATAAAATATGAATATATTAAAATATATATAAATATATAAAATTT
Found at i:91876 original size:17 final size:15
Alignment explanation
Indices: 91850--91897 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
91840 TTAAAATATT
91850 TTATATATAATTTTAA
1 TTATA-ATAATTTTAA
*
91866 TTTATTAATAATTTTTA
1 -TTA-TAATAATTTTAA
*
91883 TTATAAAAATTTTAA
1 TTATAATAATTTTAA
91898 AATATTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 12 0.44
18 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATAATAATTTTAA
Found at i:92452 original size:17 final size:19
Alignment explanation
Indices: 92421--92457 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
92411 TTATCTATAA
*
92421 AAAATATAATCAAAA-ATT
1 AAAATATAATAAAAACATT
92439 AAAA-ATAATAAAAACATT
1 AAAATATAATAAAAACATT
92457 A
1 A
92458 TATATCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATATAATAAAAACATT
Found at i:93028 original size:22 final size:24
Alignment explanation
Indices: 93002--93045 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
92992 TATTACTCTA
93002 TATGT-ATAAAAT-TAAATATTTT
1 TATGTAATAAAATATAAATATTTT
*
93024 TATGTAATAATATATAAATATT
1 TATGTAATAAAATATAAATATT
93046 ATTTCATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
TATGTAATAAAATATAAATATTTT
Found at i:93238 original size:3 final size:3
Alignment explanation
Indices: 93230--93265 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
93220 ATATATATAT
93230 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT
93266 TTTTTGGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Done.