Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000786.1 Kokia drynarioides strain JFW-HI SEQ_111854, 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: 195308
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:205 original size:23 final size:23
Alignment explanation
Indices: 86--206 Score: 163
Period size: 23 Copynumber: 5.2 Consensus size: 23
76 GCGCGCGCTT
*
86 TGTTTAGCAC-GTCTCGTGCTCTC
1 TGTTTAGCACTGTGT-GTGCTCTC
109 TGTTATTAGCACTGTGTGTGCTCTC
1 TG-T-TTAGCACTGTGTGTGCTCTC
*
134 TGATTAGCACTGTGTGTGCTCTC
1 TGTTTAGCACTGTGTGTGCTCTC
* * *
157 TGATTAGTACTTTGTGTGCTCTC
1 TGTTTAGCACTGTGTGTGCTCTC
180 TGTTTAGCACTGTGTGTGCTCTC
1 TGTTTAGCACTGTGTGTGCTCTC
203 TGTT
1 TGTT
207 GCCCAGCACT
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 67 0.76
24 1 0.01
25 17 0.19
26 3 0.03
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (23 bp):
TGTTTAGCACTGTGTGTGCTCTC
Found at i:1086 original size:114 final size:116
Alignment explanation
Indices: 968--1261 Score: 328
Period size: 114 Copynumber: 2.5 Consensus size: 116
958 CCGTAATACC
* * * * *
968 ATATTGAGCTGACAGTGACATTATAAACACTGTG-TAGCTATATTGAATTGGCAGTGACACTGTA
1 ATATTGAACTGACAGTGACACTATAAACACTGCGATA-CAATACTGAATTGGCAGTGACACTGTA
* * * **
1032 AACA-CAATACTATACTG-AATTGGCAGTGACACTGTAAACACTGTGACACT
65 AACACCAATACTATACTGAAATGGGCAATGACACTATAAACACTACGACACT
* * * *
1082 ATATTGAATTGGCAGTGACACTGTAAACACTGCGATACAATACTGAATTGGCAGTGACATTGTAA
1 ATATTGAACTGACAGTGACACTATAAACACTGCGATACAATACTGAATTGGCAGTGACACTGTAA
*
1147 ACACTGCAATACTATACTGAAATGGGCAATGACACTATAAACACTACGACGCT
66 ACAC--CAATACTATACTGAAATGGGCAATGACACTATAAACACTACGACACT
* * * * * *
1200 ATATTGAATTG-TAGTGACACTGTAAACACTGCGATACTACACTG-ATCTGACAGTGACACTGT
1 ATATTGAACTGACAGTGACACTATAAACACTGCGATACAATACTGAAT-TGGCAGTGACACTGT
1262 GACCACTGCA
Statistics
Matches: 154, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
114 56 0.36
115 2 0.01
116 2 0.01
117 56 0.36
118 38 0.25
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (116 bp):
ATATTGAACTGACAGTGACACTATAAACACTGCGATACAATACTGAATTGGCAGTGACACTGTAA
ACACCAATACTATACTGAAATGGGCAATGACACTATAAACACTACGACACT
Found at i:1094 original size:39 final size:39
Alignment explanation
Indices: 980--1305 Score: 317
Period size: 39 Copynumber: 8.4 Consensus size: 39
970 ATTGAGCTGA
* * * *
980 CAGTGACATTATAAACACTGTG-TAGCTATATTGAATTGG
1 CAGTGACACTGTAAACACTGCGATA-CTATACTGAATTGG
*
1019 CAGTGACACTGTAAACA---CAATACTATACTGAATTGG
1 CAGTGACACTGTAAACACTGCGATACTATACTGAATTGG
* * *
1055 CAGTGACACTGTAAACACTGTGACACTATATTGAATTGG
1 CAGTGACACTGTAAACACTGCGATACTATACTGAATTGG
*
1094 CAGTGACACTGTAAACACTGCGATACAATACTGAATTGG
1 CAGTGACACTGTAAACACTGCGATACTATACTGAATTGG
* * *
1133 CAGTGACATTGTAAACACTGCAATACTATACTGAAATGGG
1 CAGTGACACTGTAAACACTGCGATACTATACTG-AATTGG
* * * ** *
1173 CAATGACACTATAAACACTACGACGCTATATTGAATT-G
1 CAGTGACACTGTAAACACTGCGATACTATACTGAATTGG
* * *
1211 TAGTGACACTGTAAACACTGCGATACTACACTG-ATCTGA
1 CAGTGACACTGTAAACACTGCGATACTATACTGAAT-TGG
* * * *
1250 CAGTGACACTGTGACCACTGCAATATTATTA-TG-ATTAGG
1 CAGTGACACTGTAAACACTGCGATACTA-TACTGAATT-GG
*
1289 CAGTGACATTGTAAACA
1 CAGTGACACTGTAAACA
1306 TTGTATAACT
Statistics
Matches: 233, Mismatches: 45, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
36 30 0.13
37 4 0.02
38 28 0.12
39 140 0.60
40 31 0.13
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (39 bp):
CAGTGACACTGTAAACACTGCGATACTATACTGAATTGG
Found at i:1227 original size:117 final size:117
Alignment explanation
Indices: 1011--1274 Score: 358
Period size: 117 Copynumber: 2.3 Consensus size: 117
1001 GTAGCTATAT
* * *
1011 TGAATTGGCAGTGACACTGTAAACA---CAATACTATACTGAATTGGCAGTGACACTGTAAACAC
1 TGAATTGGCAGTGACACTGTAAACACTGCAATACTATACTGAATGGGCAATGACACTATAAACAC
** *
1073 TGTGACACTATATTGAATTGGCAGTGACACTGTAAACACTGCGATACAATAC
66 TACGACACTATATTGAATTGGCAGTGACACTGTAAACACTGCGATACAACAC
*
1125 TGAATTGGCAGTGACATTGTAAACACTGCAATACTATACTGAAATGGGCAATGACACTATAAACA
1 TGAATTGGCAGTGACACTGTAAACACTGCAATACTATACTG-AATGGGCAATGACACTATAAACA
* * *
1190 CTACGACGCTATATTGAATT-GTAGTGACACTGTAAACACTGCGATACTACAC
65 CTACGACACTATATTGAATTGGCAGTGACACTGTAAACACTGCGATACAACAC
* * *
1242 TG-ATCTGACAGTGACACTGTGACCACTGCAATA
1 TGAAT-TGGCAGTGACACTGTAAACACTGCAATA
1275 TTATTATGAT
Statistics
Matches: 131, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
114 24 0.18
116 2 0.02
117 68 0.52
118 37 0.28
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (117 bp):
TGAATTGGCAGTGACACTGTAAACACTGCAATACTATACTGAATGGGCAATGACACTATAAACAC
TACGACACTATATTGAATTGGCAGTGACACTGTAAACACTGCGATACAACAC
Found at i:2160 original size:172 final size:172
Alignment explanation
Indices: 1860--2198 Score: 497
Period size: 172 Copynumber: 2.0 Consensus size: 172
1850 CCTGGGTGCC
* * *
1860 GCCTGTCAGATAACCTCCATAAAAAGTATAATTTTCGATATTATACCCCGTATATGACCCGTATA
1 GCCTGTCAGATAACCTCCAAAAAAAGTACAATTTTAGATATTATACCCCGTATATGACCCGTATA
* * * * * *
1925 AAAAAATGGGTGCCGCCTATCTAACAGCCTCCACCTATTAAAATATTTTTTATTTTTATTTTTAT
66 AAAAAATGAGTACCACCTATCTAACAACCTCCACCCATTAAAATATTTTTTATTTTAATTTTTAT
*
1990 ATGACACATGGCAGAAATTAGGGGTGGTGTCGCCTACCTGGT
131 ATGACACATGGAAGAAATTAGGGGTGGTGTCGCCTACCTGGT
2032 GCCTGTCAGATAGA-CTCCACAAAAAAGTACAATTTTTAG-TATTATACCCCGTATATGACCCGT
1 GCCTGTCAGATA-ACCTCCA-AAAAAAGTACAA-TTTTAGATATTATACCCCGTATATGACCCGT
* *
2095 AT-AAAAAATGAGTACTACCTATCTGACAACCTCCACCCATTAAAATATTGTTTT-TTTTAATTT
63 ATAAAAAAATGAGTACCACCTATCTAACAACCTCCACCCATTAAAATATT-TTTTATTTTAATTT
*
2158 TTATCTGACACATGGAAGAAATTAGGGGTGGTGTCGCCTAC
127 TTATATGACACATGGAAGAAATTAGGGGTGGTGTCGCCTAC
2199 TTGACAGTAT
Statistics
Matches: 150, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
172 104 0.69
173 41 0.27
174 5 0.03
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (172 bp):
GCCTGTCAGATAACCTCCAAAAAAAGTACAATTTTAGATATTATACCCCGTATATGACCCGTATA
AAAAAATGAGTACCACCTATCTAACAACCTCCACCCATTAAAATATTTTTTATTTTAATTTTTAT
ATGACACATGGAAGAAATTAGGGGTGGTGTCGCCTACCTGGT
Found at i:5107 original size:16 final size:16
Alignment explanation
Indices: 5085--5118 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5075 AGCTTAAATC
*
5085 TGTTTTTGTTGATTTTT
1 TGTTTTGGTT-ATTTTT
5102 TGTTTTGGTTATTTTT
1 TGTTTTGGTTATTTTT
5118 T
1 T
5119 TTAGCTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.06, C:0.00, G:0.18, T:0.76
Consensus pattern (16 bp):
TGTTTTGGTTATTTTT
Found at i:7252 original size:21 final size:20
Alignment explanation
Indices: 7195--7253 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 20
7185 TCCAATTTAA
7195 TTAAATAAAT-TATTAAAATTT
1 TTAAA-AAATATA-TAAAATTT
*
7216 TATAAAATAA-AAATAAAATTGT
1 T-TAAAA-AATATATAAAATT-T
7238 TTAAAAAATATATAAA
1 TTAAAAAATATATAAA
7254 TTTGGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
20 2 0.06
21 20 0.65
22 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TTAAAAAATATATAAAATTT
Found at i:8043 original size:13 final size:13
Alignment explanation
Indices: 8025--8056 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
8015 GCTCCGTATT
8025 AAAAAAAAAGGGA
1 AAAAAAAAAGGGA
*
8038 AAAAAAAAATGGA
1 AAAAAAAAAGGGA
8051 AAAAAA
1 AAAAAA
8057 TTCTTCCGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGGGA
Found at i:11490 original size:59 final size:54
Alignment explanation
Indices: 11386--11493 Score: 130
Period size: 59 Copynumber: 1.9 Consensus size: 54
11376 TAGTCCCCCA
11386 ATTAGTAATTTTTTTTGTCATCCAACTATAAAAAGTTACAAAATAGTCATCTATT
1 ATTAGTAATTTTTTTTGTCATCCAACTATAAAAAG-TACAAAATAGTCATCTATT
11441 ATTAGTAAATTTTTTATTTGGTCA-CTCAACTATGAAAAA-TACAAAAATAGTCA
1 ATTAGT-AA-TTTTT-TTT-GTCATC-CAACTAT-AAAAAGTAC-AAAATAGTCA
11494 CCAAGTATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
55 6 0.13
56 2 0.04
57 5 0.11
58 7 0.15
59 21 0.46
60 5 0.11
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (54 bp):
ATTAGTAATTTTTTTTGTCATCCAACTATAAAAAGTACAAAATAGTCATCTATT
Found at i:11950 original size:31 final size:31
Alignment explanation
Indices: 11915--12041 Score: 111
Period size: 31 Copynumber: 4.2 Consensus size: 31
11905 TTGGTATTTG
* *
11915 AACTTGACACTTTTTCCTAATGTGGTACCTA
1 AACTTGACACTTTTTCTTAATTTGGTACCTA
* * *
11946 AACTT-----TTTTTGGATTCAATTTGGTTCTTA
1 AACTTGACACTTTTT--CTT-AATTTGGTACCTA
*
11975 AACTTGACATTTTTTCTTAATTTGGTACCTA
1 AACTTGACACTTTTTCTTAATTTGGTACCTA
* * *
12006 AACTTGACACTTTTTTTTAAGTTGGTACTTA
1 AACTTGACACTTTTTCTTAATTTGGTACCTA
12037 AACTT
1 AACTT
12042 TTTGAGGTCC
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.07
28 1 0.01
29 15 0.20
31 48 0.63
32 2 0.03
34 5 0.07
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (31 bp):
AACTTGACACTTTTTCTTAATTTGGTACCTA
Found at i:12039 original size:91 final size:90
Alignment explanation
Indices: 11915--12096 Score: 224
Period size: 90 Copynumber: 2.0 Consensus size: 90
11905 TTGGTATTTG
** * * * *
11915 AACTTGACACTTTTTCCTAATGTGGTACCTAAACTTTTTTTGGATTCAATTTGGTTCTTAAACTT
1 AACTTGACACTTTTTCCTAATGTGGTACCTAAACTTTTTGAGG-TCCAATTTGATACATAAACTT
*
11980 GACAT-TTTTTCTTAATTTGGTACCTA
65 GAC-TCTTTTTCCTAATTTGGTACCTA
** *
12006 AACTTGACACTTTTTTTTAA-GTTGGTACTTAAACTTTTTGAGGTCCAATTTGATACATAAACTT
1 AACTTGACACTTTTTCCTAATG-TGGTACCTAAACTTTTTGAGGTCCAATTTGATACATAAACTT
*
12070 GACTCTTTTTCCTAATTTGGTATCTA
65 GACTCTTTTTCCTAATTTGGTACCTA
12096 A
1 A
12097 TCCTTTTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
89 1 0.01
90 41 0.53
91 36 0.46
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (90 bp):
AACTTGACACTTTTTCCTAATGTGGTACCTAAACTTTTTGAGGTCCAATTTGATACATAAACTTG
ACTCTTTTTCCTAATTTGGTACCTA
Found at i:12362 original size:59 final size:58
Alignment explanation
Indices: 12265--12436 Score: 195
Period size: 59 Copynumber: 2.9 Consensus size: 58
12255 AATTGAATCT
* ** *
12265 AAAAAAAGCTTAGGTACCAAATTGGGAAAAATGCCAAGTTCAAGTACCAAATT-GTGTC
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAATGTCAAGTTCAAGTACCAAATTAG-GTC
* *
12323 AAAAAAAATTTAGGTACCAAATT-AGAAATAATTGTCAAGTTCAGGTACCAAATTAGGTC
1 AAAAAAAGTTTAGGTACCAAATTAAGAAA-AA-TGTCAAGTTCAAGTACCAAATTAGGTC
* * *
12382 AAAAAAAGTTTAAGTACCAAATTAAAAAAAAAAGTGTCAAGTTCAAGTATCAAAT
1 AAAAAAAGTTTAGGTACCAAATT--AAGAAAAA-TGTCAAGTTCAAGTACCAAAT
12437 GTTATATTAA
Statistics
Matches: 97, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
57 4 0.04
58 23 0.24
59 44 0.45
60 1 0.01
61 21 0.22
62 4 0.04
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAAGAAAAATGTCAAGTTCAAGTACCAAATTAGGTC
Found at i:19498 original size:17 final size:16
Alignment explanation
Indices: 19449--19516 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 16
19439 ATCTTCTCAA
19449 TTTTATTT-TTTATTG
1 TTTTATTTATTTATTG
*
19464 TTCTAATCTTTGATTTATTG
1 TT-T--TATTT-ATTTATTG
19484 TTTTATTTTATTTATCT-
1 TTTTA-TTTATTTAT-TG
19501 TATTTATTTATTTATT
1 T-TTTATTTATTTATT
19517 TTAATTGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 17 0.40
18 12 0.28
19 1 0.02
20 9 0.21
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (16 bp):
TTTTATTTATTTATTG
Found at i:19514 original size:26 final size:26
Alignment explanation
Indices: 19476--19544 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
19466 CTAATCTTTG
19476 ATTTATTGT-TTTATTTTATTTATCTT
1 ATTTATT-TATTTATTTTATTTATCTT
* * *
19502 ATTTATTTATTTATTTTAATTGTTTT
1 ATTTATTTATTTATTTTATTTATCTT
*
19528 ATTTA-ATATTT-TTTTAT
1 ATTTATTTATTTATTTTAT
19545 CTAACTTGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 5 0.14
25 6 0.16
26 26 0.70
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (26 bp):
ATTTATTTATTTATTTTATTTATCTT
Found at i:19532 original size:4 final size:4
Alignment explanation
Indices: 19476--19517 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
19466 CTAATCTTTG
19476 ATTT ATTGT -TTT ATTTT ATTT ATCTT ATTT ATTT ATTT ATTT
1 ATTT ATT-T ATTT A-TTT ATTT AT-TT ATTT ATTT ATTT ATTT
19518 TAATTGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 1 0.03
4 24 0.71
5 9 0.26
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:19534 original size:13 final size:12
Alignment explanation
Indices: 19476--19517 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
19466 CTAATCTTTG
19476 ATTTATTGT-TTT
1 ATTTATT-TATTT
19488 ATTTTATTTATCTT
1 A-TTTATTTAT-TT
19502 ATTTATTTATTT
1 ATTTATTTATTT
19514 ATTT
1 ATTT
19518 TAATTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.30
13 16 0.59
14 3 0.11
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
ATTTATTTATTT
Found at i:24054 original size:2 final size:2
Alignment explanation
Indices: 24047--24100 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
24037 ACGAGAATGA
24047 AT AT AT AT AT AT 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 AT AT AT AT AT AT
24089 AT AT AT AT AT AT
1 AT AT AT AT AT AT
24101 TATCTAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24726 original size:37 final size:37
Alignment explanation
Indices: 24680--24756 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
24670 ATTTTGATTA
* *
24680 ATTCGATTAATTTTTATATTTTGGACTTATATAATGT
1 ATTCAATTAATTTTTATATTTTAGACTTATATAATGT
**
24717 ATTCAATTAATTTTTATATTTTAGTTTTATATAATGT
1 ATTCAATTAATTTTTATATTTTAGACTTATATAATGT
24754 ATT
1 ATT
24757 GGACCTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (37 bp):
ATTCAATTAATTTTTATATTTTAGACTTATATAATGT
Found at i:25975 original size:97 final size:95
Alignment explanation
Indices: 25821--26000 Score: 234
Period size: 97 Copynumber: 1.9 Consensus size: 95
25811 TTAATTATTG
* * * * *
25821 AACTCCTCTAAGAAAACGTTCGAATTAAAATTCAATTATTTTGTTAAAGAAATCTTATTAATATA
1 AACTCCTCCAAGAAAACGTACAAATTAAAATTCAATTATTTTATTAAACAAATCTTATTAATATA
*
25886 TTTAAATTAAAATATTTATTAACTTGAATA
66 TTGAAATTAAAATATTTATTAACTTGAATA
* * * *
25916 AACTCCTCCAATGAAAATGTACAAATTAAAACTTTAATTGTTTTATTAAACAAATCTTATTGATA
1 AACTCCTCCAA-GAAAACGTACAAATTAAAA-TTCAATTATTTTATTAAACAAATCTTATTAATA
* *
25981 TGTTGGAATTAAAATATTTA
64 TATTGAAATTAAAATATTTA
26001 ACTCCTTACT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 10 0.14
96 16 0.23
97 45 0.63
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (95 bp):
AACTCCTCCAAGAAAACGTACAAATTAAAATTCAATTATTTTATTAAACAAATCTTATTAATATA
TTGAAATTAAAATATTTATTAACTTGAATA
Found at i:39204 original size:18 final size:18
Alignment explanation
Indices: 39181--39235 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
39171 ACAATTCATA
* *
39181 TCACTTTCAATTCCAATT
1 TCACTTTCACTTTCAATT
* *
39199 TCACTTTTACTTTCACTT
1 TCACTTTCACTTTCAATT
39217 TCACTTTCACTTTCAATT
1 TCACTTTCACTTTCAATT
39235 T
1 T
39236 TGTTCACAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (18 bp):
TCACTTTCACTTTCAATT
Found at i:39210 original size:6 final size:6
Alignment explanation
Indices: 39181--39231 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
39171 ACAATTCATA
* * * *
39181 TCACTT TCAATT CCAATT TCACTT TTACTT TCACTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
39229 TCA
1 TCA
39232 ATTTTGTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:39402 original size:16 final size:17
Alignment explanation
Indices: 39381--39413 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39371 TTAAACACGT
39381 AATATT-TCACATATAC
1 AATATTATCACATATAC
39397 AATATTCATCACATATA
1 AATATT-ATCACATATA
39414 TATCCTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATTATCACATATAC
Found at i:53716 original size:24 final size:25
Alignment explanation
Indices: 53688--53734 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
53678 TTTACATTTC
53688 TCTTATT-TCATT-TCCATTTTTTAA
1 TCTTATTCT-ATTCTCCATTTTTTAA
53712 TCTTATTCTATTCTCCATTTTTT
1 TCTTATTCTATTCTCCATTTTTT
53735 GCCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (25 bp):
TCTTATTCTATTCTCCATTTTTTAA
Found at i:58912 original size:46 final size:46
Alignment explanation
Indices: 58859--58951 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
58849 CTTATTTATG
58859 AGTTGGAATTGGACTATAGATATTTCTAGATATTATTTCAAAAAGA
1 AGTTGGAATTGGACTATAGATATTTCTAGATATTATTTCAAAAAGA
58905 AGTTGGAATTGGACTATAGATATTTCTAGATATTATTTCAAAAAGA
1 AGTTGGAATTGGACTATAGATATTTCTAGATATTATTTCAAAAAGA
58951 A
1 A
58952 CAAATATGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (46 bp):
AGTTGGAATTGGACTATAGATATTTCTAGATATTATTTCAAAAAGA
Found at i:63835 original size:21 final size:21
Alignment explanation
Indices: 63809--63883 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
63799 AACAAAACAC
*
63809 AAAACCAACAACCTCTCTTGG
1 AAAACCAGCAACCTCTCTTGG
* *
63830 AAAACCAGCAGCATCCTCTT-G
1 AAAACCAGCAACCT-CTCTTGG
63851 AAATACCAGCAGCACCT-TCTTGG
1 AAA-ACCAGCA--ACCTCTCTTGG
63874 AAAACCAGCA
1 AAAACCAGCA
63884 GCCAGGAACC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
21 15 0.34
22 23 0.52
23 4 0.09
24 2 0.05
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.17
Consensus pattern (21 bp):
AAAACCAGCAACCTCTCTTGG
Found at i:63858 original size:22 final size:21
Alignment explanation
Indices: 63823--63885 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 21
63813 CCAACAACCT
63823 CTCTTGGAAAACCAGCAGCATC
1 CTCTTGGAAAACCAGCAGCA-C
63845 CTCTT-GAAATACCAGCAGCAC
1 CTCTTGGAAA-ACCAGCAGCAC
63866 CTTCTTGGAAAACCAGCAGC
1 C-TCTTGGAAAACCAGCAGC
63886 CAGGAACCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.16
22 28 0.74
23 4 0.11
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (21 bp):
CTCTTGGAAAACCAGCAGCAC
Found at i:74944 original size:19 final size:19
Alignment explanation
Indices: 74920--74959 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
74910 CTTACAAATA
*
74920 TTCGAGCTGGAATCAATGT
1 TTCGAGCTAGAATCAATGT
74939 TTCGAGCTAGAATCAATGT
1 TTCGAGCTAGAATCAATGT
74958 TT
1 TT
74960 TAGGTGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (19 bp):
TTCGAGCTAGAATCAATGT
Found at i:75462 original size:171 final size:171
Alignment explanation
Indices: 75148--75471 Score: 411
Period size: 171 Copynumber: 1.9 Consensus size: 171
75138 GTTTATTCAG
* *** * * *
75148 TGATTTCATGGTAATATCTGTTCAAACTTTCTTAATTTTTTGACAAGGCACACACACCTTATACA
1 TGATTACATGGTAATATCTGTTCAAACTTTCTTAACCCTTTGACAACGCACACACACATTACACA
* * * *
75213 CATAGACGCTCGAACCCAAGACCTCTAAAATGAATAACATCATCTTTTCCACTAGATCCACTTAC
66 CATAGACGCTCGAACCCAAAACCTCTAAAATGAACAACATCATCTTTACCACTAGAACCACTTAC
* * *
75278 TGGGTTTAATTTGGATTCATTTTTTTTTTAATATGCTTGTA
131 TAGATTCAATTTGGATTCATTTTTTTTTTAATATGCTTGTA
*
75319 TGATTACATGGTAATATCTGTTCATACTTTCTTAACCCTTTGACAACGCACACACACATTGCACA
1 TGATTACATGGTAATATCTGTTCAAACTTTCTTAACCCTTTGACAACGCACACACACATT--ACA
* * * *
75384 CACA-AG-CGCTCGAACCCAAAA-ATCCTAAGATGAACAACATCCTCTTTACCACTGGAACCACT
64 CACATAGACGCTCGAACCCAAAACCT-CTAAAATGAACAACATCATCTTTACCACTAGAACCACT
**
75446 TGTTAGATTCAATTTGGATTCATTTT
128 TACTAGATTCAATTTGGATTCATTTT
75472 AAATGTATTC
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
170 1 0.01
171 120 0.93
172 2 0.02
173 6 0.05
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (171 bp):
TGATTACATGGTAATATCTGTTCAAACTTTCTTAACCCTTTGACAACGCACACACACATTACACA
CATAGACGCTCGAACCCAAAACCTCTAAAATGAACAACATCATCTTTACCACTAGAACCACTTAC
TAGATTCAATTTGGATTCATTTTTTTTTTAATATGCTTGTA
Found at i:87269 original size:82 final size:82
Alignment explanation
Indices: 87132--87287 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 82
87122 TGTATAATTT
* *
87132 TGTCAATTCATGGCACCAGATGCCTAGCGGATAAATCGCAATAAGTGAGCCCAGCTCTAGTTGGA
1 TGTCAATTCATGGCACCAGATGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGA
87197 TTAACCAACAATGATTC
66 TTAACCAACAATGATTC
* *
87214 TGTCAATTCCTGGTACCCA-ATGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGG
1 TGTCAATTCATGGCA-CCAGATGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGG
87278 ATTAACCAAC
65 ATTAACCAAC
87288 GGTTTTGCAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
82 66 0.96
83 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (82 bp):
TGTCAATTCATGGCACCAGATGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGA
TTAACCAACAATGATTC
Found at i:87474 original size:181 final size:184
Alignment explanation
Indices: 87142--87508 Score: 519
Period size: 181 Copynumber: 2.0 Consensus size: 184
87132 TGTCAATTCA
*
87142 TGGCACCAGATGCCTAGCGGATAAATCGCAATAAGTGAGCCCAGCTCTAGTTGGATTAACCAACA
1 TGGCACCAGATGCCTAGCGGATAAATCGCAATAAGTGAGCCCAGATCTAGTTGGATTAACCAACA
* * * *
87207 ATGATTCTGTCAATTCCTGGTACCCAATGCCTAGCAGATAAACCGCAATAAGTGAGCCCAGCTCT
66 ATGA-TCCGTCAAATCCTGGCACCCAATGCCTAACAGATAAACCGCAATAAGTGAGCCCAGCTCT
* * * **
87272 AGTTGGATTAACCAACGGTTTTGCACCTAGCGCTAGTCGAATAAATTGACGATCC
130 AATTGAATTAACCAACGGTTTTGCACCCAGCGCTAGTCGAATAAACCGACGATCC
**
87327 TGGCACCTAG-TGCCTAGCGGATAAA-CTGCAA-AAGTGAGCCCAGATCTAGTTGGATTAGTCAA
1 TGGCACC-AGATGCCTAGCGGATAAATC-GCAATAAGTGAGCCCAGATCTAGTTGGATTAACCAA
* * *
87389 CAATG-TCCGTCAAATCTTGGCACTCAATGCCTAACAGATAAAGCGCAA-AAGTGAGCCCAGCTC
64 CAATGATCCGTCAAATCCTGGCACCCAATGCCTAACAGATAAACCGCAATAAGTGAGCCCAGCTC
* *
87452 TAATTGAATTAACCAACGGTTTTGCGCCCAGCGCTAGTCGGATAAACCGACGATCC
129 TAATTGAATTAACCAACGGTTTTGCACCCAGCGCTAGTCGAATAAACCGACGATCC
87508 T
1 T
87509 TTAATAATTC
Statistics
Matches: 163, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
181 65 0.40
182 36 0.22
184 34 0.21
185 26 0.16
186 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (184 bp):
TGGCACCAGATGCCTAGCGGATAAATCGCAATAAGTGAGCCCAGATCTAGTTGGATTAACCAACA
ATGATCCGTCAAATCCTGGCACCCAATGCCTAACAGATAAACCGCAATAAGTGAGCCCAGCTCTA
ATTGAATTAACCAACGGTTTTGCACCCAGCGCTAGTCGAATAAACCGACGATCC
Found at i:92622 original size:61 final size:61
Alignment explanation
Indices: 92432--92698 Score: 366
Period size: 62 Copynumber: 4.4 Consensus size: 61
92422 TGTCAGACAT
** * *
92432 AAAAAATTTGAAATTTTTTTATTTGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCA
1 AAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGGCCAACA-CA
* * * * *
92494 ACAAATTTTGAAAATTTTTTATCCAAGAACAGGGGATGTCGGCCATTGCATGGCCAACAC-
1 AAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGGCCAACACA
*
92554 -----ATTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGACCATTGCATGGCCAACACA
1 AAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGGCCAACACA
* *
92610 AAAAAATTTGAAATTTTTTTATCCGAGAACAAGGGGTGTCGGCCATTGCATGGCCAATACAA
1 AAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGGCCAACAC-A
92672 AAAAAATTTGAAATTTTTTTATCCGAG
1 AAAAAATTTGAAATTTTTTTATCCGAG
92699 CCATTGCATG
Statistics
Matches: 181, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
55 50 0.28
61 53 0.29
62 78 0.43
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (61 bp):
AAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGGCCAACACA
Found at i:92663 original size:116 final size:117
Alignment explanation
Indices: 92437--92666 Score: 356
Period size: 117 Copynumber: 2.0 Consensus size: 117
92427 GACATAAAAA
** * * *
92437 ATTTGAAATTTTTTTATTTGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAACAAATTT
1 ATTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCATGACCAACACCAAAAAAATT
92502 TGAAAATTTTTTATCCAAGAACAGGGGATGTCGGCCATTGCATGGCCAACAC
66 TGAAAATTTTTTATCCAAGAACAGGGGATGTCGGCCATTGCATGGCCAACAC
* *
92554 ATTTGAAATTTTTTTATCCGAGAACAGGGGGTGTCGACCATTGCATGGCCAACA-CAAAAAAATT
1 ATTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCATGACCAACACCAAAAAAATT
* *
92618 TGAAATTTTTTTATCCGAGAACAAGGGG-TGTCGGCCATTGCATGGCCAA
66 TGAAAATTTTTTATCCAAGAAC-AGGGGATGTCGGCCATTGCATGGCCAA
92667 TACAAAAAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
116 49 0.48
117 54 0.52
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (117 bp):
ATTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCATGACCAACACCAAAAAAATT
TGAAAATTTTTTATCCAAGAACAGGGGATGTCGGCCATTGCATGGCCAACAC
Found at i:92679 original size:116 final size:117
Alignment explanation
Indices: 92442--92680 Score: 329
Period size: 116 Copynumber: 2.1 Consensus size: 117
92432 AAAAAATTTG
** * * *
92442 AAATTTTTTTATTTGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACCAACAAATTTTGAAA
1 AAATTTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCATGACCAACACCAAAAAAATTTGAAA
****
92507 ATTTTTTATCCAAGAACAGGGGATGTCGGCCATTGCATGGCCAACACATTTG
66 ATTTTTTATCCAAGAACAGGGGATGTCGGCCATTGCATGGCCAACACAAAAA
* *
92559 AAATTTTTTTATCCGAGAACAGGGGGTGTCGACCATTGCATGGCCAACA-CAAAAAAATTTGAAA
1 AAATTTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCATGACCAACACCAAAAAAATTTGAAA
* * *
92623 TTTTTTTATCCGAGAACAAGGGG-TGTCGGCCATTGCATGGCCAATACAAAAA
66 ATTTTTTATCCAAGAAC-AGGGGATGTCGGCCATTGCATGGCCAACACAAAAA
92675 AAATTT
1 AAATTT
92681 GAAATTTTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
116 58 0.54
117 49 0.46
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (117 bp):
AAATTTTTTTATCCGAGAAAAGGGGGTGTCGACCATTGCATGACCAACACCAAAAAAATTTGAAA
ATTTTTTATCCAAGAACAGGGGATGTCGGCCATTGCATGGCCAACACAAAAA
Found at i:95179 original size:21 final size:21
Alignment explanation
Indices: 95153--95192 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
95143 TTATATTACA
*
95153 TCAGTAATTTTATTTTGAATT
1 TCAGTAATTTTATTATGAATT
*
95174 TCAGTATTTTTATTATGAA
1 TCAGTAATTTTATTATGAA
95193 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (21 bp):
TCAGTAATTTTATTATGAATT
Found at i:96693 original size:7 final size:7
Alignment explanation
Indices: 96681--96711 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
96671 ATCTAATAAA
96681 TTTATAT
1 TTTATAT
96688 TTTATAT
1 TTTATAT
*
96695 TTTTTAT
1 TTTATAT
96702 TTTATAT
1 TTTATAT
96709 TTT
1 TTT
96712 TTGTAGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTATAT
Found at i:100975 original size:7 final size:7
Alignment explanation
Indices: 100963--100990 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
100953 CACCCTTTTC
100963 GACAACA
1 GACAACA
100970 GACAACA
1 GACAACA
100977 GACAACA
1 GACAACA
100984 GACAACA
1 GACAACA
100991 ATTGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.29, G:0.14, T:0.00
Consensus pattern (7 bp):
GACAACA
Found at i:101596 original size:20 final size:19
Alignment explanation
Indices: 101559--101599 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
101549 GAAATTATTA
*
101559 TTTTAGAAAATTTTAAATT
1 TTTTAGAAAATTTAAAATT
*
101578 TTTTATAAATATTTAAAATT
1 TTTTAGAAA-ATTTAAAATT
101598 TT
1 TT
101600 AAAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTAGAAAATTTAAAATT
Found at i:101606 original size:29 final size:27
Alignment explanation
Indices: 101565--101620 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
101555 ATTATTTTAG
101565 AAAATTTTAAATT-TTTTATAAATATTT
1 AAAATTTTAAATTATTTT-TAAATATTT
*
101592 AAAATTTTAAAAATTATTTTTAATTATTT
1 AAAATTTT--AAATTATTTTTAAATATTT
101621 TTATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 8 0.32
29 13 0.52
30 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AAAATTTTAAATTATTTTTAAATATTT
Found at i:101780 original size:29 final size:28
Alignment explanation
Indices: 101713--101780 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
101703 TCGAAGAGTA
* *
101713 GAATTCAACTCGATTCGGATTACTTATTC
1 GAATT-AACTCGATTCGAATAACTTATTC
*
101742 GAATTGACTCGATATCGAATAACTTGATTC
1 GAATTAACTCGAT-TCGAATAACTT-ATTC
101772 G-ATTAACTC
1 GAATTAACTC
101781 AAAATTTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.21
29 21 0.64
30 5 0.15
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (28 bp):
GAATTAACTCGATTCGAATAACTTATTC
Found at i:102862 original size:33 final size:31
Alignment explanation
Indices: 102823--102897 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
102813 CCTGTTATTT
* *
102823 ATTTTTTGGTTAATTTAGTA-CTCAAATTTGAC
1 ATTTTTT-CTTAATTTAGTACCT-AAACTTGAC
*
102855 ACTTTTTTCTTAATTTGGTACCTAAACTTGAC
1 A-TTTTTTCTTAATTTAGTACCTAAACTTGAC
102887 A-TTTTTCTTAA
1 ATTTTTTCTTAA
102898 GTTGATGCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 10 0.26
32 20 0.53
33 8 0.21
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (31 bp):
ATTTTTTCTTAATTTAGTACCTAAACTTGAC
Found at i:104549 original size:12 final size:11
Alignment explanation
Indices: 104532--104579 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
104522 TAAATTTATT
104532 TTAATTAGTTA
1 TTAATTAGTTA
104543 GTTAATTAAGTT-
1 -TTAATT-AGTTA
*
104555 TGAATTAGTTA
1 TTAATTAGTTA
104566 TTAAATTAGTTA
1 TT-AATTAGTTA
104578 TT
1 TT
104580 CAAATCAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 4 0.13
11 6 0.19
12 17 0.55
13 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (11 bp):
TTAATTAGTTA
Found at i:109225 original size:6 final size:6
Alignment explanation
Indices: 109214--109246 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
109204 CTTTTTACTC
*
109214 CCACTG CCACTG CCACTG CCACTG CCATTG CCA
1 CCACTG CCACTG CCACTG CCACTG CCACTG CCA
109247 GTTTTCTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.48, G:0.15, T:0.18
Consensus pattern (6 bp):
CCACTG
Found at i:110344 original size:24 final size:24
Alignment explanation
Indices: 110317--110367 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
110307 CTTCAACTTC
* *
110317 TTTAGGTTCATGTTTGGTTTCTGG
1 TTTAGATTCATGTTTAGTTTCTGG
**
110341 TTTAGATTTTTGTTTAGTTTCTGG
1 TTTAGATTCATGTTTAGTTTCTGG
110365 TTT
1 TTT
110368 TCCATCTGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.06, G:0.24, T:0.61
Consensus pattern (24 bp):
TTTAGATTCATGTTTAGTTTCTGG
Found at i:115269 original size:18 final size:18
Alignment explanation
Indices: 115246--115285 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
115236 TGGGATCATG
115246 TAAACTACTTGATGGGCC
1 TAAACTACTTGATGGGCC
115264 TAAACTACTTGATGGGCC
1 TAAACTACTTGATGGGCC
115282 TAAA
1 TAAA
115286 GGAGGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (18 bp):
TAAACTACTTGATGGGCC
Found at i:119173 original size:30 final size:30
Alignment explanation
Indices: 119117--119174 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
119107 ATAATTAAAT
* *
119117 TTTTTTTAGAAGGTAAATAATTAAATTTGA
1 TTTTTTTAAAAGGTAAATAATCAAATTTGA
*
119147 TTTTTTTAAAATGTTAAA-AATCAAATTT
1 TTTTTTTAAAA-GGTAAATAATCAAATTT
119175 AACTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTTTTTAAAAGGTAAATAATCAAATTTGA
Found at i:122817 original size:42 final size:42
Alignment explanation
Indices: 122765--122848 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
122755 CAAATATTTT
122765 TAAACCCAAATATAATTTCA-TTCTTCAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTTC-T-AAATAACACTCATAAAC
* *
122807 TAAACTCAAATATAATTTTATTTCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTTCTAAATAACACTCATAAAC
122849 AACTCTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 32 0.84
43 3 0.08
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTTCTAAATAACACTCATAAAC
Found at i:129065 original size:235 final size:235
Alignment explanation
Indices: 128743--129213 Score: 924
Period size: 235 Copynumber: 2.0 Consensus size: 235
128733 TGGTAAAACC
128743 ACAGTTAAGTCCTTCACAAATTATAAAGTTATAAATTAATATGATGGTAAAAAAATTGCAATTTG
1 ACAGTTAAGTCCTTCACAAATTATAAAGTTATAAATTAATATGATGGTAAAAAAATTGCAATTTG
128808 ACATTTAAAAAGTTATAATTCATAGGGATGGCAATGATATCCAATATATCTTTTACAGATTTGGA
66 ACATTTAAAAAGTTATAATTCATAGGGATGGCAATGATATCCAATATATCTTTTACAGATTTGGA
*
128873 TAATATTCGGATTCAACTTTTAAAAATACTATCGGTTACAAATTTTGAGTGAAAATAGATGAATA
131 TAATATTCGGATTCAACTTTTAAAAATACTATCGGTTACAAATTTTAAGTGAAAATAGATGAATA
128938 TCTCGAATATCCATCATTCAAATCTATATTATTTATTCGA
196 TCTCGAATATCCATCATTCAAATCTATATTATTTATTCGA
128978 ACAGTTAAGTCCTTCACAAATTATAAAGTTATAAATTAATATGATGGTAAAAAAATTGCAATTTG
1 ACAGTTAAGTCCTTCACAAATTATAAAGTTATAAATTAATATGATGGTAAAAAAATTGCAATTTG
*
129043 ACATTTAAAAAGTTATAATTCATAGGGATGGCAATGATATCCAATATATCTTTTATAGATTTGGA
66 ACATTTAAAAAGTTATAATTCATAGGGATGGCAATGATATCCAATATATCTTTTACAGATTTGGA
129108 TAATATTCGGATTCAACTTTTAAAAATACTATCGGTTACAAATTTTAAGTGAAAATAGATGAATA
131 TAATATTCGGATTCAACTTTTAAAAATACTATCGGTTACAAATTTTAAGTGAAAATAGATGAATA
129173 TCTCGAATATCCATCATTCAAATCTATATTATTTATTCGA
196 TCTCGAATATCCATCATTCAAATCTATATTATTTATTCGA
129213 A
1 A
129214 TGACGGATAC
Statistics
Matches: 234, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
235 234 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (235 bp):
ACAGTTAAGTCCTTCACAAATTATAAAGTTATAAATTAATATGATGGTAAAAAAATTGCAATTTG
ACATTTAAAAAGTTATAATTCATAGGGATGGCAATGATATCCAATATATCTTTTACAGATTTGGA
TAATATTCGGATTCAACTTTTAAAAATACTATCGGTTACAAATTTTAAGTGAAAATAGATGAATA
TCTCGAATATCCATCATTCAAATCTATATTATTTATTCGA
Found at i:134423 original size:2 final size:2
Alignment explanation
Indices: 134416--134445 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
134406 ATGGACCATT
134416 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
134446 ATCTTTTAAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:141737 original size:17 final size:17
Alignment explanation
Indices: 141715--141750 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
141705 CGTGGTAGGT
*
141715 CCGATTCTCAAACCAAC
1 CCGATTCCCAAACCAAC
*
141732 CCGATTCCCATACCAAC
1 CCGATTCCCAAACCAAC
141749 CC
1 CC
141751 ACAACCCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.47, G:0.06, T:0.17
Consensus pattern (17 bp):
CCGATTCCCAAACCAAC
Found at i:145102 original size:29 final size:28
Alignment explanation
Indices: 145054--145117 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
145044 TCTAATTTTG
* * *
145054 TACTAT-AATATATTATGTAATTTATTA
1 TACTATAAAAATATTATGTAATATATAA
145081 TAC-ATAAAAATATCTATAGTAATATATAA
1 TACTATAAAAATAT-TAT-GTAATATATAA
145110 TACTATAA
1 TACTATAA
145118 TGTAAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.07
27 9 0.30
28 3 0.10
29 12 0.40
30 4 0.13
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (28 bp):
TACTATAAAAATATTATGTAATATATAA
Found at i:162732 original size:67 final size:67
Alignment explanation
Indices: 162621--162758 Score: 258
Period size: 67 Copynumber: 2.1 Consensus size: 67
162611 TCTAATAACT
*
162621 CCTTTGAATGCTATCCCTCCCGATATTCACCACTATCAATCATTCATGTTTCATTTAACTTCCCT
1 CCTTTGAATGCTATCCCTCCCGATATTCACCACTATCAAACATTCATGTTTCATTTAACTTCCCT
162686 TC
66 TC
*
162688 CCTTTGAATGCTATCTCTCCCGATATTCACCACTATCAAACATTCATGTTTCATTTAACTTCCCT
1 CCTTTGAATGCTATCCCTCCCGATATTCACCACTATCAAACATTCATGTTTCATTTAACTTCCCT
162753 TC
66 TC
162755 CCTT
1 CCTT
162759 CTACATAATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (67 bp):
CCTTTGAATGCTATCCCTCCCGATATTCACCACTATCAAACATTCATGTTTCATTTAACTTCCCT
TC
Found at i:164478 original size:16 final size:17
Alignment explanation
Indices: 164448--164480 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
164438 AACTTGAACA
*
164448 CATTTTTTTCTTCTTTC
1 CATTTTCTTCTTCTTTC
164465 CATTTTCTTC-TCTTTC
1 CATTTTCTTCTTCTTTC
164481 TTTTTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (17 bp):
CATTTTCTTCTTCTTTC
Found at i:165702 original size:19 final size:19
Alignment explanation
Indices: 165678--165714 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
165668 AATGCGACTG
165678 AAATATCATTTTAATATTT
1 AAATATCATTTTAATATTT
* *
165697 AAATATTATTTTTATATT
1 AAATATCATTTTAATATT
165715 ATTCAAGTGT
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:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATATCATTTTAATATTT
Found at i:167654 original size:38 final size:37
Alignment explanation
Indices: 167594--167672 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 37
167584 GATGATATTT
167594 GATATTAAAATTTAAATTGAATACTTTAAGGTGATTG
1 GATATTAAAATTTAAATTGAATACTTTAAGGTGATTG
167631 GATATTAAAATTTTAAATTGAATACTTTAAGGTGATTG
1 GATATTAAAA-TTTAAATTGAATACTTTAAGGTGATTG
167669 GATA
1 GATA
167673 AGTAGTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 10 0.24
38 31 0.76
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.41
Consensus pattern (37 bp):
GATATTAAAATTTAAATTGAATACTTTAAGGTGATTG
Found at i:171138 original size:6 final size:6
Alignment explanation
Indices: 171129--171162 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
171119 TGAAAGAGAG
171129 GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT GAAG
1 GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT GAAG
171163 ATGGAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
GAAGGT
Found at i:172642 original size:26 final size:26
Alignment explanation
Indices: 172613--172664 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
172603 AAATATACCG
* **
172613 TTAATAAAATTAATTGCTCAAATCAA
1 TTAATAAAATCAATTAATCAAATCAA
*
172639 TTAATAGAATCAATTAATCAAATCAA
1 TTAATAAAATCAATTAATCAAATCAA
172665 CCATTACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (26 bp):
TTAATAAAATCAATTAATCAAATCAA
Found at i:172662 original size:13 final size:13
Alignment explanation
Indices: 172630--172664 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
172620 AATTAATTGC
172630 TCAAATCAATTAA
1 TCAAATCAATTAA
172643 T-AGAATCAATTAA
1 TCA-AATCAATTAA
172656 TCAAATCAA
1 TCAAATCAA
172665 CCATTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (13 bp):
TCAAATCAATTAA
Found at i:182074 original size:18 final size:19
Alignment explanation
Indices: 182053--182089 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
182043 TTCACTCATT
182053 TTTTCAAGTTTTA-TTTTA
1 TTTTCAAGTTTTACTTTTA
*
182071 TTTTCAATTTTTACTTTTA
1 TTTTCAAGTTTTACTTTTA
182090 AAAGTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTCAAGTTTTACTTTTA
Found at i:182928 original size:29 final size:28
Alignment explanation
Indices: 182896--183089 Score: 88
Period size: 29 Copynumber: 6.6 Consensus size: 28
182886 TAGAATTCTG
* *
182896 GAAAGTTTAAGGGTAGAAATGCAATTTTC
1 GAAAGTTT-AGGGTAAAAATGCAATTTTA
* * *
182925 GAAAAATTTGGGGTTAAAAATGGAATTTTA
1 G-AAAGTTTAGGG-TAAAAATGCAATTTTA
* *
182955 GAAAGTTTGAGGGT--AAATGGTAACTTTTG
1 GAAAGTTT-AGGGTAAAAAT-GCAA-TTTTA
** * *
182984 GAAAAATTAGGGTAAAAAATGGAAATTTAA
1 GAAAGTTTAGGGT-AAAAAT-GCAATTTTA
* * * *
183014 AAAATTTTGGGGTAAAAATGCAATTTTTG
1 GAAAGTTTAGGGTAAAAATGCAA-TTTTA
* * *
183043 GAAATTTTA-GGTCAAAAAATGGAATTTTG
1 GAAAGTTTAGGGT--AAAAATGCAATTTTA
*
183072 GAAAGTTTGAAGGTAAAA
1 GAAAGTTT-AGGGTAAAA
183090 TAGTAATTTT
Statistics
Matches: 127, Mismatches: 25, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
27 4 0.03
28 14 0.11
29 53 0.42
30 45 0.35
31 11 0.09
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.31
Consensus pattern (28 bp):
GAAAGTTTAGGGTAAAAATGCAATTTTA
Found at i:182952 original size:30 final size:30
Alignment explanation
Indices: 182853--183194 Score: 112
Period size: 30 Copynumber: 11.6 Consensus size: 30
182843 ATTCGGGGGT
* * *
182853 AAAATGGTAATTTTGG-GAAA-TCGGGGTCA
1 AAAATGG-AATTTTGGAAAAATTTGGGGTTA
* * * *
182882 AAAATAGAATTCTGG-AAAGTTTAAGGG-TA
1 AAAATGGAATTTTGGAAAAATTT-GGGGTTA
* * *
182911 GAAATGCAATTTTCGAAAAATTTGGGGTTA
1 AAAATGGAATTTTGGAAAAATTTGGGGTTA
* *
182941 AAAATGGAATTTTAG-AAAGTTTGAGGG-T-
1 AAAATGGAATTTTGGAAAAATTTG-GGGTTA
* *
182969 -AAATGGTAACTTTTGGAAAAA-TTAGGGTAA
1 AAAATGG-AA-TTTTGGAAAAATTTGGGGTTA
* *
182999 AAAATGGAAATTT-AAAAAATTTTGGGG-TA
1 AAAATGGAATTTTGGAAAAA-TTTGGGGTTA
* ** *
183028 AAAATGCAATTTTTGG--AAATTTTAGGTCAA
1 AAAATGGAA-TTTTGGAAAAATTTGGGGT-TA
* *
183058 AAAATGGAATTTTGG-AAAGTTTGAAGG-T-
1 AAAATGGAATTTTGGAAAAATTTG-GGGTTA
* ***
183086 AAAATAGTAATTTTTGGAAAAA-GCAGGGTT-
1 AAAAT-GGAA-TTTTGGAAAAATTTGGGGTTA
** *
183116 AAAATGGAATTTTTGG-AAGTTTTGGGGTAA
1 AAAATGGAA-TTTTGGAAAAATTTGGGGTTA
** * * *
183146 AAAATATAATTTT-CAAAAAGTTCGAGGTTA
1 AAAATGGAATTTTGGAAAAA-TTTGGGGTTA
*
183176 AAAATGAAATTTTGGAAAA
1 AAAATGGAATTTTGGAAAA
183195 GTTCAAGGAT
Statistics
Matches: 225, Mismatches: 60, Indels: 54
0.66 0.18 0.16
Matches are distributed among these distances:
27 6 0.03
28 31 0.14
29 82 0.36
30 90 0.40
31 16 0.07
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTGGAAAAATTTGGGGTTA
Found at i:182988 original size:59 final size:57
Alignment explanation
Indices: 182849--183147 Score: 223
Period size: 59 Copynumber: 5.1 Consensus size: 57
182839 AGATATTCGG
* ** * * * * *
182849 GGGTAAAATGGTAATTTTGG-GAAATCGGGGTCAAAAATAGAATTCTGGAAAGTTTAA
1 GGGTAAAAT-GTAATTTTGGAAAAATTAGGGTAAAAAATGGAATTTTAGAAAGTTTGA
* * * *
182906 GGGTAGAAATGCAATTTTCGAAAAATTTGGGGTTAAAAATGGAATTTTAGAAAGTTTGA
1 GGGTA-AAATGTAATTTTGGAAAAA-TTAGGGTAAAAAATGGAATTTTAGAAAGTTTGA
* * *
182965 GGGT-AAATGGTAACTTTTGGAAAAATTAGGGTAAAAAATGGAAATTTAAAAAATTTTG-
1 GGGTAAAAT-GTAA-TTTTGGAAAAATTAGGGTAAAAAATGG-AATTTTAGAAAGTTTGA
* ** *
183023 GGGTAAAAATGCAATTTTTGGAAATTTTA-GGTCAAAAAATGGAATTTTGGAAAGTTTGA
1 GGGT-AAAATGTAA-TTTTGGAAAAATTAGGGT-AAAAAATGGAATTTTAGAAAGTTTGA
* ** * * *
183082 AGGTAAAATAGTAATTTTTGGAAAAAGCAGGGT-TAAAATGGAATTTTTGGAAGTTTTG-
1 GGGTAAAAT-GTAA-TTTTGGAAAAATTAGGGTAAAAAATGGAATTTTAGAAAG-TTTGA
183140 GGGTAAAA
1 GGGTAAAA
183148 AATATAATTT
Statistics
Matches: 195, Mismatches: 34, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
57 17 0.09
58 72 0.37
59 99 0.51
60 7 0.04
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.31
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTGGAAAAATTAGGGTAAAAAATGGAATTTTAGAAAGTTTGA
Found at i:183217 original size:30 final size:30
Alignment explanation
Indices: 183145--183222 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
183135 TTTTGGGGTA
** * *
183145 AAAAATATAATTTTCAAAAAGTTCGAGGTT
1 AAAAATATAATTTTGGAAAAGTTCAAGGAT
183175 AAAAATGA-AATTTTGGAAAAGTTCAAGGAT
1 AAAAAT-ATAATTTTGGAAAAGTTCAAGGAT
*
183205 CAAAATATAATTTCTGGA
1 AAAAATATAATTT-TGGA
183223 CAGTTTAGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 34 0.85
31 5 0.12
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.31
Consensus pattern (30 bp):
AAAAATATAATTTTGGAAAAGTTCAAGGAT
Found at i:184331 original size:3 final size:3
Alignment explanation
Indices: 184323--184348 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
184313 TAACTGTTAC
184323 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
184349 CTAATTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:185033 original size:6 final size:6
Alignment explanation
Indices: 185022--185100 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
185012 ATATTTATAA
* * *
185022 TAAATT TAAATT TAAATA TAAATC TAAACT TAAA-T TAAATT TAAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT
* * *
185070 TAAA-A TAAATT TAAATT CAAA-A TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA
185101 TCTTAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 12 0.20
6 41 0.69
7 6 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:185044 original size:18 final size:17
Alignment explanation
Indices: 185014--185115 Score: 125
Period size: 17 Copynumber: 5.9 Consensus size: 17
185004 CACTTTCAAT
*
185014 ATTTATAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
185031 ATTTAAATATAAATCTAA
1 ATTTAAA-ATAAATTTAA
* *
185049 ACTTAAATTAAATTTAAA
1 ATTTAAAATAAATTT-AA
185067 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
185084 ATTCAAAATAAATTT-A
1 ATTTAAAATAAATTTAA
185100 ATCTTAAAATAAATTT
1 AT-TTAAAATAAATTT
185116 TAAAATGGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
16 3 0.04
17 40 0.55
18 30 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:185119 original size:35 final size:34
Alignment explanation
Indices: 185020--185115 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 34
185010 CAATATTTAT
*
185020 AATAAATTTAAATTTAAATATAAATCTAAACTTAA
1 AATAAATTTAAATTTAAA-ATAAATTTAAACTTAA
*
185055 ATTAAATTTAAAATTTAAAATAAATTTAAA-TTCAA
1 AATAAATTT-AAATTTAAAATAAATTTAAACTT-AA
185090 AATAAATTT-AATCTTAAAATAAATTT
1 AATAAATTTAAAT-TTAAAATAAATTT
185116 TAAAATGGGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
33 3 0.05
34 15 0.27
35 28 0.51
36 9 0.16
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
AATAAATTTAAATTTAAAATAAATTTAAACTTAA
Found at i:187049 original size:16 final size:16
Alignment explanation
Indices: 187030--187088 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
187020 TCCGAATTCG
187030 AAATGACTCAAATCCA
1 AAATGACTCAAATCCA
*
187046 AAATGA-TCAAA-CTCG
1 AAATGACTCAAATC-CA
* *
187061 AAATAAGTCAAATCCAA
1 AAATGACTCAAATCC-A
187078 AAATGAC-CAAA
1 AAATGACTCAAA
187089 CCTGAAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 16 0.47
17 6 0.18
ACGTcount: A:0.54, C:0.20, G:0.08, T:0.17
Consensus pattern (16 bp):
AAATGACTCAAATCCA
Found at i:187064 original size:31 final size:32
Alignment explanation
Indices: 187027--187099 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
187017 TGATCCGAAT
*
187027 TCGAAATGACTCAAATCC-AAAATGATCAAAC
1 TCGAAATGACTCAAATCCAAAAATGACCAAAC
* *
187058 TCGAAATAAGTCAAATCCAAAAATGACCAAAC
1 TCGAAATGACTCAAATCCAAAAATGACCAAAC
187090 -CTGAAATGAC
1 TC-GAAATGAC
187100 CCAACTCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (32 bp):
TCGAAATGACTCAAATCCAAAAATGACCAAAC
Found at i:187096 original size:32 final size:31
Alignment explanation
Indices: 187027--187089 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
187017 TGATCCGAAT
* * *
187027 TCGAAATGACTCAAATCCAAAATGATCAAAC
1 TCGAAATAAGTCAAATCCAAAATGACCAAAC
187058 TCGAAATAAGTCAAATCCAAAAATGACCAAAC
1 TCGAAATAAGTCAAATCC-AAAATGACCAAAC
187090 CTGAAATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.17
Consensus pattern (31 bp):
TCGAAATAAGTCAAATCCAAAATGACCAAAC
Found at i:190701 original size:3 final size:3
Alignment explanation
Indices: 190695--190723 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
190685 TTGCTGCTGT
190695 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
190724 CTGTTTCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Done.