Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010590.1 Kokia drynarioides strain JFW-HI SEQ_125517, 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: 70319
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 195 characters in sequence are not A, C, G, or T
Found at i:206 original size:6 final size:6
Alignment explanation
Indices: 181--219 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
171 ACAATTCATA
* * *
181 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
220 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:2066 original size:44 final size:45
Alignment explanation
Indices: 1999--2128 Score: 181
Period size: 44 Copynumber: 2.9 Consensus size: 45
1989 GTTTACCATG
*
1999 ATGCCATAGCGTCTTTCAACTATGGTCTTACTCATTTTTGTCCT-
1 ATGCCATAGCATCTTTCAACTATGGTCTTACTCATTTTTGTCCTA
* * * *
2043 GTGTCATAGCATCTTTCAACTATGGTCTTACTCATTTTTATCTTA
1 ATGCCATAGCATCTTTCAACTATGGTCTTACTCATTTTTGTCCTA
* *
2088 ATGCCATAGCATCTTTTAGCTATGGTCTTACTCATCTTTTG
1 ATGCCATAGCATCTTTCAACTATGGTCTTACTCAT-TTTTG
2129 CATATAGCCT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 39 0.53
45 31 0.42
46 4 0.05
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (45 bp):
ATGCCATAGCATCTTTCAACTATGGTCTTACTCATTTTTGTCCTA
Found at i:5683 original size:30 final size:30
Alignment explanation
Indices: 5647--5924 Score: 265
Period size: 30 Copynumber: 9.2 Consensus size: 30
5637 CATTTTATTT
5647 AAAAATTATGTTTTGACCCCTAAACTTTCA
1 AAAAATTATGTTTTGACCCCTAAACTTTCA
* *
5677 AAAAATTATGTTTTGAGCCCTAAACTATCA
1 AAAAATTATGTTTTGACCCCTAAACTTTCA
* *
5707 AAAAATTA--TTTTGACCCCCAAACTCTCA
1 AAAAATTATGTTTTGACCCCTAAACTTTCA
* * * **
5735 AAAAATTATGTTTTAACCCTTAAGCTTTTT
1 AAAAATTATGTTTTGACCCCTAAACTTTCA
* * *
5765 AAAAATTATTTTTTAACCACTAAACTTTCAAA
1 AAAAATTATGTTTTGACCCCTAAACTTTC--A
* * * *
5797 AAAAAATATGTTTTGACCCCCAAACTATCC
1 AAAAATTATGTTTTGACCCCTAAACTTTCA
*
5827 AAAAATTATGTTTTGACCCCTAAACTTTCC
1 AAAAATTATGTTTTGACCCCTAAACTTTCA
* * ** *
5857 AAAATTTCTAATTTGACCCCTAAACTTTCC
1 AAAAATTATGTTTTGACCCCTAAACTTTCA
** * *
5887 AAAAATTCA-AATTTGGCCCCAAAACTTTCCA
1 AAAAATT-ATGTTTTGACCCCTAAACTTT-CA
5918 AAAAATT
1 AAAAATT
5925 TTTGACCAGA
Statistics
Matches: 205, Mismatches: 37, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
28 25 0.12
30 149 0.73
31 8 0.04
32 23 0.11
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAAATTATGTTTTGACCCCTAAACTTTCA
Found at i:5880 original size:92 final size:90
Alignment explanation
Indices: 5647--5891 Score: 287
Period size: 92 Copynumber: 2.7 Consensus size: 90
5637 CATTTTATTT
* * *
5647 AAAAATTATGTTTTGACCCCTAAACTTTCAAAAAATTATGTTTTGAGCCCTAAACTATC--AAAA
1 AAAAATTATGTTTTGACCCCTAAACTTTCAAAAAATTATATTTTGACCCCTAAACTTTCAAAAAA
*
5710 AATTATTTTGACCCCCAAACTCTCA
66 AATTATTTTGACCCCCAAACTATCA
* * * ** * * *
5735 AAAAATTATGTTTTAACCCTTAAGCTTTTTAAAAATTATTTTTTAACCACTAAACTTTCAAAAAA
1 AAAAATTATGTTTTGACCCCTAAACTTTCAAAAAATTATATTTTGACCCCTAAACTTTC-AAAAA
* *
5800 AAATATGTTTTGACCCCCAAACTATCC
65 AAAT-TATTTTGACCCCCAAACTATCA
* * * * *
5827 AAAAATTATGTTTTGACCCCTAAACTTTCCAAAATTTCTAATTTGACCCCTAAACTTTCCAAAAA
1 AAAAATTATGTTTTGACCCCTAAACTTTCAAAAAATTATATTTTGACCCCTAAACTTTCAAAAAA
5892 TTCAAATTTG
Statistics
Matches: 128, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
88 49 0.38
91 12 0.09
92 67 0.52
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (90 bp):
AAAAATTATGTTTTGACCCCTAAACTTTCAAAAAATTATATTTTGACCCCTAAACTTTCAAAAAA
AATTATTTTGACCCCCAAACTATCA
Found at i:6041 original size:28 final size:25
Alignment explanation
Indices: 5968--6044 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 25
5958 ACCCTAAAAT
5968 TTTCTTTTTTGTTTTAATA-TAATCC
1 TTTCTTTTTT-TTTTAATATTAATCC
*
5993 TTTATTTGTATTTCTTCTAATATTAATCCC
1 TTTCTTT-T-TTT-TT-TAATATTAAT-CC
6023 GTCTTCTTTTTTTTTTAATATT
1 -T-TTCTTTTTTTTTTAATATT
6045 TCGATTTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
25 6 0.14
26 2 0.05
27 4 0.10
28 12 0.29
29 6 0.14
30 5 0.12
31 2 0.05
32 5 0.12
ACGTcount: A:0.19, C:0.13, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTCTTTTTTTTTTAATATTAATCC
Found at i:7804 original size:17 final size:17
Alignment explanation
Indices: 7784--7826 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
7774 GTTCCCTTGA
*
7784 TCTTTAACCTTTCATCT
1 TCTTTAACCTTTCATAT
7801 TCTTTAACCTTTCATAT
1 TCTTTAACCTTTCATAT
7818 TCTTGTAAC
1 TCTT-TAAC
7827 TACTTTTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (17 bp):
TCTTTAACCTTTCATAT
Found at i:11297 original size:11 final size:11
Alignment explanation
Indices: 11267--11299 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
11257 AAAAATCATT
*
11267 GAAAGAAAGGA
1 GAAAGAAATGA
11278 GAAAGAAATGA
1 GAAAGAAATGA
11289 GAAAGAAATGA
1 GAAAGAAATGA
11300 AGATGGTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (11 bp):
GAAAGAAATGA
Found at i:12996 original size:24 final size:24
Alignment explanation
Indices: 12962--13009 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12952 ATAGATGTTC
* *
12962 AACCTTTCATCTCCTTTGACCTTT
1 AACCTTCCATCTCCTTTAACCTTT
*
12986 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTCCTTTAACCTTT
13010 CATATTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
AACCTTCCATCTCCTTTAACCTTT
Found at i:13239 original size:19 final size:21
Alignment explanation
Indices: 13215--13264 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
13205 CTTTAAATTA
13215 TTTTTAAAATTAT-TATA-AT
1 TTTTTAAAATTATATATATAT
*
13234 TTTTTAATA-TATATATATAT
1 TTTTTAAAATTATATATATAT
*
13254 TTTTTGAAATT
1 TTTTTAAAATT
13265 TTTGTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
19 12 0.48
20 9 0.36
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTTAAAATTATATATATAT
Found at i:13285 original size:19 final size:19
Alignment explanation
Indices: 13255--13307 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
13245 TATATATATT
13255 TTTTGAAATTTTTGTAAATA
1 TTTTG-AATTTTTGTAAATA
***
13275 TTTTGAATTTTAAAAAATA
1 TTTTGAATTTTTGTAAATA
*
13294 TTTTAAATTTTTGT
1 TTTTGAATTTTTGT
13308 TAAGAGAGAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TTTTGAATTTTTGTAAATA
Found at i:22331 original size:17 final size:18
Alignment explanation
Indices: 22290--22331 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
22280 AAAATTATAA
*
22290 AATTATTTTTAAAAAATT
1 AATTAATTTTAAAAAATT
*
22308 AA-GAATTTT-AAAAATT
1 AATTAATTTTAAAAAATT
22324 AATTAATT
1 AATTAATT
22332 GTTGATGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 9 0.45
17 9 0.45
18 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTAATTTTAAAAAATT
Found at i:24434 original size:18 final size:17
Alignment explanation
Indices: 24411--24448 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
24401 AGTGCTTTTT
24411 AAAAACACTTTTGACATA
1 AAAAACACTTTTGA-ATA
24429 AAAAACACTTTTGAATA
1 AAAAACACTTTTGAATA
24446 AAA
1 AAA
24449 GTAATGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAAACACTTTTGAATA
Found at i:24882 original size:12 final size:13
Alignment explanation
Indices: 24859--24898 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
24849 CTTCAAAATT
24859 ACTTTTTCAAAA-C
1 ACTTTTT-AAAAGC
24872 ACTTTTTAAAAGC
1 ACTTTTTAAAAGC
*
24885 ACTTCTTAAAAGC
1 ACTTTTTAAAAGC
24898 A
1 A
24899 ATACTAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (13 bp):
ACTTTTTAAAAGC
Found at i:26364 original size:50 final size:50
Alignment explanation
Indices: 26228--26629 Score: 255
Period size: 50 Copynumber: 7.9 Consensus size: 50
26218 TCCTTCTTGT
* *
26228 TTTTTAAGGTACCGGGTTCACCGTTGC-AGCCTCAACCTTTCCCTTCATCTCATC
1 TTTTT-AGGTACCGGGTTCGCCGTTACGA-CCTCAACCTTTCCCTTCA---CATC
* * * * * *
26282 TTCTTAGGTACTGGGTTTGTCGTTGC-AGCCTCAACCTTTCCATTCACATC
1 TTTTTAGGTACCGGGTTCGCCGTTACGA-CCTCAACCTTTCCCTTCACATC
* *
26332 TTTTTAGGTACCGGGTTTGCCGTTACGACCTCAACCTTTCCCTTTACAT-
1 TTTTTAGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCACATC
* * * ** *
26381 TTGTTTAAGGTATCGGATTCACTATTACGGCCTCAATCC--TCCTCTGT--CATC
1 TT-TTT-AGGTACCGGGTTCGCCGTTACGACCTCAA-CCTTTCC-CT-TCACATC
* * * *
26432 TCTTCATGGTACTGGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCAAATCTCATC
1 TTTTTA-GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTC--A---CATC
* * * * * *
26488 TTCTTAAGTATCGAGTTCGCCGTTATGACCTCAACCTTTCCCTTCACGTC
1 TTTTTAGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCACATC
* * * *
26538 TTCTTAGGTACCGGGTTCGCCATTGCGACCTTAACCTTTCCCTTCA-ATC
1 TTTTTAGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCACATC
* * * * **
26587 TTTTAAGGTACCAGATTTGCCGTCGCGACCTCAATCC-TTCCCT
1 TTTTTAGGTACCGGGTTCGCCGTTACGACCTCAA-CCTTTCCCT
26630 ATCAAACCAG
Statistics
Matches: 277, Mismatches: 53, Indels: 41
0.75 0.14 0.11
Matches are distributed among these distances:
49 40 0.14
50 124 0.45
51 29 0.10
52 3 0.01
53 37 0.13
54 4 0.01
55 33 0.12
56 7 0.03
ACGTcount: A:0.17, C:0.31, G:0.16, T:0.36
Consensus pattern (50 bp):
TTTTTAGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCACATC
Found at i:26557 original size:105 final size:103
Alignment explanation
Indices: 26234--26584 Score: 287
Period size: 105 Copynumber: 3.4 Consensus size: 103
26224 TTGTTTTTTA
* * * *
26234 AGGTACCGGGTTCACCGTTGC-AGCCTCAACCTTTCCCTTC--ATCTCATCTTCTTAGGTACTGG
1 AGGTACCGGGTTCGCCGTTACGA-CCTCAACCTTTCCCTTCAAATCTCATCTTCTTAAGTA-TCG
* * * *
26296 GTTTGTCG-T-TGCAGCCTCAACCTTTCCATTCACATCTTTTT
64 GTTCGCCGTTATG-A-CCTCAACCTTTCCCTTCAC-TCTTCTT
* * * *
26337 AGGTACCGGGTTTGCCGTTACGACCTCAACCTTTCCCTTTACAT-T--T-GT-TTAAGGTATCGG
1 AGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCAAATCTCATCTTCTTAA-GTATCGG
* ** * * *
26397 ATTCACTATTACGGCCTCAATCC--TCCTCTGTCATCTCTTCAT
65 -TTCGCCGTTATGACCTCAA-CCTTTCC-CT-TCA-CTCTTCTT
* *
26439 -GGTACTGGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCAAATCTCATCTTCTTAAGTATCGAG
1 AGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCAAATCTCATCTTCTTAAGTATCG-G
26503 TTCGCCGTTATGACCTCAACCTTTCCCTTCACGTCTTCTT
65 TTCGCCGTTATGACCTCAACCTTTCCCTTCAC-TCTTCTT
* * *
26543 AGGTACCGGGTTCGCCATTGCGACCTTAACCTTTCCCTTCAA
1 AGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCAA
26585 TCTTTTAAGG
Statistics
Matches: 193, Mismatches: 34, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
100 9 0.05
101 51 0.26
102 13 0.07
103 37 0.19
104 14 0.07
105 61 0.32
106 8 0.04
ACGTcount: A:0.17, C:0.31, G:0.16, T:0.35
Consensus pattern (103 bp):
AGGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCTTCAAATCTCATCTTCTTAAGTATCGGT
TCGCCGTTATGACCTCAACCTTTCCCTTCACTCTTCTT
Found at i:26617 original size:49 final size:49
Alignment explanation
Indices: 26514--26634 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 49
26504 TCGCCGTTAT
* * * *
26514 GACCTCAACCTTTCCCTTCACGTCTTCTTAGGTACCGGGTTCGCCATTGC
1 GACCTCAACCTTTCCCTTCA-ATCTTCTTAGGTACCAGATTCGCCATCGC
* * *
26564 GACCTTAACCTTTCCCTTCAATCTT-TTAAGGTACCAGATTTGCCGTCGC
1 GACCTCAACCTTTCCCTTCAATCTTCTT-AGGTACCAGATTCGCCATCGC
26613 GACCTCAATCC-TTCCCTATCAA
1 GACCTCAA-CCTTTCCCT-TCAA
26635 ACCAGTAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
48 2 0.03
49 33 0.55
50 25 0.42
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (49 bp):
GACCTCAACCTTTCCCTTCAATCTTCTTAGGTACCAGATTCGCCATCGC
Found at i:27553 original size:23 final size:23
Alignment explanation
Indices: 27518--27594 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
27508 CACCTCAACC
*
27518 TCTTC-TTTTCTTTTTTCATTTT
1 TCTTCTTTTTCTTTTTCCATTTT
*
27540 TC-TCTATTTTCTTTTTCCTTTTT
1 TCTTCT-TTTTCTTTTTCCATTTT
27563 TCTTCTTTTTCTTTTTCC-TTTT
1 TCTTCTTTTTCTTTTTCCATTTT
27585 T-TTCCTTTTT
1 TCTT-CTTTTT
27595 ATTTATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.08
22 13 0.27
23 29 0.59
24 3 0.06
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (23 bp):
TCTTCTTTTTCTTTTTCCATTTT
Found at i:28306 original size:14 final size:13
Alignment explanation
Indices: 28286--28314 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28276 TCATCTTGAC
28286 TTTTCT-TTCTTT
1 TTTTCTCTTCTTT
28298 TTTTCTCTTCTTT
1 TTTTCTCTTCTTT
28311 TTTT
1 TTTT
28315 TTTGTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTCTTT
Found at i:29193 original size:17 final size:19
Alignment explanation
Indices: 29171--29205 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29161 GATTTAATGT
29171 ATGAAATG-T-AAATGCAC
1 ATGAAATGATAAAATGCAC
29188 ATGAAATGATAAAATGCA
1 ATGAAATGATAAAATGCA
29206 TGCAACAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (19 bp):
ATGAAATGATAAAATGCAC
Found at i:32680 original size:29 final size:29
Alignment explanation
Indices: 32614--32974 Score: 182
Period size: 29 Copynumber: 12.6 Consensus size: 29
32604 AAACAGAGTC
*
32614 AAAAATGTAATTTTTGG--ATGTCGAGGG-
1 AAAAATGTAATTTTTGGACAT-TCGGGGGT
*
32641 AAAAATGGTAATTTTTGGACACTCGGGGGT
1 AAAAAT-GTAATTTTTGGACATTCGGGGGT
* *
32671 AAAAATGTAATTTTTGAACATTCGAGGGT
1 AAAAATGTAATTTTTGGACATTCGGGGGT
* **
32700 -AAAATGGTAATTTTTGGAAACTT-GGGGAC
1 AAAAAT-GTAATTTTTGGACA-TTCGGGGGT
32729 AAAAATGTAATTTTTGGACATTC-GGGGT
1 AAAAATGTAATTTTTGGACATTCGGGGGT
* * * * * *
32757 TAAAACGATATTTTTTGGAAAGTT-AGAGGT
1 AAAAATG-TAATTTTTGGACA-TTCGGGGGT
* *
32787 CAAAAATGTAA-TTTTGGATATTCGAGGGT
1 -AAAAATGTAATTTTTGGACATTCGGGGGT
* **
32816 -AAAATGGTAATTTTTGGAAAGTTC-AAGGT
1 AAAAAT-GTAATTTTTGGACA-TTCGGGGGT
* * **
32845 CAAATAT-T-ATTTTTGGAAATTTAGGGGT
1 -AAAAATGTAATTTTTGGACATTCGGGGGT
**
32873 -AAAATGGTAA-TTTTGGA-AGTT-TAGGGT
1 AAAAAT-GTAATTTTTGGACA-TTCGGGGGT
* *
32900 AAAAATGTGATTTTTTGGA-AGTTCGAGGGT
1 AAAAATGT-AATTTTTGGACA-TTCGGGGGT
* * ** *
32930 -AAAATGCAATTTTTGGAAAGTTCAAGGGA
1 AAAAATGTAATTTTTGGACA-TTCGGGGGT
32959 AAAAATGTAATTTTTG
1 AAAAATGTAATTTTTG
32975 TGAAGTTCAA
Statistics
Matches: 264, Mismatches: 41, Indels: 55
0.73 0.11 0.15
Matches are distributed among these distances:
26 4 0.02
27 20 0.08
28 71 0.27
29 116 0.44
30 44 0.17
31 9 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGACATTCGGGGGT
Found at i:32708 original size:58 final size:58
Alignment explanation
Indices: 32614--32974 Score: 312
Period size: 58 Copynumber: 6.3 Consensus size: 58
32604 AAACAGAGTC
* * *
32614 AAAAATGTAATTTTTGG--ATGTCGAGGGAAAAATGGTAATTTTTGGACACTCGGGGGT
1 AAAAATGTAATTTTTGGACAT-TCGAGGGTAAAATGGTAATTTTTGGAAACTTGGGGGT
* **
32671 AAAAATGTAATTTTTGAACATTCGAGGGTAAAATGGTAATTTTTGGAAACTTGGGGAC
1 AAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAACTTGGGGGT
* * * * * *
32729 AAAAATGTAATTTTTGGACATTCG-GGGTTAAAACGATATTTTTTGGAAAGTTAGAGGT
1 AAAAATGTAATTTTTGGACATTCGAGGG-TAAAATGGTAATTTTTGGAAACTTGGGGGT
* * ***
32787 CAAAAATGTAA-TTTTGGATATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGT
1 -AAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAACTTGGGGGT
* * * * **
32845 CAAATAT-T-ATTTTTGGAAATT-TAGGGGTAAAATGGTAA-TTTTGG-AAGTTTAGGGT
1 -AAAAATGTAATTTTTGGACATTCGA-GGGTAAAATGGTAATTTTTGGAAACTTGGGGGT
* * * ** *
32900 AAAAATGTGATTTTTTGGA-AGTTCGAGGGTAAAAT-GCAATTTTTGGAAAGTTCAAGGGA
1 AAAAATGT-AATTTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTGGAAACTT-GGGGGT
32959 AAAAATGTAATTTTTG
1 AAAAATGTAATTTTTG
32975 TGAAGTTCAA
Statistics
Matches: 256, Mismatches: 33, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
54 5 0.02
55 10 0.04
56 12 0.05
57 69 0.27
58 133 0.52
59 27 0.11
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (58 bp):
AAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAACTTGGGGGT
Found at i:32826 original size:87 final size:88
Alignment explanation
Indices: 32611--32833 Score: 241
Period size: 87 Copynumber: 2.6 Consensus size: 88
32601 AGCAAACAGA
*
32611 GTCAAAAATGTAATTTTTGGAT-GTCGAGGGAAAAATGGTAATTTTTGGACACTCGGGGGTAAAA
1 GTCAAAAATGTAATTTTTGGATATTCGAGGGAAAAATGGTAATTTTTGGACACTCGGGGGTAAAA
* *
32675 ATGTAATTTTTGAACATTCGAGG
66 ACGTAATTTTTGAACATTAGAGG
* *
32698 GT--AAAATGGTAATTTTTGGAAACTT-G-GGGACAAAAAT-GTAATTTTTGGACATTC-GGGGT
1 GTCAAAAAT-GTAATTTTTGGATA-TTCGAGGG--AAAAATGGTAATTTTTGGACACTCGGGGGT
* *
32757 TAAAACGATATTTTTTGGAA-AGTTAGA-G
62 AAAAACG-TAATTTTT-GAACA-TTAGAGG
*
32785 GTCAAAAATGTAA-TTTTGGATATTCGAGGGTAAAATGGTAATTTTTGGA
1 GTCAAAAATGTAATTTTTGGATATTCGAGGGAAAAATGGTAATTTTTGGA
32834 AAGTTCAAGG
Statistics
Matches: 114, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
85 5 0.04
86 32 0.28
87 51 0.45
88 21 0.18
89 5 0.04
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (88 bp):
GTCAAAAATGTAATTTTTGGATATTCGAGGGAAAAATGGTAATTTTTGGACACTCGGGGGTAAAA
ACGTAATTTTTGAACATTAGAGG
Found at i:32877 original size:28 final size:28
Alignment explanation
Indices: 32768--32903 Score: 73
Period size: 28 Copynumber: 4.8 Consensus size: 28
32758 AAAACGATAT
* *
32768 TTTTTGGAAAGTTAGAGGTCAAAA-ATGTA
1 TTTTTGGAAATTTAGGGGT-AAAATAT-TA
* * * * *
32797 ATTTTGGATA-TTCGAGGGTAAAATGGTAA
1 TTTTTGGAAATTTAG-GGGTAAAAT-ATTA
* * *
32826 TTTTTGGAAAGTTCA-AGGTCAAATATTA
1 TTTTTGGAAA-TTTAGGGGTAAAATATTA
**
32854 TTTTTGGAAATTTAGGGGTAAAATGGTA
1 TTTTTGGAAATTTAGGGGTAAAATATTA
* *
32882 ATTTTGGAAGTTTA-GGGTAAAA
1 TTTTTGGAAATTTAGGGGTAAAA
32904 ATGTGATTTT
Statistics
Matches: 80, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
27 11 0.14
28 40 0.50
29 27 0.34
30 1 0.01
31 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (28 bp):
TTTTTGGAAATTTAGGGGTAAAATATTA
Found at i:33011 original size:30 final size:29
Alignment explanation
Indices: 32930--33007 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
32920 GTTCGAGGGT
* *
32930 AAAATGCAATTTTTGGAAAGTTCAAGGGAA
1 AAAATGTAA-TTTTGGAAAGTTCAAGAGAA
**
32960 AAAATGTAATTTTTGTG-AAGTTCAAGAGTT
1 AAAATGTAA-TTTTG-GAAAGTTCAAGAGAA
*
32990 AAAATGTGATTTTGGAAA
1 AAAATGTAATTTTGGAAA
33008 AGTTTGAGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.02
29 7 0.17
30 32 0.78
31 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTCAAGAGAA
Found at i:33021 original size:30 final size:30
Alignment explanation
Indices: 32667--33068 Score: 190
Period size: 29 Copynumber: 13.8 Consensus size: 30
32657 GGACACTCGG
* **
32667 GGGTAAAAATGTAATTTTT-GAACA-TTCGA
1 GGGTTAAAATGTAATTTTTGGAA-AGTTTAA
* *
32696 GGG-TAAAATGGTAATTTTTGGAAA-CTT-G
1 GGGTTAAAAT-GTAATTTTTGGAAAGTTTAA
** * **
32724 GGGACAAAAATGTAATTTTTGGACA--TTCG
1 GGG-TTAAAATGTAATTTTTGGAAAGTTTAA
* *
32753 GGGTTAAAACGATATTTTTTGGAAAG-TT-A
1 GGGTTAAAATG-TAATTTTTGGAAAGTTTAA
* * **
32782 GAGGTCAAAAATGTAA-TTTTGGATA-TTCGA
1 G-GGT-TAAAATGTAATTTTTGGAAAGTTTAA
*
32812 GGG-TAAAATGGTAATTTTTGGAAAGTTCAA
1 GGGTTAAAAT-GTAATTTTTGGAAAGTTTAA
*
32842 -GGTCAAATAT-T-ATTTTTGGAAA-TTT-A
1 GGGTTAAA-ATGTAATTTTTGGAAAGTTTAA
*
32868 GGGGTAAAATGGTAA-TTTTGG-AAGTTT-A
1 GGGTTAAAAT-GTAATTTTTGGAAAGTTTAA
* * **
32896 GGGTAAAAATGTGATTTTTTGG-AAGTTCGA
1 GGGTTAAAATGT-AATTTTTGGAAAGTTTAA
* *
32926 GGG-TAAAATGCAATTTTTGGAAAGTTCAA
1 GGGTTAAAATGTAATTTTTGGAAAGTTTAA
** *
32955 GGGAAAAAATGTAATTTTTGTG-AAGTTCAA
1 GGGTTAAAATGTAATTTTTG-GAAAGTTTAA
* * *
32985 GAGTTAAAATGTGA-TTTTGGAAAAGTTTGA
1 GGGTTAAAATGTAATTTTTGG-AAAGTTTAA
*
33015 GGGTT-AAATAATAATTTTTGGAAAGTTTAA
1 GGGTTAAAAT-GTAATTTTTGGAAAGTTTAA
* *
33045 AGGTT-AAATCGTGATTTTTGGAAA
1 GGGTTAAAAT-GTAATTTTTGGAAA
33069 ATTCAAGGAC
Statistics
Matches: 294, Mismatches: 48, Indels: 61
0.73 0.12 0.15
Matches are distributed among these distances:
26 3 0.01
27 16 0.05
28 59 0.20
29 102 0.35
30 100 0.34
31 14 0.05
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTTGGAAAGTTTAA
Found at i:33037 original size:31 final size:31
Alignment explanation
Indices: 32999--33069 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
32989 TAAAATGTGA
* *
32999 TTTTGGAAAAGTTTGAGGGTTAAATAATAAT
1 TTTTGGAAAAGTTTAAAGGTTAAATAATAAT
** *
33030 TTTTGG-AAAGTTTAAAGGTTAAATCGTGAT
1 TTTTGGAAAAGTTTAAAGGTTAAATAATAAT
33060 TTTTGGAAAA
1 TTTTGGAAAA
33070 TTCAAGGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.39
Consensus pattern (31 bp):
TTTTGGAAAAGTTTAAAGGTTAAATAATAAT
Found at i:34928 original size:17 final size:17
Alignment explanation
Indices: 34891--34929 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
34881 TTTTGAATCT
* * *
34891 AAAATAATTTTAAACTT
1 AAAATAAATTTAAAATA
34908 AAAATAAATTTAAAATA
1 AAAATAAATTTAAAATA
34925 AAAAT
1 AAAAT
34930 TAGTTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAAATTTAAAATA
Found at i:43906 original size:19 final size:19
Alignment explanation
Indices: 43882--43921 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43872 TTTGTTAGAT
43882 TGCTTTGATTCTTATTTAA
1 TGCTTTGATTCTTATTTAA
43901 TGCTTTGATTCTTATTTAA
1 TGCTTTGATTCTTATTTAA
43920 TG
1 TG
43922 TTTTTCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.57
Consensus pattern (19 bp):
TGCTTTGATTCTTATTTAA
Found at i:45589 original size:101 final size:102
Alignment explanation
Indices: 45437--45668 Score: 265
Period size: 101 Copynumber: 2.3 Consensus size: 102
45427 GGACATAACA
** * * **
45437 TTCTCGAATTTTCGAAAAT-AAAGAACATTTATTAATTTTAAATAGAATATTCAATTA-TTAAGG
1 TTCTCGAATTCCCTAAAATAAAAGAACATTGAACAATTTTAAATAGAATATTCAATTACTT-AGG
* *
45500 TTCAAAGAAAAACCATACCCAACATGTTA-GAGCATAAT
65 TTCAAAGAAAAACCATACCCAACACGTTATG-GCACAAT
* * *
45538 TTCTCGAGTTCCCTAAAATAAAAGAACATTGAACAA-TTTAAATAGGATATTCAATTACTTCGGT
1 TTCTCGAATTCCCTAAAATAAAAGAACATTGAACAATTTTAAATAGAATATTCAATTACTTAGGT
* * *
45602 TCAACGAAAGACCATACCCAATACGTTATGGCACAAT
66 TCAAAGAAAAACCATACCCAACACGTTATGGCACAAT
* * *
45639 TTCTCGAATTTCTTAAAATAGAAGAACATT
1 TTCTCGAATTCCCTAAAATAAAAGAACATT
45669 ACCTCGGTTT
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
101 94 0.85
102 16 0.15
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (102 bp):
TTCTCGAATTCCCTAAAATAAAAGAACATTGAACAATTTTAAATAGAATATTCAATTACTTAGGT
TCAAAGAAAAACCATACCCAACACGTTATGGCACAAT
Found at i:46362 original size:21 final size:21
Alignment explanation
Indices: 46338--46377 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
46328 ATGAAAGAAT
46338 ATACAA-AATAAAATAAATACG
1 ATACAAGAAT-AAATAAATACG
46359 ATACAAGAATAAATAAATA
1 ATACAAGAATAAATAAATA
46378 AAATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (21 bp):
ATACAAGAATAAATAAATACG
Found at i:47385 original size:19 final size:19
Alignment explanation
Indices: 47363--47405 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
47353 CTATTTTACA
47363 TTTGTTTTTGCATTTT-TCT
1 TTTGTTTTT-CATTTTGTCT
* *
47382 TTTGCTTTTCCTTTTGTCT
1 TTTGTTTTTCATTTTGTCT
47401 TTTGT
1 TTTGT
47406 AGGTAATCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.02, C:0.14, G:0.12, T:0.72
Consensus pattern (19 bp):
TTTGTTTTTCATTTTGTCT
Found at i:51604 original size:30 final size:30
Alignment explanation
Indices: 51557--51838 Score: 265
Period size: 30 Copynumber: 9.5 Consensus size: 30
51547 CTAAACTATT
* *
51557 AAAAGATTACATTTTTACCCTCG-AGCTTCC
1 AAAA-ATTCCATTTTTACCCTCGAAACTTCC
* * *
51587 AAAAATCCCATTTTTTA-CCTCGAAGCTTCA
1 AAAAATTCCA-TTTTTACCCTCGAAACTTCC
*
51617 AAAAATTCCATTTTTGACCCT-GAAACTTCT
1 AAAAATTCCATTTTT-ACCCTCGAAACTTCC
*
51647 AAAAATTCCATTTTTACCCTCG-AACTTCT
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
* *
51676 AAAAATTCCATTTTTAACCTCGAAACTCCC
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
* * * *
51706 AAAAATTACATTTTTACCCTTG-AACCTCT
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
* * *
51735 AAAATTTCCATTTTTAACCC-CAAAACTTCA
1 AAAAATTCCATTTTT-ACCCTCGAAACTTCC
* *
51765 AAAAATTCTATTTTTACCCTC-AAACCTCC
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
* * *
51794 AAAATTTTCATTTTTGA-CCTCGAAACTTTC
1 AAAAATTCCATTTTT-ACCCTCGAAACTTCC
51824 AAAAATTACCATTTT
1 AAAAATT-CCATTTT
51839 CCCCCGAATG
Statistics
Matches: 208, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
29 90 0.43
30 109 0.52
31 9 0.04
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAAATTCCATTTTTACCCTCGAAACTTCC
Found at i:51680 original size:59 final size:60
Alignment explanation
Indices: 51556--51922 Score: 280
Period size: 59 Copynumber: 6.2 Consensus size: 60
51546 CCTAAACTAT
* * * *
51556 TAAAAGATTACATTTTT-ACCCTCG-AGCTTCCAAAAATCCCATTTTTTA-CCTCGAAGCTTC
1 TAAAA-ATTCCATTTTTGACCCTCGAAACTTCTAAAAATTCCA-TTTTTACCCTCGAA-CTTC
*
51616 AAAAAATTCCATTTTTGACCCT-GAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTC
1 TAAAAATTCCATTTTTGACCCTCGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTC
* * * * * *
51675 TAAAAATTCCATTTTT-AACCTCGAAACTCCCAAAAATTACATTTTTACCCTTGAACCTC
1 TAAAAATTCCATTTTTGACCCTCGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTC
* * * * * * *
51734 TAAAATTTCCATTTTTAACCC-CAAAACTTCAAAAAATTCTATTTTTACCCTCAAACCTC
1 TAAAAATTCCATTTTTGACCCTCGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTC
* * * *
51793 CAAAATTTTCATTTTTGA-CCTCGAAACTT-TCAAAAATTACCA-TTTT-CCCCCGAA-TGTC
1 TAAAAATTCCATTTTTGACCCTCGAAACTTCT-AAAAATT-CCATTTTTACCCTCGAACT-TC
* * * ** * *
51851 CAAAAACTCCA-TTTTGA-CCACGAAAC-TCTCGAAATTACC-CTTTTACTCTCGAA-TGTC
1 TAAAAATTCCATTTTTGACCCTCGAAACTTCTAAAAATT-CCATTTTTACCCTCGAACT-TC
*
51908 TAAAAAATCCATTTT
1 TAAAAATTCCATTTT
51923 AACCCTAAAT
Statistics
Matches: 254, Mismatches: 40, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
56 13 0.05
57 34 0.13
58 25 0.10
59 147 0.58
60 35 0.14
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (60 bp):
TAAAAATTCCATTTTTGACCCTCGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTC
Found at i:51875 original size:57 final size:57
Alignment explanation
Indices: 51805--51922 Score: 148
Period size: 57 Copynumber: 2.1 Consensus size: 57
51795 AAATTTTCAT
* * *
51805 TTTTGACCTCGAAACTTTCAAAAATTACCATTTT-CCCCCGAATGTCCAAAAACTCCA
1 TTTTGACCACGAAACTCTC-AAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCA
* * * * *
51862 TTTTGACCACGAAACTCTCGAAATTACCCTTTTACTCTCGAATGTCTAAAAAATCCA
1 TTTTGACCACGAAACTCTCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCA
51919 TTTT
1 TTTT
51923 AACCCTAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 12 0.23
57 40 0.77
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (57 bp):
TTTTGACCACGAAACTCTCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCA
Found at i:51996 original size:28 final size:28
Alignment explanation
Indices: 51936--51996 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
51926 CCTAAATTTT
* * *
51936 CCCAAAATTACCTTTTTGCCCTCGAGAA
1 CCCAAAATTACCATTTTGCCCCCAAGAA
* *
51964 TCCAAAATTACCATTTTGCCCCCAAGTA
1 CCCAAAATTACCATTTTGCCCCCAAGAA
51992 CCCAA
1 CCCAA
51997 TAGGTTTCAT
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:0.31, C:0.34, G:0.08, T:0.26
Consensus pattern (28 bp):
CCCAAAATTACCATTTTGCCCCCAAGAA
Found at i:63983 original size:115 final size:115
Alignment explanation
Indices: 63840--64093 Score: 336
Period size: 115 Copynumber: 2.2 Consensus size: 115
63830 ATGCAGACAT
*
63840 CTTCCTGATGAGATACAGAGAAGAATACCAACTCGA-GGCTCAATACGAGCAAATCTTCGAATCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACT-GAGGGCTCAATACGAGCAAATCTTCGAATCC
* * * *
63904 TAGCTTCCTGATGAGA-TACTGAGAAGCA-GGTCGAAGTAATAAAATGGTTAG
65 CAGCTTCCTAATGAGACAACTAAGAAGCAGGGT-GAAGTAATAAAA-GGTTAG
* * **
63955 CTTCCTGATGAGATACAGAGAAGTATACCAACTTAGGGCTCGATGTGAGCAAATCTTCGAATCCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTGAGGGCTCAATACGAGCAAATCTTCGAATCCC
* **
64020 ATCTTTTTAATGAGACAACTAAGAAGCAGGGTGAAGTAATAAAAGGTTAG
66 AGCTTCCTAATGAGACAACTAAGAAGCAGGGTGAAGTAATAAAAGGTTAG
64070 CTTCCTGATGAGATACTA-AGAAGT
1 CTTCCTGATGAGATAC-AGAGAAGT
64094 GAACCAGATT
Statistics
Matches: 123, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
114 1 0.01
115 96 0.78
116 23 0.19
117 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (115 bp):
CTTCCTGATGAGATACAGAGAAGTATACCAACTGAGGGCTCAATACGAGCAAATCTTCGAATCCC
AGCTTCCTAATGAGACAACTAAGAAGCAGGGTGAAGTAATAAAAGGTTAG
Found at i:64264 original size:201 final size:203
Alignment explanation
Indices: 63955--64383 Score: 618
Period size: 202 Copynumber: 2.1 Consensus size: 203
63945 AAATGGTTAG
* * * * *
63955 CTTCCTGATGAGATACAGAGAAGTATACCAACTTAGGGCTCGATGTGAGCAAATCTTCGAATCCC
1 CTTCCTGATGAGATACAGAGAAGAATACCAACTGAGGGCTCAATGCGAGCAAATCTTCGAACCCC
* ** *
64020 ATCTTTTTAATGAGACAACTAAGAAGCAGGGTGAAGTAATAAAA-GGTTAGCTTCCTGATGAGAT
66 AGCTTCCTAATGAGACAACTAAGAAGCAGGGTGAAGCAATAAAATGGTTAGCTTCCTGATGAGAT
* *
64084 ACTAAGAAGTGAACCAGATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA-CAAGCAAT
131 ACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACCAAGCAAT
64148 GCGATCAT
196 GCGATCAT
64156 CTTCCTGATGAGATACAGAGAAGAATACCAACTCGA-GGCTCAATGCGAGCAAATCTTCGAACCC
1 CTTCCTGATGAGATACAGAGAAGAATACCAACT-GAGGGCTCAATGCGAGCAAATCTTCGAA-CC
* *
64220 CCAGCTTCCTGATGAGA-TAC-AGAGAAGCA-GGTCGAAGCAATAAAATGGTTAGCTTCCTGATG
64 CCAGCTTCCTAATGAGACAACTA-AGAAGCAGGGT-GAAGCAATAAAATGGTTAGCTTCCTGATG
* *
64282 CGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACCAAG
127 AGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACCAAG
* *
64347 CTATGCGGTCAT
192 CAATGCGATCAT
*
64359 CTTCCTGATGAGATACTGAGAAGAA
1 CTTCCTGATGAGATACAGAGAAGAA
64384 GGACAAGTCG
Statistics
Matches: 204, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
200 4 0.02
201 75 0.37
202 87 0.43
203 38 0.19
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (203 bp):
CTTCCTGATGAGATACAGAGAAGAATACCAACTGAGGGCTCAATGCGAGCAAATCTTCGAACCCC
AGCTTCCTAATGAGACAACTAAGAAGCAGGGTGAAGCAATAAAATGGTTAGCTTCCTGATGAGAT
ACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACCAAGCAAT
GCGATCAT
Found at i:64758 original size:22 final size:22
Alignment explanation
Indices: 64732--64773 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
64722 CAAGTTTGAT
64732 TTTAAAATTAGGTTTAAATTAG
1 TTTAAAATTAGGTTTAAATTAG
* **
64754 TTTAAATTTATTTTTAAATT
1 TTTAAAATTAGGTTTAAATT
64774 TAAACTTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTAAAATTAGGTTTAAATTAG
Found at i:64789 original size:17 final size:16
Alignment explanation
Indices: 64744--64833 Score: 64
Period size: 17 Copynumber: 5.5 Consensus size: 16
64734 TAAAATTAGG
64744 TTTAAATTAGT-TTAAA
1 TTTAAATTA-TCTTAAA
64760 TTT--ATT-T-TTAAA
1 TTTAAATTATCTTAAA
64772 TTTAAACTTATCTTAAA
1 TTTAAA-TTATCTTAAA
64789 TTTAAATTGATCTTTTTAAA
1 TTTAAATT-ATC---TTAAA
* *
64809 TTTAAATTTGTTTTAAA
1 TTTAAA-TTATCTTAAA
64826 TTTAAATT
1 TTTAAATT
64834 TAATCAAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
12 9 0.15
14 4 0.06
15 2 0.03
16 8 0.13
17 25 0.40
20 12 0.19
21 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTAAATTATCTTAAA
Found at i:64834 original size:17 final size:18
Alignment explanation
Indices: 64754--64835 Score: 96
Period size: 17 Copynumber: 4.6 Consensus size: 18
64744 TTTAAATTAG
64754 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
* *
64772 TTTAAACTTA-TCTTAAA
1 TTTAAATTTATTTTTAAA
*
64789 TTTAAATTGATCTTTTTAAA
1 TTTAAATT--TATTTTTAAA
*
64809 TTTAAATTT-GTTTTAAA
1 TTTAAATTTATTTTTAAA
64826 TTTAAATTTA
1 TTTAAATTTA
64836 ATCAAATTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
17 29 0.54
18 10 0.19
19 1 0.02
20 14 0.26
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:65676 original size:3 final size:3
Alignment explanation
Indices: 65621--65658 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
65611 ATCAATAATA
* *
65621 ATT ATT -TT AAT ATT ATT ATT ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
65659 GATAATAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:66147 original size:11 final size:11
Alignment explanation
Indices: 66131--66156 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
66121 CTACGCATGG
66131 CGGATGTGGAT
1 CGGATGTGGAT
66142 CGGATGTGGAT
1 CGGATGTGGAT
66153 CGGA
1 CGGA
66157 GTCCGACTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.12, G:0.46, T:0.23
Consensus pattern (11 bp):
CGGATGTGGAT
Found at i:66823 original size:30 final size:29
Alignment explanation
Indices: 66758--67057 Score: 243
Period size: 30 Copynumber: 10.2 Consensus size: 29
66748 AAAGGTCCCT
* *
66758 AAACTATCCAAAAATTACATTTTTACCCCCG
1 AAACT-TCCAAAAATTCCATTTTGA-CCCCG
* *
66789 -AGCTTCCAAAAATCCCATTCTTGACCCCG
1 AAACTTCCAAAAATTCCATT-TTGACCCCG
* * *
66818 AAGCTTCCAAAAATTCCATTTTTA-CCCT
1 AAACTTCCAAAAATTCCATTTTGACCCCG
* *
66846 AAACTTCCAAAAATTCCATTTTTGATCCCA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCG
*
66876 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGACCC-CG
*
66906 -AACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCG
** * * *
66935 AAACACCCAAAAAATACATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGACCC-CG
* * *
66965 -AACCTCTAAAATTTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCG
** *
66994 AAACTTTAAAAAATTACCATTTTGCCCCCG
1 AAACTTCCAAAAATT-CCATTTTGACCCCG
* *
67024 -AA-TGTCCAAAAACTCCATTTTGGACCTCG
1 AAACT-TCCAAAAATTCCATTTT-GACCCCG
67053 AAACT
1 AAACT
67058 CTCAAAATTA
Statistics
Matches: 216, Mismatches: 38, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
28 28 0.13
29 86 0.40
30 98 0.45
31 4 0.02
ACGTcount: A:0.35, C:0.30, G:0.06, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCCCG
Found at i:66935 original size:59 final size:59
Alignment explanation
Indices: 66758--67133 Score: 345
Period size: 59 Copynumber: 6.4 Consensus size: 59
66748 AAAGGTCCCT
* * * * * *
66758 AAACTATCCAAAAATTACATTTTTACCCCCGAGCTTCCAAAAATCCCATTCTTGACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
* * *
66818 AAGCTTCCAAAAATTCCATTTTTACCCT-AAACTTCCAAAAATTCCATTTTTGATCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
66876 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
** * * * * * *
66935 AAACACCCAAAAAATACATTTTTACCCTCGAACCTCTAAAATTTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
** * * * * * *
66994 AAACTTTAAAAAATTACCA-TTTTGCCCCCGAA-TGTCCAAAAACTCCATTTTGGACCTCG
1 AAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGACCCCA
* * * * *
67053 AAAC-TCTC-AAAATTACC-CTTTTACCCTCGAA-TGTCTAAGAATTCCATTTTTAACCCTA
1 AAACTTC-CAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGACCCCA
*
67111 AAATTTCTC-AAAATTACCATTTT
1 AAACTTC-CAAAAATT-CCATTTT
67134 GCCCCCGAGA
Statistics
Matches: 261, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
58 94 0.36
59 158 0.61
60 9 0.03
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
Found at i:66976 original size:117 final size:118
Alignment explanation
Indices: 66753--67141 Score: 382
Period size: 117 Copynumber: 3.3 Consensus size: 118
66743 CCCTAAAAGG
* * * *
66753 TCCCTAAACTATCCAAAAATTA-CATTTTTACCCCCGAGCTTCCAAAAATCCCATTCTTGACCCC
1 TCCCAAAACT-TCCAAAAATTACCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCC
* * * * * *
66817 GAAGCTTCCAAAAATTCCATTTTTACCCT-AAACTTCCAAAAATTCCATTTTTGA
65 GAAACTCCCAAAAATTACATTTTTACCCTCGAACCT-CTAAAATTCCATTTTTGA
* *
66871 TCCCAAAACTTCCAAAAATT-CCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCA
1 TCCCAAAACTTCCAAAAATTACCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
* *
66935 AAACACCCAAAAAATACATTTTTACCCTCGAACCTCTAAAATTTCCATTTTTGA
66 AAACTCCCAAAAATTACATTTTTACCCTCGAACCTCTAAAA-TTCCATTTTTGA
* * ** * * * *
66989 CCCCGAAACTTTAAAAAATTACCA-TTTTGCCCCCGAA-TGTCCAAAAACTCCATTTTGGACCTC
1 TCCCAAAACTTCCAAAAATTACCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGACCCC
* ** **
67052 GAAACTCTC-AAAATTACCCTTTTACCCTCGAATGTCTAAGAATTCCATTTTT-A
65 GAAACTCCCAAAAATTACATTTTTACCCTCGAACCTCTAA-AATTCCATTTTTGA
* * *
67105 ACCCTAAAATTTCTC-AAAATTACCA-TTTTGCCCCCGA
1 TCCC-AAAACTTC-CAAAAATTACCATTTTTACCCCCGA
67142 GAATCCAAAA
Statistics
Matches: 227, Mismatches: 36, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
116 4 0.02
117 139 0.61
118 81 0.36
119 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (118 bp):
TCCCAAAACTTCCAAAAATTACCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
AAACTCCCAAAAATTACATTTTTACCCTCGAACCTCTAAAATTCCATTTTTGA
Found at i:67064 original size:30 final size:29
Alignment explanation
Indices: 66795--67162 Score: 181
Period size: 30 Copynumber: 12.6 Consensus size: 29
66785 CCCGAGCTTC
* *
66795 CAAAAATCCCATTCTTGACCCCGAAGCT-T
1 CAAAAATTCCATT-TTGACCCCGAAACTCT
* *
66824 CCAAAAATTCCATTTTTA-CCCTAAACT-T
1 -CAAAAATTCCATTTTGACCCCGAAACTCT
* *
66852 CCAAAAATTCCATTTTTGATCCCAAAACT-T
1 -CAAAAATTCCA-TTTTGACCCCGAAACTCT
*
66882 CCAAAAATTCCATTTTTACCCTCG-AACT-T
1 -CAAAAATTCCATTTTGACCC-CGAAACTCT
* * *
66911 CCAAAAATTCCATTTTTGACCCCAAAACACC
1 -CAAAAATTCCA-TTTTGACCCCGAAACTCT
* * * *
66942 CAAAAAATACATTTTTACCCTCGAACCTCT
1 CAAAAATTCCATTTTGACCC-CGAAACTCT
* *
66972 -AAAATTTCCATTTTTGACCCCGAAACTTT
1 CAAAAATTCCA-TTTTGACCCCGAAACTCT
* * **
67001 AAAAAATTACCATTTTGCCCCCGAATGTC-
1 CAAAAATT-CCATTTTGACCCCGAAACTCT
* *
67030 CAAAAACTCCATTTTGGACCTCGAAACTCT
1 CAAAAATTCCATTTT-GACCCCGAAACTCT
* **
67060 C-AAAATTACCCTTTT-ACCCTCGAATGTCT
1 CAAAAATT-CCATTTTGACCC-CGAAACTCT
* * ** *
67089 -AAGAATTCCATTTTTAACCCTAAAATTTCT
1 CAAAAATTCCA-TTTTGACCCCGAAA-CTCT
*
67119 C-AAAATTACCATTTTGCCCCCGAGAA-TC-
1 CAAAAATT-CCATTTTGACCCCGA-AACTCT
67147 C-AAAATTACCATTTTG
1 CAAAAATT-CCATTTTG
67163 CCTCGAGTAC
Statistics
Matches: 264, Mismatches: 53, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
28 48 0.18
29 95 0.36
30 113 0.43
31 8 0.03
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (29 bp):
CAAAAATTCCATTTTGACCCCGAAACTCT
Found at i:67103 original size:29 final size:28
Alignment explanation
Indices: 66827--67109 Score: 116
Period size: 29 Copynumber: 9.7 Consensus size: 28
66817 GAAGCTTCCA
*
66827 AAAATTCCATTTTTACCCT--AAACTTCCA
1 AAAATTCCATTTTTACCCTCGAAAC-T-CT
* * *
66855 AAAATTCCATTTTTGATCC-CAAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCGAAAC-T-CT
*
66885 AAAATTCCATTTTTACCCTCG-AACTTCCA
1 AAAATTCCATTTTTACCCTCGAAAC-T-CT
* * *
66914 AAAATTCCATTTTTGACCC-CAAAACACCCA
1 AAAATTCCATTTTT-ACCCTC-GAA-ACTCT
* * *
66944 AAAAATACATTTTTACCCTCGAACCTCT
1 AAAATTCCATTTTTACCCTCGAAACTCT
*
66972 AAAATTTCCATTTTTGACCC-CGAAACTTT
1 AAAA-TTCCATTTTT-ACCCTCGAAACTCT
* * ** *
67001 AAAAAATTACCA-TTTTGCCCCCGAATGTCCA
1 --AAAATT-CCATTTTTACCCTCGAAACT-CT
* *
67032 AAAACTCCATTTTGGA-CCTCGAAACTCT
1 AAAATTCCATTTT-TACCCTCGAAACTCT
* **
67060 CAAAATTACC-CTTTTACCCTCGAATGTCT
1 -AAAATT-CCATTTTTACCCTCGAAACTCT
67089 AAGAATTCCATTTTTAACCCT
1 AA-AATTCCATTTTT-ACCCT
67110 AAAATTTCTC
Statistics
Matches: 198, Mismatches: 33, Indels: 46
0.71 0.12 0.17
Matches are distributed among these distances:
28 29 0.15
29 94 0.47
30 65 0.33
31 8 0.04
32 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTCGAAACTCT
Found at i:67177 original size:27 final size:28
Alignment explanation
Indices: 67119--67178 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
67109 TAAAATTTCT
*
67119 CAAAATTACCATTTTGCCCCCGAGAATC
1 CAAAATTACCATTTTGCCCCCGAGAACC
* *
67147 CAAAATTACCATTTTG-CCTCGAGTACC
1 CAAAATTACCATTTTGCCCCCGAGAACC
67174 CAAAA
1 CAAAA
67179 GGTCTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (28 bp):
CAAAATTACCATTTTGCCCCCGAGAACC
Found at i:69303 original size:12 final size:12
Alignment explanation
Indices: 69278--69408 Score: 59
Period size: 12 Copynumber: 10.8 Consensus size: 12
69268 TTTTACAGGA
69278 TAAATATTAAAT
1 TAAATATTAAAT
69290 TAAAT-TTAATAT
1 TAAATATTAA-AT
* * *
69302 TAAGATAATCACT
1 TAA-ATATTAAAT
* *
69315 TTAATATTAAAA
1 TAAATATTAAAT
* *
69327 TAAGTATTAGAT
1 TAAATATTAAAT
* *
69339 TAAATTTTATAT
1 TAAATATTAAAT
* *
69351 TATACTATTAAAA
1 TA-AATATTAAAT
* * *
69364 TAAGTACTAGAT
1 TAAATATTAAAT
* *
69376 TAAATTTTATAT
1 TAAATATTAAAT
*
69388 TAAACTATTAAAA
1 TAAA-TATTAAAT
69401 T-AATATTA
1 TAAATATTA
69409 TTTTAAGAAT
Statistics
Matches: 84, Mismatches: 30, Indels: 11
0.67 0.24 0.09
Matches are distributed among these distances:
11 9 0.11
12 54 0.64
13 19 0.23
14 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:69360 original size:37 final size:37
Alignment explanation
Indices: 69319--69408 Score: 155
Period size: 37 Copynumber: 2.5 Consensus size: 37
69309 ATCACTTTAA
*
69319 TATTAAAATAAGTATTAGATTAAATTTTATATTATAC
1 TATTAAAATAAGTATTAGATTAAATTTTATATTAAAC
*
69356 TATTAAAATAAGTACTAGATTAAATTTTATATTAAAC
1 TATTAAAATAAGTATTAGATTAAATTTTATATTAAAC
69393 TATTAAAATAA-TATTA
1 TATTAAAATAAGTATTA
69409 TTTTAAGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
36 4 0.08
37 46 0.92
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (37 bp):
TATTAAAATAAGTATTAGATTAAATTTTATATTAAAC
Found at i:69362 original size:20 final size:20
Alignment explanation
Indices: 69337--69399 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
69327 TAAGTATTAG
69337 ATTAAATTTTATATTATACT
1 ATTAAATTTTATATTATACT
* * *
69357 ATTAAA--ATA-AGTACTA-G
1 ATTAAATTTTATATTA-TACT
*
69374 ATTAAATTTTATATTAAACT
1 ATTAAATTTTATATTATACT
69394 ATTAAA
1 ATTAAA
69400 ATAATATTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
17 9 0.29
18 4 0.13
19 3 0.10
20 15 0.48
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTAAATTTTATATTATACT
Done.