Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008062.1 Hibiscus syriacus cultivar Beakdansim tig00110557_pilon, 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: 2089609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:2550 original size:8 final size:8
Alignment explanation
Indices: 2537--2577 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2527 CTCATTTTCA
2537 GAGAATTT
1 GAGAATTT
2545 GAGAATTT
1 GAGAATTT
*
2553 -AGAGTTT
1 GAGAATTT
*
2560 GGGAATTT
1 GAGAATTT
2568 GAGAATTT
1 GAGAATTT
2576 GA
1 GA
2578 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2875 original size:128 final size:127
Alignment explanation
Indices: 2647--3269 Score: 1074
Period size: 128 Copynumber: 4.9 Consensus size: 127
2637 TAATCGGAGT
*
2647 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCC-CGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* *
2712 CATTGCCCTATTATGTCACTCATGTCCCTTGGGGACACTAGATATATTAGTACCTATTATTTC
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
2775 ACTATTCACATGAAGGCGCATTCCCAGGGGTGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
2840 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
2903 ACTATTCACATGAAGGCGCGTTCCCGGGG-G-GCCTTCCA-TATTTCGTCAGAGAATATGTTATC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
*
2965 GTTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
3027 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* * *
3092 CATTGCCCTATTATGTCACTCATGTCCCTTGGTGACACTAGATATATCAGTACCTATTATTGC
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
3155 ACTATTCACATGAAGGTGCGTT-CCGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
3219 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
3270 AATCAGGTAA
Statistics
Matches: 473, Mismatches: 17, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
124 109 0.23
125 12 0.03
126 89 0.19
127 14 0.03
128 249 0.53
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (127 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:3141 original size:252 final size:254
Alignment explanation
Indices: 2647--3269 Score: 1097
Period size: 252 Copynumber: 2.5 Consensus size: 254
2637 TAATCGGAGT
2647 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCC-GGGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* *
2712 CATTGCCCTATTATGTCACTCATGTCCCTTGGGGACACTAGATATATTAGTACCTATTATTTCAC
64 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
2777 TATTCACATGAAGGCGCATTCCCAGGGGTGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
129 TATTCACATGAAGGCGCATTCCCAGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
2842 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
194 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTGC
* * *
2903 ACTATTCACATGAAGGCGCGTTCCCGGGGG-GCCTTCCA-TATTTCGTCAGAGAATATGTTATCG
1 ACTATTCACATGAAGGCGCGTTCCGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
2966 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
* * *
3031 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
131 TTCACATGAAGGCGCATTCCCAGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
* *
3096 GCCCTATTATGTCACTCATGTCCCTTGGTGACACTAGATATATCAGTACCTATTATTGC
196 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTGC
*
3155 ACTATTCACATGAAGGTGCGTTCCGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 ACTATTCACATGAAGGCGCGTTCCGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
3220 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
3270 AATCAGGTAA
Statistics
Matches: 349, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
252 231 0.66
253 16 0.05
254 74 0.21
255 4 0.01
256 24 0.07
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (254 bp):
ACTATTCACATGAAGGCGCGTTCCGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
TTCACATGAAGGCGCATTCCCAGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTGC
Found at i:3727 original size:27 final size:28
Alignment explanation
Indices: 3682--3757 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
3672 TTTGAATACT
* *
3682 ATAAT-TTATTTTAAATTTAAATTT-GA
1 ATAATATTATTTTTATTTTAAATTTCGA
3708 ATAATATTATTTTTATTTTAAATTTCGA
1 ATAATATTATTTTTATTTTAAATTTCGA
* *
3736 ATAATATAATTTGTATTTTAAA
1 ATAATATTATTTTTATTTTAAA
3758 AACATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.11
27 17 0.39
28 22 0.50
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (28 bp):
ATAATATTATTTTTATTTTAAATTTCGA
Found at i:3755 original size:33 final size:30
Alignment explanation
Indices: 3659--3756 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 30
3649 TAAGTTGAAA
*
3659 TTTAATGTTAAATTTTGAATACTATAATTTAT
1 TTTAAT-TTAAA-TTTGAATAATATAATTTAT
*
3691 TTTAAATTTAAATTTGAATAATAT--TAT-T
1 TTT-AATTTAAATTTGAATAATATAATTTAT
*
3719 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTT-GAATAATATAA-TT-TAT
3752 TTTAA
1 TTTAA
3757 AAACATTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
27 10 0.19
28 13 0.24
29 2 0.04
31 12 0.22
32 9 0.17
33 8 0.15
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (30 bp):
TTTAATTTAAATTTGAATAATATAATTTAT
Found at i:4359 original size:21 final size:21
Alignment explanation
Indices: 4271--4364 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
4261 TATGGTATAA
*
4271 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
4292 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
4313 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
4334 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
4355 AACCCTGCGG
1 AACCCTGCGG
4365 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:4394 original size:21 final size:21
Alignment explanation
Indices: 4368--4415 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4358 CCTGCGGAGA
*
4368 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
4389 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
4410 GGGCAT
1 TGGCAT
4416 GTACCCTGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:6189 original size:32 final size:29
Alignment explanation
Indices: 6143--6209 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
6133 TCTAATAAGT
*
6143 AATAATTATATAAATATTATTTTAATAAAAAA
1 AATAATTACATAAATA-TA--TTAATAAAAAA
* *
6175 AATATTTACATAAATATATTAATATAAAA
1 AATAATTACATAAATATATTAATAAAAAA
6204 AATAAT
1 AATAAT
6210 AATTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 15 0.48
31 2 0.06
32 14 0.45
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
AATAATTACATAAATATATTAATAAAAAA
Found at i:6895 original size:25 final size:26
Alignment explanation
Indices: 6843--6896 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
6833 TAGTAACATG
* * * *
6843 AAAATTGTTTTATGTCAAAATTACTT
1 AAAACTGTTTTACGTCAAAATAAATT
6869 AAAACTGTTTTACGT-AAAATAAATT
1 AAAACTGTTTTACGTCAAAATAAATT
6894 AAA
1 AAA
6897 TTTTCTGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (26 bp):
AAAACTGTTTTACGTCAAAATAAATT
Found at i:7240 original size:25 final size:26
Alignment explanation
Indices: 7231--7303 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 26
7221 TAATATTAAA
7231 AATAT-AATATTATTAAAATTATAAT
1 AATATAAATATTATTAAAATTATAAT
7256 AATATAAATATT-TTAATAA-T-TAAT
1 AATATAAATATTATTAA-AATTATAAT
*
7280 -AT-T--TTATTATTAAAATTATAAT
1 AATATAAATATTATTAAAATTATAAT
7302 AA
1 AA
7304 GATATTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
20 6 0.15
21 5 0.12
22 5 0.12
23 3 0.07
24 4 0.10
25 10 0.24
26 8 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AATATAAATATTATTAAAATTATAAT
Found at i:7246 original size:17 final size:17
Alignment explanation
Indices: 7224--7256 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7214 ATTAATTTAA
7224 TATTAAAAATATAATAT
1 TATTAAAAATATAATAT
*
7241 TATTAAAATTATAATA
1 TATTAAAAATATAATA
7257 ATATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTAAAAATATAATAT
Found at i:7291 original size:14 final size:15
Alignment explanation
Indices: 7242--7303 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
7232 ATATAATATT
* *
7242 ATTAAAATTATAATA
1 ATTAATATTTTAATA
7257 ATATAAATATTTTAATA
1 AT-T-AATATTTTAATA
*
7274 ATTAATATTTT-ATT
1 ATTAATATTTTAATA
* *
7288 ATTAAAATTATAATA
1 ATTAATATTTTAATA
7303 A
1 A
7304 GATATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 11 0.29
15 13 0.34
16 2 0.05
17 12 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAATATTTTAATA
Found at i:7467 original size:19 final size:18
Alignment explanation
Indices: 7429--7463 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7419 ACAAAGAAAC
*
7429 TAGAAAAATGAATTACAT
1 TAGAAAAATCAATTACAT
7447 TAGAAAAATCAATTACA
1 TAGAAAAATCAATTACA
7464 ATTATCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (18 bp):
TAGAAAAATCAATTACAT
Found at i:8244 original size:2 final size:2
Alignment explanation
Indices: 8233--8304 Score: 123
Period size: 2 Copynumber: 37.5 Consensus size: 2
8223 AAATAACCAT
8233 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8273 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8305 TATGATGTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 64 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8315 original size:21 final size:20
Alignment explanation
Indices: 8232--8304 Score: 105
Period size: 19 Copynumber: 3.7 Consensus size: 20
8222 TAAATAACCA
8232 TTATA-ATATATATATATAT
1 TTATATATATATATATATAT
*
8251 ATATATATATATATATA-AT
1 TTATATATATATATATATAT
*
8270 ATATATATATATATATATAT
1 TTATATATATATATATATAT
8290 ATTATATATATATAT
1 -TTATATATATATAT
8305 TATGATGTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.47
20 13 0.27
21 13 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATATATATATATATATAT
Found at i:8355 original size:20 final size:21
Alignment explanation
Indices: 8326--8365 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
8316 TTAATATATC
8326 AAATACAATC-TAAAATTATT
1 AAATACAATCATAAAATTATT
* *
8346 AAATATAATCATAATATTAT
1 AAATACAATCATAAAATTAT
8366 ATTTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATACAATCATAAAATTATT
Found at i:9449 original size:283 final size:284
Alignment explanation
Indices: 8899--9450 Score: 688
Period size: 283 Copynumber: 1.9 Consensus size: 284
8889 CCCTAAGTAT
*
8899 TTTTAGATTTTCTATGTATTTTTTTTTGAAAATTTATTTTCGCTTCCTAGAATTTTATAAATTCA
1 TTTTAGATTTTATATGTATTTTTTTTTGAAAATTTATTTTCGCTTCCTAGAATTTTATAAATTCA
* * * *
8964 AGATCGCCCATTAACATAAAATCTTGCATCCAGGGAGGGGCGAACTAGAATCTATAAAATTCTAG
66 AGATCACCCACTAACATAAAATCCTGCATCCAGGGAGGGGCGAACTAAAATCTATAAAATTCTAG
* * *
9029 GGAGGGGCAAAATTCAATAGAAAATATATAAAAAATCTAAAATTTATGGTAATTTTTAATTTTAT
131 GGAGGGGCAAAATTCAATAAAAAATACATAAAAAATCTAAAATTTATGATAATTTTTAATTTTAT
* ** * * * * *
9094 GGGAGCGTTTGCCCTCACCCGCTCCTGTCTCATTACAAAGGAAGCTAGAGGAAAACCTCTAACAA
196 GGAAGCGAGTGCCCTCACCCACGCCTATCTCAGTACAAAGGAAGCTAGAGGAAAAACTCTAACAA
9159 CACTATTTTATAAATTATTATATA
261 CACTATTTTATAAATTATTATATA
9183 TTTTAGATTTTTATATGTATTTTTTATTT--AAATATT-TTTTCG-TTCCTAGAATTTTATAAAT
1 TTTTAGA-TTTTATATGTATTTTTT-TTTGAAAAT-TTATTTTCGCTTCCTAGAATTTTATAAAT
* * * * ** *
9244 TTACGTTCACCCCCTAACATAAAATCCTGTGTCCAGGGAGGGGGCGAACTAAAATTTATAAAATT
63 TCAAGATCACCCACTAACATAAAATCCTGCATCCAGGGA-GGGGCGAACTAAAATCTATAAAATT
* * *
9309 -TAGGGATGGGCGAAATTCAATAAAAAAATACATAAATAATCTAAAATTTATGATAA-TTTTAAT
127 CTAGGGAGGGGCAAAATTCAAT-AAAAAATACATAAAAAATCTAAAATTTATGATAATTTTTAAT
** * * *
9372 TTT-TTTAAGGGAGTGCCCTCACCCACGCCTATCTGAGTACAGA-GAACGCTAGAGGAAAAAACT
191 TTTATGGAAGCGAGTGCCCTCACCCACGCCTATCTCAGTACAAAGGAA-GCTAGAGG-AAAAACT
* *
9435 CTAATAATACTATTTT
254 CTAACAACACTATTTT
9451 TATTAGTTTA
Statistics
Matches: 228, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
281 3 0.01
282 36 0.16
283 98 0.43
284 70 0.31
285 18 0.08
286 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (284 bp):
TTTTAGATTTTATATGTATTTTTTTTTGAAAATTTATTTTCGCTTCCTAGAATTTTATAAATTCA
AGATCACCCACTAACATAAAATCCTGCATCCAGGGAGGGGCGAACTAAAATCTATAAAATTCTAG
GGAGGGGCAAAATTCAATAAAAAATACATAAAAAATCTAAAATTTATGATAATTTTTAATTTTAT
GGAAGCGAGTGCCCTCACCCACGCCTATCTCAGTACAAAGGAAGCTAGAGGAAAAACTCTAACAA
CACTATTTTATAAATTATTATATA
Found at i:11844 original size:21 final size:21
Alignment explanation
Indices: 11818--11859 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11808 CCAGAATGGG
*
11818 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
11839 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
11860 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:12109 original size:29 final size:31
Alignment explanation
Indices: 12068--12136 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
12058 TATTTTTGTA
*
12068 AATTTTGAATAAATTCAATT-AAGTCCAAATAC
1 AATTTTG--TAAATTCAATTCAAGTCCAAAAAC
12100 -ATTTTGTAAATTCAATTCAAGTCCAAAAAC
1 AATTTTGTAAATTCAATTCAAGTCCAAAAAC
12130 AATTTTG
1 AATTTTG
12137 CCTTAAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 11 0.32
30 11 0.32
31 12 0.35
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
AATTTTGTAAATTCAATTCAAGTCCAAAAAC
Found at i:12145 original size:34 final size:29
Alignment explanation
Indices: 12077--12136 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
12067 AAATTTTGAA
*
12077 TAAATTCAATTAAGTCCAAATACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
12106 TAAATTCAATTCAAGTCCAAAAACAATTTTG
1 TAAATTCAATT-AAGTCCAAAAAC-ATTTTG
12137 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:15718 original size:21 final size:21
Alignment explanation
Indices: 15694--15734 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
15684 GATAAAAAGT
*
15694 TATTTAAAATATTATTATTTA
1 TATTTAAAATATTAATATTTA
15715 TATTTAAAATATTAATATTT
1 TATTTAAAATATTAATATTT
15735 TTTTATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTAAAATATTAATATTTA
Found at i:19632 original size:19 final size:20
Alignment explanation
Indices: 19605--19646 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
19595 TTAACAAAAT
*
19605 ATTCTAAAA-AATTATTAAA
1 ATTCCAAAATAATTATTAAA
*
19624 ATTCCAAAATTAATTTTTAAA
1 ATTCCAAAA-TAATTATTAAA
19645 AT
1 AT
19647 AATAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTCCAAAATAATTATTAAA
Found at i:20967 original size:17 final size:17
Alignment explanation
Indices: 20945--20978 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20935 TTAGAGAGAC
20945 AAAAATAAATTATCAAT
1 AAAAATAAATTATCAAT
*
20962 AAAAATATATTATCAAT
1 AAAAATAAATTATCAAT
20979 TCATTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATAAATTATCAAT
Found at i:22546 original size:15 final size:16
Alignment explanation
Indices: 22528--22560 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
22518 GTGGCAGATC
22528 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
22543 AAAATCCAGAACGGGA
1 AAAATCCAGAACGGGA
22559 AA
1 AA
22561 GAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:28136 original size:2 final size:2
Alignment explanation
Indices: 28129--28159 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28119 TGTTACGTTA
28129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28160 AAACTCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29059 original size:18 final size:18
Alignment explanation
Indices: 29025--29079 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
29015 AGTATTTTAA
29025 TTGAAAATTAGTGAATATTT
1 TTGAAAATT--TGAATATTT
29045 TTGAAAATTTGAATATATT
1 TTGAAAATTTGAATAT-TT
*
29064 TT-TAAATTT-AATATTT
1 TTGAAAATTTGAATATTT
29080 ACAAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 13 0.39
19 4 0.12
20 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TTGAAAATTTGAATATTT
Found at i:31755 original size:2 final size:2
Alignment explanation
Indices: 31748--31773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31738 AAATACTCTC
31748 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
31774 TCCTTCACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34523 original size:23 final size:23
Alignment explanation
Indices: 34493--34538 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
34483 ATATTTTAAT
34493 TGACGTGGCGTGGTGCATGTCCA
1 TGACGTGGCGTGGTGCATGTCCA
34516 TGACGTGGCGTGGTGCATGTCCA
1 TGACGTGGCGTGGTGCATGTCCA
34539 ACCTGGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.39, T:0.26
Consensus pattern (23 bp):
TGACGTGGCGTGGTGCATGTCCA
Found at i:37211 original size:12 final size:13
Alignment explanation
Indices: 37185--37217 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
37175 AAGCAAAGGC
*
37185 AATACAAATTTAA
1 AATACAAATTAAA
37198 AATA-AAATTAAA
1 AATACAAATTAAA
37210 AATACAAA
1 AATACAAA
37218 AGAACAGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AATACAAATTAAA
Found at i:42423 original size:31 final size:31
Alignment explanation
Indices: 42388--42450 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
42378 TCAATAAAGT
*
42388 TTAAAAAATTATAAAA-TACTTATTAAATTTA
1 TTAAAAAATTATAAAATTA-TTAATAAATTTA
*
42419 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAATTATTAATAAATTTA
42450 T
1 T
42451 CCAAATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATTATTAATAAATTTA
Found at i:42450 original size:20 final size:20
Alignment explanation
Indices: 42383--42450 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
42373 TTTTGTCAAT
*
42383 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
42401 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
42422 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
42441 ATAA-ATTTAT
1 A-AAGATTTAT
42451 CCAAATACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:52224 original size:31 final size:31
Alignment explanation
Indices: 52189--52257 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
52179 GAGCTGCTCA
* *
52189 CGAGCTTCAGTTCAG-GATTTCGAGTTCGAGT
1 CGAGCTCCAGTTCAGAGATTTCGAG-TCAAGT
* *
52220 CGAGCTCCATTTCAGAGTTTTCGAGTCAAGT
1 CGAGCTCCAGTTCAGAGATTTCGAGTCAAGT
52251 CGAGCTC
1 CGAGCTC
52258 AACAATACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.30
Consensus pattern (31 bp):
CGAGCTCCAGTTCAGAGATTTCGAGTCAAGT
Found at i:52508 original size:24 final size:24
Alignment explanation
Indices: 52463--52509 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
52453 TTTTTATATA
*
52463 TAATAATATTACACATTTAATTAT
1 TAATAATATTACACATTAAATTAT
* * *
52487 TAATAATTTTATATATTAAATTA
1 TAATAATATTACACATTAAATTA
52510 AACTAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATAATATTACACATTAAATTAT
Found at i:53249 original size:31 final size:31
Alignment explanation
Indices: 53211--53273 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
53201 CATTCATGCA
53211 TTGTTATTGGAAGAGAAGGGGAAAGGGAAGG
1 TTGTTATTGGAAGAGAAGGGGAAAGGGAAGG
53242 TTGTTATTGGAAGAGAAGGGGAAAGGGAAGG
1 TTGTTATTGGAAGAGAAGGGGAAAGGGAAGG
53273 T
1 T
53274 GATAAGTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.44, T:0.21
Consensus pattern (31 bp):
TTGTTATTGGAAGAGAAGGGGAAAGGGAAGG
Found at i:63857 original size:27 final size:27
Alignment explanation
Indices: 63819--63887 Score: 131
Period size: 26 Copynumber: 2.6 Consensus size: 27
63809 ATAATATTTT
63819 CTCTAACAACAGTTTTTTTTATAAGAA
1 CTCTAACAACAGTTTTTTTTATAAGAA
63846 CTCTAACAACAG-TTTTTTTATAAGAA
1 CTCTAACAACAGTTTTTTTTATAAGAA
63872 CTCTAACAACAGTTTT
1 CTCTAACAACAGTTTT
63888 AGATGTCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 26 0.63
27 15 0.37
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (27 bp):
CTCTAACAACAGTTTTTTTTATAAGAA
Found at i:65414 original size:239 final size:241
Alignment explanation
Indices: 64993--65480 Score: 944
Period size: 239 Copynumber: 2.0 Consensus size: 241
64983 ATCAGTTATG
64993 TATTGAGCAATGTGATAACAAGGTTGAGACTGTAAATGCTAGTACTTTGCACATATAGTTAGTTA
1 TATTGAGCAATGTGATAACAAGGTTGAGACTGTAAATGCTAGTACTTTGCACATATAGTTAGTTA
65058 TTTATTCAAGTTCTCACATAAAGATGTGATAAATATAGCATGTTAAGATATGATACATTGGTGTG
66 TTTATTCAAGTTCTCACATAAAGATGTGATAAATATAGCATGTTAAGATATGATACATTGGTGTG
*
65123 GCTTCTTGATTGTGACACGGAGTTCTAGTTTTCAACTTTCAGTTCATAAAAACAACTTTTTGTGG
131 GCTTCTTGATCGTGACACGGAGTTCTAGTTTTCAACTTTCAGTTCATAAAAACAACTTTTTGTGG
65188 AGCAGGGTTAAGCCTCCTGCATCTCCCCTCCCCTCCCCTTGCATGT
196 AGCAGGGTTAAGCCTCCTGCATCTCCCCTCCCCTCCCCTTGCATGT
65234 TATTGAGCAATGTGATAACAAGGTTGAGACTGTAAATGCTAGTACTTTGCACATATAGTTA-TT-
1 TATTGAGCAATGTGATAACAAGGTTGAGACTGTAAATGCTAGTACTTTGCACATATAGTTAGTTA
65297 TTTATTCAAGTTCTCACATAAAGATGTGATAAATATAGCATGTTAAGATATGATACATTGGTGTG
66 TTTATTCAAGTTCTCACATAAAGATGTGATAAATATAGCATGTTAAGATATGATACATTGGTGTG
65362 GCTTCTTGATCGTGACACGGAGTTCTAGTTTTCAACTTTCAGTTCATAAAAACAACTTTTTGTGG
131 GCTTCTTGATCGTGACACGGAGTTCTAGTTTTCAACTTTCAGTTCATAAAAACAACTTTTTGTGG
*
65427 AGCAGGGTTAAGCCTCTTGCATCTCCCCTCCCCTCCCCTTGCATGT
196 AGCAGGGTTAAGCCTCCTGCATCTCCCCTCCCCTCCCCTTGCATGT
65473 TATTGAGC
1 TATTGAGC
65481 TTTGTGTACT
Statistics
Matches: 245, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
239 182 0.74
240 2 0.01
241 61 0.25
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (241 bp):
TATTGAGCAATGTGATAACAAGGTTGAGACTGTAAATGCTAGTACTTTGCACATATAGTTAGTTA
TTTATTCAAGTTCTCACATAAAGATGTGATAAATATAGCATGTTAAGATATGATACATTGGTGTG
GCTTCTTGATCGTGACACGGAGTTCTAGTTTTCAACTTTCAGTTCATAAAAACAACTTTTTGTGG
AGCAGGGTTAAGCCTCCTGCATCTCCCCTCCCCTCCCCTTGCATGT
Found at i:71226 original size:2 final size:2
Alignment explanation
Indices: 71219--71311 Score: 62
Period size: 2 Copynumber: 51.5 Consensus size: 2
71209 CCGCCCTGAT
* * * *
71219 TA TA TA TA TG TA TA AA TA TA TT TA TA T- TT TA TA T- TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
71257 TA TA TA TA TA -A TA TT TA TA TA T- TT TA TA T- TA -A T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71294 TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA T
71312 TTTATATTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
1 10 0.14
2 61 0.86
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (2 bp):
TA
Found at i:71273 original size:24 final size:22
Alignment explanation
Indices: 71246--71319 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 22
71236 ATATTTATAT
71246 TTTATATTAATTATATATATAATA
1 TTTATA-T-ATTATATATATAATA
*
71270 TTTATATATTTTATAT-TAAT-
1 TTTATATATTATATATATAATA
*
71290 TATATATA-TATATATATAATA
1 TTTATATATTATATATATAATA
71311 TTT-TATATT
1 TTTATATATT
71320 TTTATATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 6 0.14
20 15 0.35
21 7 0.16
22 8 0.19
23 1 0.02
24 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATATATTATATATATAATA
Found at i:71278 original size:33 final size:33
Alignment explanation
Indices: 71223--71319 Score: 135
Period size: 33 Copynumber: 2.9 Consensus size: 33
71213 CCTGATTATA
*
71223 TATATGTATAAATATATT-TATATTTTATATTAAT
1 TATATATAT-AATAT-TTATATATTTTATATTAAT
71257 TATATATATAATATTTATATATTTTATATTAAT
1 TATATATATAATATTTATATATTTTATATTAAT
*
71290 TATATATAT-ATATATATAATATTTTATATT
1 TATATATATAATATTTAT-ATATTTTATATT
71320 TTTATATTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
32 9 0.15
33 42 0.71
34 8 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TATATATATAATATTTATATATTTTATATTAAT
Found at i:71323 original size:41 final size:41
Alignment explanation
Indices: 71234--71334 Score: 140
Period size: 41 Copynumber: 2.5 Consensus size: 41
71224 ATATGTATAA
71234 ATATA-TTTATATT--TTATAT-TAATTATATATATAATATTT
1 ATATATTTTATATTAATTATATAT-A-TATATATATAATATTT
71273 ATATATTTTATATTAATTATATATATATATATATAATATTT
1 ATATATTTTATATTAATTATATATATATATATATAATATTT
71314 -TATATTTTTATATTAATTATA
1 ATATA-TTTTATATTAATTATA
71335 CAATACAAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
39 5 0.09
40 12 0.21
41 32 0.56
42 7 0.12
43 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (41 bp):
ATATATTTTATATTAATTATATATATATATATATAATATTT
Found at i:72117 original size:21 final size:20
Alignment explanation
Indices: 72093--72153 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
72083 TACTGTTACA
72093 ATGTTAGCGTGGTAGTCCAAT
1 ATGTT-GCGTGGTAGTCCAAT
72114 ATGTTGGCGTGGTAGTCCAAT
1 ATGTT-GCGTGGTAGTCCAAT
* *
72135 ATATTGACGTGGTTGTCCA
1 ATGTTG-CGTGGTAGTCCA
72154 CTGCGACTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (20 bp):
ATGTTGCGTGGTAGTCCAAT
Found at i:72335 original size:18 final size:19
Alignment explanation
Indices: 72287--72324 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
72277 TAAATTATTC
72287 AAATATTAAAAAAAATAAA
1 AAATATTAAAAAAAATAAA
*
72306 AAATACTAAAAAAAATAAA
1 AAATATTAAAAAAAATAAA
72325 TTATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATATTAAAAAAAATAAA
Found at i:74614 original size:58 final size:57
Alignment explanation
Indices: 74467--74614 Score: 210
Period size: 58 Copynumber: 2.6 Consensus size: 57
74457 ATTAAGTAAT
* *
74467 TTATTTATTGAACATGATTAATT-AAATTAATTATAATAATTACAAGTTAAAATAAT
1 TTATTTATTGAACATGATTAATTAAAATTAATTATAATAATTAAAAGTTAAAATAAG
* *
74523 TTATTGGCATTGAACATGATTAA-TAAAATTAATTATAATCATTAAAAGTTAAAATAAG
1 TTATT--TATTGAACATGATTAATTAAAATTAATTATAATAATTAAAAGTTAAAATAAG
*
74581 TTATTTATTGAACATGATTAATTGAAAAATAATT
1 TTATTTATTGAACATGATTAATT-AAAATTAATT
74615 TAAATGTATA
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
56 20 0.25
57 2 0.02
58 59 0.73
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (57 bp):
TTATTTATTGAACATGATTAATTAAAATTAATTATAATAATTAAAAGTTAAAATAAG
Found at i:75490 original size:18 final size:19
Alignment explanation
Indices: 75469--75504 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
75459 TCGAAATATT
*
75469 AATAAAATTAA-AATTTAA
1 AATAAAATGAATAATTTAA
75487 AATAAAATGAATAATTTA
1 AATAAAATGAATAATTTA
75505 TTTACCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATAAAATGAATAATTTAA
Found at i:78238 original size:21 final size:22
Alignment explanation
Indices: 78212--78257 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
78202 CAGAAAATAT
*
78212 TAAAAAA-ATTAATATTTTAGA
1 TAAAAAATACTAATATTTTAGA
78233 TAAAAAATACTAATATTTTAGA
1 TAAAAAATACTAATATTTTAGA
78255 TAA
1 TAA
78258 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
TAAAAAATACTAATATTTTAGA
Found at i:80657 original size:2 final size:2
Alignment explanation
Indices: 80611--80641 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
80601 GAAACATTTG
*
80611 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80642 GCATAGGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:102822 original size:40 final size:39
Alignment explanation
Indices: 102773--102885 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 39
102763 ACGATAAATT
102773 AATT-TATGTTAATTTATTTAAATGAATGAACATAAATAA
1 AATTATATGTT-ATTTATTTAAATGAATGAACATAAATAA
* * * *
102812 AATTATATGTTTGTTTATTTAAATAAATGGACATGAATAA
1 AATTATATG-TTATTTATTTAAATGAATGAACATAAATAA
* *
102852 AATTATATATCTTTTTATTTAAATGAATGAACAT
1 AATTATATGT-TATTTATTTAAATGAATGAACAT
102886 TCGATAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
39 5 0.08
40 56 0.89
41 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (39 bp):
AATTATATGTTATTTATTTAAATGAATGAACATAAATAA
Found at i:103170 original size:14 final size:14
Alignment explanation
Indices: 103151--103189 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
103141 GGTTAGTTTA
103151 TGTTCGTTTATTTG
1 TGTTCGTTTATTTG
*
103165 TGTTCGTTCATTTG
1 TGTTCGTTTATTTG
*
103179 TGTTCATTTAT
1 TGTTCGTTTAT
103190 AATTTAAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.62
Consensus pattern (14 bp):
TGTTCGTTTATTTG
Found at i:103465 original size:10 final size:11
Alignment explanation
Indices: 103452--103497 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
103442 ACTTTAACTG
103452 ATATTATAA-A
1 ATATTATAATA
103462 ATATTATAATA
1 ATATTATAATA
*
103473 ATATT-TTATA
1 ATATTATAATA
103483 AT-TTATATATA
1 ATATTATA-ATA
103494 ATAT
1 ATAT
103498 ATTTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 2 0.07
10 16 0.53
11 11 0.37
12 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATTATAATA
Found at i:103477 original size:21 final size:21
Alignment explanation
Indices: 103452--103497 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
103442 ACTTTAACTG
103452 ATATTATAAAATATTATA-ATA
1 ATATTATAAAAT-TTATATATA
* *
103473 ATATTTTATAATTTATATATA
1 ATATTATAAAATTTATATATA
103494 ATAT
1 ATAT
103498 ATTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTATAAAATTTATATATA
Found at i:103482 original size:23 final size:23
Alignment explanation
Indices: 103455--103514 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
103445 TTAACTGATA
103455 TTATAAAATAT-TATAATAATATT
1 TTATAAAATATATATAAT-ATATT
**
103478 TTATAATTTATATATAATATATT
1 TTATAAAATATATATAATATATT
*
103501 TT-T-AAATAAATATA
1 TTATAAAATATATATA
103515 GTTAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 8 0.26
22 1 0.03
23 16 0.52
24 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATAAAATATATATAATATATT
Found at i:103498 original size:16 final size:16
Alignment explanation
Indices: 103479--103560 Score: 50
Period size: 16 Copynumber: 5.4 Consensus size: 16
103469 AATAATATTT
103479 TATAATTTATATATAA
1 TATAATTTATATATAA
* *
103495 TAT-ATTTTTAAATAAA
1 TATAATTTATATAT-AA
* * *
103511 TATAGTTAAT-TTTAA
1 TATAATTTATATATAA
103526 TCATAATTTA-ATATAA
1 T-ATAATTTATATATAA
*
103542 -AT-ATTTTTAT-TAA
1 TATAATTTATATATAA
103555 TATAAT
1 TATAAT
103561 AAATTATTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 15
0.65 0.15 0.20
Matches are distributed among these distances:
13 7 0.15
14 6 0.12
15 13 0.27
16 19 0.40
17 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (16 bp):
TATAATTTATATATAA
Found at i:103513 original size:21 final size:24
Alignment explanation
Indices: 103466--103514 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 24
103456 TATAAAATAT
* *
103466 TATAATAATATTTTATAATTTATA
1 TATAATAATATTTTATAATATAAA
103490 TATAAT-ATATTTT-TAA-ATAAA
1 TATAATAATATTTTATAATATAAA
103511 TATA
1 TATA
103515 GTTAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 3 0.13
23 7 0.30
24 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAATAATATTTTATAATATAAA
Found at i:104633 original size:27 final size:27
Alignment explanation
Indices: 104603--104689 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
104593 TTAGAAATAT
104603 AAATATAAAAATAATGAATTTAATTTA
1 AAATATAAAAATAATGAATTTAATTTA
*
104630 AAAT-TATTAAATAAT--A---AATTT-
1 AAATATA-AAAATAATGAATTTAATTTA
104651 -AATATGAAAAATAATGAATTTAATTTAA
1 AAATAT-AAAAATAATGAATTTAATTT-A
*
104679 AAATACAAAAA
1 AAATATAAAAA
104690 ACAATAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 21
0.66 0.04 0.30
Matches are distributed among these distances:
20 3 0.07
21 8 0.17
22 6 0.13
23 1 0.02
25 1 0.02
26 7 0.15
27 11 0.24
28 5 0.11
29 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAATATAAAAATAATGAATTTAATTTA
Found at i:104682 original size:20 final size:21
Alignment explanation
Indices: 104638--104683 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
104628 TAAAATTATT
104638 AAATAATAAATTTAATATGAA
1 AAATAATAAATTTAATATGAA
* *
104659 AAATAATGAATTTAAT-TTAA
1 AAATAATAAATTTAATATGAA
104679 AAATA
1 AAATA
104684 CAAAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATAATAAATTTAATATGAA
Found at i:105612 original size:20 final size:19
Alignment explanation
Indices: 105584--105680 Score: 108
Period size: 18 Copynumber: 5.1 Consensus size: 19
105574 TTACTTTGCT
*
105584 TTTGATTTTGATTATTTTCC
1 TTTGCTTTTGATT-TTTTCC
*
105604 TTTGCTTTT-AATTTTTCC
1 TTTGCTTTTGATTTTTTCC
*
105622 TTTGATTTTGATTCTTTTCC
1 TTTGCTTTTGATT-TTTTCC
* *
105642 TTTGC-TTTCAATTTTTCC
1 TTTGCTTTTGATTTTTTCC
105660 TTTGCTTTTGATTCTTTTCC
1 TTTGCTTTTGATT-TTTTCC
105680 T
1 T
105681 AATAGTCTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
18 25 0.39
19 14 0.22
20 25 0.39
ACGTcount: A:0.10, C:0.16, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTGCTTTTGATTTTTTCC
Found at i:105626 original size:38 final size:38
Alignment explanation
Indices: 105584--105680 Score: 167
Period size: 38 Copynumber: 2.6 Consensus size: 38
105574 TTACTTTGCT
* *
105584 TTTGATTTTGATTATTTTCCTTTGCTTTTAATTTTTCC
1 TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
105622 TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
1 TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
*
105660 TTTGCTTTTGATTCTTTTCCT
1 TTTGATTTTGATTCTTTTCCT
105681 AATAGTCTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.10, C:0.16, G:0.08, T:0.65
Consensus pattern (38 bp):
TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
Found at i:105693 original size:38 final size:37
Alignment explanation
Indices: 105584--105693 Score: 123
Period size: 38 Copynumber: 2.9 Consensus size: 37
105574 TTACTTTGCT
* * *
105584 TTTGATTTTGATTATTTTCCTTTGCTTTTAATTTTTCC
1 TTTGATTTTGATTCTTTTCCTTAGC-TCTAATTTTTCC
* *
105622 TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
1 TTTGATTTTGATTCTTTTCCTTAGCTCT-AATTTTTCC
*
105660 TTTGCTTTTGATTCTTTTCCTAATAG-TCTAATTT
1 TTTGATTTTGATTCTTTTCCT--TAGCTCTAATTT
105694 CAACAACTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
37 3 0.05
38 58 0.89
39 2 0.03
40 2 0.03
ACGTcount: A:0.14, C:0.15, G:0.08, T:0.63
Consensus pattern (37 bp):
TTTGATTTTGATTCTTTTCCTTAGCTCTAATTTTTCC
Found at i:111256 original size:21 final size:21
Alignment explanation
Indices: 111231--111270 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
111221 AAAAAATAAA
* *
111231 ATTTATATATATATAATTTTT
1 ATTTAAATATATAGAATTTTT
*
111252 ATTTAAATATTTAGAATTT
1 ATTTAAATATATAGAATTT
111271 CACTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
ATTTAAATATATAGAATTTTT
Found at i:111455 original size:20 final size:20
Alignment explanation
Indices: 111419--111456 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
111409 ATCATATTCC
**
111419 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
111439 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
111457 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:111716 original size:25 final size:24
Alignment explanation
Indices: 111669--111716 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
111659 ATTTATATAC
* *
111669 TTTTTAATAAAATTTATATATAAT
1 TTTTTAATAAAATTTAAAGATAAT
*
111693 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
111717 ATGGGTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTTAATAAAATTTAAAGATAAT
Found at i:114398 original size:30 final size:30
Alignment explanation
Indices: 114362--114494 Score: 230
Period size: 30 Copynumber: 4.4 Consensus size: 30
114352 TTCGAATGAC
114362 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
114392 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
114422 CTATTCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
114452 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
114482 CTGTCCATAGGTC
1 CTATCCAGAGGTC
114495 CCGAAAAACC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:114511 original size:60 final size:60
Alignment explanation
Indices: 114362--114519 Score: 201
Period size: 60 Copynumber: 2.6 Consensus size: 60
114352 TTCGAATGAC
* * *
114362 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCAGAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * *
114422 CTATTCAGAGGTCATAAAGATCCTTGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCAGAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * *
114482 CTGTCCATAGGTCCCGAAA-AACCTAGGTAAACTATCCA
1 CTATCCAGAGGT-CAGAAAGAACCTAGGT-AACTATCCA
114520 TATGTTCCTT
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 74 0.85
61 13 0.15
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (60 bp):
CTATCCAGAGGTCAGAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:115639 original size:20 final size:20
Alignment explanation
Indices: 115614--115687 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
115604 CTCTTGAAGC
115614 GCATCGATGCATTCAACAGT
1 GCATCGATGCATTCAACAGT
*
115634 GCATCGATGCATTCTTTAGCATGT
1 GCATCGATGCATTC---AACA-GT
* * *
115658 GCATCGATGCAGT-ACCCGT
1 GCATCGATGCATTCAACAGT
115677 GCATCGATGCA
1 GCATCGATGCA
115688 CAAATCACCT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
19 13 0.28
20 16 0.35
23 3 0.07
24 14 0.30
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (20 bp):
GCATCGATGCATTCAACAGT
Found at i:115731 original size:64 final size:64
Alignment explanation
Indices: 115657--115796 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 64
115647 CTTTAGCATG
* * * * *
115657 TGCATCGATGCAGTACC-CGTGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGGGA
1 TGCATCGATGCACT-CCTCATGCAGCGATGCACAAATCACATTCGATGTTTCCATTTTAAGGGGA
* * * **
115721 TGCATCGATGCACTCCTTATGCAGCGATGCACCAATTACATTCGATGTTTCCATTTTAATAGG-
1 TGCATCGATGCACTCCTCATGCAGCGATGCACAAATCACATTCGATGTTTCCATTTTAAGGGGA
*
115784 TGTATCGATGCAC
1 TGCATCGATGCAC
115797 ATAGCTCAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
63 14 0.22
64 50 0.78
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCACTCCTCATGCAGCGATGCACAAATCACATTCGATGTTTCCATTTTAAGGGGA
Found at i:119166 original size:30 final size:30
Alignment explanation
Indices: 119130--119262 Score: 248
Period size: 30 Copynumber: 4.4 Consensus size: 30
119120 TCTGAATGAC
119130 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
119160 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
119190 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
119220 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
119250 CTATCTAGAGGTC
1 CTATCCAGAGGTC
119263 CCGAATAACC
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 100 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:119279 original size:60 final size:60
Alignment explanation
Indices: 119130--119279 Score: 201
Period size: 60 Copynumber: 2.5 Consensus size: 60
119120 TCTGAATGAC
* * *
119130 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCAGTAA
* * * *
119190 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCAGTAA
* * * *
119250 CTATCTAGAGGTCCCGAATAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAA
119280 AATATCAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:119528 original size:8 final size:8
Alignment explanation
Indices: 119515--119619 Score: 129
Period size: 8 Copynumber: 13.1 Consensus size: 8
119505 ATATAACCAT
*
119515 TACATATA
1 TACATACA
119523 TACATACA
1 TACATACA
119531 TACATACA
1 TACATACA
*
119539 TACATGCA
1 TACATACA
*
119547 TACATGCA
1 TACATACA
*
119555 TACATGCA
1 TACATACA
*
119563 TACATGCA
1 TACATACA
*
119571 TACATGCA
1 TACATACA
*
119579 TACATGCA
1 TACATACA
*
119587 TACATGCA
1 TACATACA
*
119595 TATATACA
1 TACATACA
119603 TACATACA
1 TACATACA
119611 TACATACA
1 TACATACA
119619 T
1 T
119620 GTCATCATTT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 92 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.28
Consensus pattern (8 bp):
TACATACA
Found at i:119536 original size:16 final size:16
Alignment explanation
Indices: 119515--119619 Score: 147
Period size: 16 Copynumber: 6.6 Consensus size: 16
119505 ATATAACCAT
* *
119515 TACATATATACATACA
1 TACATACATACATGCA
119531 TACATACATACATGCA
1 TACATACATACATGCA
*
119547 TACATGCATACATGCA
1 TACATACATACATGCA
*
119563 TACATGCATACATGCA
1 TACATACATACATGCA
*
119579 TACATGCATACATGCA
1 TACATACATACATGCA
* *
119595 TATATACATACATACA
1 TACATACATACATGCA
119611 TACATACAT
1 TACATACAT
119620 GTCATCATTT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 82 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.28
Consensus pattern (16 bp):
TACATACATACATGCA
Found at i:119549 original size:24 final size:24
Alignment explanation
Indices: 119522--119615 Score: 143
Period size: 24 Copynumber: 3.9 Consensus size: 24
119512 CATTACATAT
119522 ATACATACATACATACATACATGC
1 ATACATACATACATACATACATGC
* *
119546 ATACATGCATACATGCATACATGC
1 ATACATACATACATACATACATGC
* *
119570 ATACATGCATACATGCATACATGC
1 ATACATACATACATACATACATGC
*
119594 ATATATACATACATACATACAT
1 ATACATACATACATACATACAT
119616 ACATGTCATC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (24 bp):
ATACATACATACATACATACATGC
Found at i:120508 original size:24 final size:20
Alignment explanation
Indices: 120455--120531 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
120445 TTTCTCTTGA
120455 AGTGCATCGATGCATTCAAC
1 AGTGCATCGATGCATTCAAC
*
120475 AGTGCATCGATGCATTCTTTAGC
1 AGTGCATCGATGCATTC---AAC
* *
120498 ATGTGCATCGATGCAAT-ACC
1 A-GTGCATCGATGCATTCAAC
*
120518 CGTGCATCGATGCA
1 AGTGCATCGATGCA
120532 CAAATCACCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.27
20 19 0.39
23 3 0.06
24 14 0.29
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAC
Found at i:126103 original size:13 final size:13
Alignment explanation
Indices: 126085--126109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
126075 AGTTGAACAA
126085 TCTTCATATGCAG
1 TCTTCATATGCAG
126098 TCTTCATATGCA
1 TCTTCATATGCA
126110 TGACTTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
TCTTCATATGCAG
Found at i:127358 original size:29 final size:27
Alignment explanation
Indices: 127303--127358 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
127293 TTAAATATAT
* * *
127303 TTTAAAAATATTTTATTTTTGTTTAAA
1 TTTAAAAATATTTTATTCTTATCTAAA
127330 TTTAAAAGTATATTTTATTCTTATCTAAA
1 TTTAAAA--ATATTTTATTCTTATCTAAA
127359 CTATATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.29
29 17 0.71
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTAAAAATATTTTATTCTTATCTAAA
Found at i:127530 original size:27 final size:30
Alignment explanation
Indices: 127500--127570 Score: 94
Period size: 27 Copynumber: 2.5 Consensus size: 30
127490 TATAAATGTT
127500 TTAAAATAAAAATAAAATA-ATTTTA-AA-
1 TTAAAATAAAAATAAAATAGATTTTATAAG
* *
127527 TTAAATTAATAATAAAATAGATTTTATAAG
1 TTAAAATAAAAATAAAATAGATTTTATAAG
*
127557 TTAATATAAAAATA
1 TTAAAATAAAAATA
127571 TTTTTTAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 17 0.47
28 6 0.17
29 2 0.06
30 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
TTAAAATAAAAATAAAATAGATTTTATAAG
Found at i:127579 original size:23 final size:24
Alignment explanation
Indices: 127527--127587 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
127517 TAATTTTAAA
*
127527 TTAAATTAATAATAAAATAGATTTT
1 TTAAGTTAAT-ATAAAATAGATTTT
* *
127552 ATAAGTTAATATAAAA-ATATTTT
1 TTAAGTTAATATAAAATAGATTTT
127575 TTAAGTTAATATA
1 TTAAGTTAATATA
127588 TATAAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 18 0.56
24 6 0.19
25 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
TTAAGTTAATATAAAATAGATTTT
Found at i:127830 original size:19 final size:19
Alignment explanation
Indices: 127806--127843 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
127796 TGTATTTTTA
127806 TTTAATAAAAATAATATTT
1 TTTAATAAAAATAATATTT
* *
127825 TTTAATAAATATATTATTT
1 TTTAATAAAAATAATATTT
127844 CGAGTCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATAAAAATAATATTT
Found at i:133738 original size:16 final size:16
Alignment explanation
Indices: 133711--133764 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
133701 GGCGAGCAAT
*
133711 GAGCATTGAGCTTAAC
1 GAGCAATGAGCTTAAC
* *
133727 GAGTAATGAGCTTAAT
1 GAGCAATGAGCTTAAC
*
133743 AAGCAATGAGCTTAAC
1 GAGCAATGAGCTTAAC
133759 GAGCAA
1 GAGCAA
133765 CAAGTTTTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (16 bp):
GAGCAATGAGCTTAAC
Found at i:135470 original size:62 final size:65
Alignment explanation
Indices: 135397--135528 Score: 198
Period size: 65 Copynumber: 2.1 Consensus size: 65
135387 TATAATAGTT
* * *
135397 TTATATAAACTTTTTTTA-TTAA-ATGTATATAAAC-TTTTTAAAATTTATGCACAAGACACATC
1 TTATATAAACTTCTTTTACTAAATATATATATAAACTTTTTTAAAATTTATGCACAAGACACATC
* *
135459 TTATATAAACTTCTTTTACTAAATATATATATAAACTTTTTTTAAATTTATGCACAAGACACCTC
1 TTATATAAACTTCTTTTACTAAATATATATATAAACTTTTTTAAAATTTATGCACAAGACACATC
135524 TTATA
1 TTATA
135529 GATGTGATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
62 17 0.27
63 3 0.05
64 11 0.18
65 31 0.50
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.44
Consensus pattern (65 bp):
TTATATAAACTTCTTTTACTAAATATATATATAAACTTTTTTAAAATTTATGCACAAGACACATC
Found at i:135740 original size:2 final size:2
Alignment explanation
Indices: 135735--135777 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
135725 TATCTAAAAA
135735 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
135777 A
1 A
135778 CGGATTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:138490 original size:81 final size:83
Alignment explanation
Indices: 138308--138525 Score: 273
Period size: 81 Copynumber: 2.7 Consensus size: 83
138298 ACATTTATGG
* * * ** * * *
138308 AACATTAGGTTATATATATAAATATATACTGGAAAGCATTATGCTCCTTTTTATTTTAACATTGG
1 AACATTAGGTTATATATATAAATGTATAATGGAAAGCATTA-GGTTTTTTTTATGTGAACAATGG
138373 GCTATATATATTGACTAAT
65 GCTATATATATTGACTAAT
*
138392 AACATTAGGTAATATATATAAATGTATAATGGAAAGCATTAGGTTTTTTTTATGTGAACAAT-GG
1 AACATTAGGTTATATATATAAATGTATAATGGAAAGCATTAGGTTTTTTTTATGTGAACAATGGG
*
138456 C-CTATATATTGACTAAT
66 CTATATATATTGACTAAT
* * * *
138473 AACATTAGGTTACATATATAAATGTATAAT-GAACGTAGTAGG-TTTTTTTATGT
1 AACATTAGGTTATATATATAAATGTATAATGGAAAGCATTAGGTTTTTTTTATGT
138526 TTACATAAGG
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
79 11 0.09
80 9 0.08
81 43 0.36
82 3 0.03
83 15 0.13
84 38 0.32
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (83 bp):
AACATTAGGTTATATATATAAATGTATAATGGAAAGCATTAGGTTTTTTTTATGTGAACAATGGG
CTATATATATTGACTAAT
Found at i:138543 original size:81 final size:81
Alignment explanation
Indices: 138375--138545 Score: 220
Period size: 81 Copynumber: 2.1 Consensus size: 81
138365 AACATTGGGC
* *
138375 TATATATATTGACTAATAACATTAGGTAATATATATAAATGTATAATGGAAAGCATTAGGTTTTT
1 TATATATATTGACTAATAACATTAGGTAACATATATAAATGTATAATGGAAAGCAGTAGGTTTTT
*
138440 TTTATGTGAACAATGG
66 TTTATGTGAACAAAGG
** * * *
138456 CCTATATATTGACTAATAACATTAGGTTACATATATAAATGTATAAT-GAACGTAGTAGG-TTTT
1 TATATATATTGACTAATAACATTAGGTAACATATATAAATGTATAATGGAAAGCAGTAGGTTTTT
**
138519 TTTATGTTTACATAAGG
66 TTTATGTGAACA-AAGG
138536 TTATATATAT
1 -TATATATAT
138546 AAGGGGAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 14 0.18
80 12 0.16
81 50 0.66
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (81 bp):
TATATATATTGACTAATAACATTAGGTAACATATATAAATGTATAATGGAAAGCAGTAGGTTTTT
TTTATGTGAACAAAGG
Found at i:139226 original size:115 final size:113
Alignment explanation
Indices: 139036--139270 Score: 278
Period size: 115 Copynumber: 2.1 Consensus size: 113
139026 AGCCCCCTTA
* * * *
139036 ATTTTTTATTTATAATTAAAGTCCCTAATTTTTATAATGTCATGAAATTTTTAGTTTTTTATTCA
1 ATTTTTTATTTATAATTAAAGCCCCTAATTTTTATAATGTCATAAAATGTTTAGTTTTTTACTCA
* * *
139101 TTTATTCATTTCTTTTATTAATTTATTCAATTTTGAATTAAATTTAACC
66 TTTATTCATTTCTCTTATTAATTCATTCAA-TTTGAATTAAATCTAACC
*** * *
139150 ATTTTTATATTTATAATTTGGGCCCCTTATTTTTATAATTTCATAAAATGTTTAG-TTTTTACCC
1 ATTTTT-TATTTATAATTAAAGCCCCTAATTTTTATAATGTCATAAAATGTTTAGTTTTTTA--C
* *
139214 TC-TTT-TTCCATTTCTCTTATTTATTCATTCAATTTGAATTAAATCTAATC
63 TCATTTATT-CATTTCTCTTATTAATTCATTCAATTTGAATTAAATCTAACC
139264 ATTTTTT
1 ATTTTTT
139271 CTCTTTTTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
113 1 0.01
114 36 0.35
115 64 0.62
116 2 0.02
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.56
Consensus pattern (113 bp):
ATTTTTTATTTATAATTAAAGCCCCTAATTTTTATAATGTCATAAAATGTTTAGTTTTTTACTCA
TTTATTCATTTCTCTTATTAATTCATTCAATTTGAATTAAATCTAACC
Found at i:154605 original size:12 final size:12
Alignment explanation
Indices: 154584--154613 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
154574 GACATGACAT
*
154584 TTATTATTATTA
1 TTATTGTTATTA
154596 TTATTGTTATTA
1 TTATTGTTATTA
154608 TTATTG
1 TTATTG
154614 CCACATAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:155439 original size:21 final size:21
Alignment explanation
Indices: 155413--155487 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
155403 GTTTCCAGAT
155413 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
155434 TCGCAATGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
155455 TCGCAACGCGAACTT-GAACTA
1 TCGCAACGCGAACTTCG-ACTA
*
155476 TCGCAATGCGAA
1 TCGCAACGCGAA
155488 TATGTAAATC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 1 0.02
21 49 0.98
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:155521 original size:21 final size:19
Alignment explanation
Indices: 155413--155525 Score: 84
Period size: 21 Copynumber: 5.5 Consensus size: 19
155403 GTTTCCAGAT
*
155413 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAA--TCGACTA
155434 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAA--TCGACTA
* *
155455 TCGCAACGCGAACTTGAACTA
1 TCGCAATGCGAA-TCG-ACTA
* *
155476 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAAT-CG-ACTA
155496 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-A-TCGACTA
155517 TCGCAATGC
1 TCGCAATGC
155526 AATTTACATA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
20 16 0.21
21 61 0.78
22 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (19 bp):
TCGCAATGCGAATCGACTA
Found at i:155562 original size:21 final size:21
Alignment explanation
Indices: 155536--155610 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
155526 AATTTACATA
*
155536 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
155557 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
155578 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
155599 TTCGCATTGCGA
1 TTCGCATTGCGA
155611 ATCTGGAAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:156867 original size:6 final size:6
Alignment explanation
Indices: 156846--156882 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
156836 TCTCGTCTCG
156846 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
156883 AATACGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:157476 original size:54 final size:54
Alignment explanation
Indices: 157354--157475 Score: 183
Period size: 53 Copynumber: 2.3 Consensus size: 54
157344 CCCCATAGGA
** *
157354 GGAACCGATTCCCCCTAAATGGTTTTGGCCCCGAGATTTCCAGAATGCTCGGAG
1 GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAG
* *
157408 GGAACCGATTCCCCCTAAACAGTTTT-GCTCCGAGAATTCCAGTATGCTCGGAG
1 GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAG
*
157461 GGAACCGATCCCCCC
1 GGAACCGATTCCCCC
157476 CAAGGGGGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 38 0.61
54 24 0.39
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.22
Consensus pattern (54 bp):
GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAG
Found at i:162773 original size:23 final size:21
Alignment explanation
Indices: 162717--162778 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
162707 TTTTGGTGCA
*
162717 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
162737 GAGGGAACCAATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
162758 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
162779 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 15 0.44
ACGTcount: A:0.23, C:0.35, G:0.24, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:164740 original size:9 final size:8
Alignment explanation
Indices: 164718--164768 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
164708 TGTTTCAACA
164718 TTTTGGAT
1 TTTTGGAT
164726 ATTTTGGAT
1 -TTTTGGAT
164735 TGTTT-GAT
1 T-TTTGGAT
164743 TTTGTGGAT
1 TTT-TGGAT
*
164752 TGTTGGA-
1 TTTTGGAT
164759 TTTTGGAT
1 TTTTGGAT
164767 TT
1 TT
164769 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:164752 original size:17 final size:17
Alignment explanation
Indices: 164720--164763 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
164710 TTTCAACATT
164720 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
164737 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
164754 TTGGATTTTG
1 TTGGATTTTG
164764 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:165504 original size:76 final size:77
Alignment explanation
Indices: 165352--165558 Score: 287
Period size: 76 Copynumber: 2.7 Consensus size: 77
165342 CAAAGCCAAA
* * * **
165352 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
165416 TTTGGCCTCGAG
66 TTTGGCCTCGAG
*
165428 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
165493 TTT-G-CTCCGAG
66 TTTGGCCT-CGAG
* * * *
165504 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
165559 TTGTACAACG
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
75 19 0.16
76 85 0.72
77 14 0.12
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCTCGAG
Found at i:166326 original size:21 final size:21
Alignment explanation
Indices: 166255--166353 Score: 105
Period size: 21 Copynumber: 4.8 Consensus size: 21
166245 ATTAACTCAA
*
166255 CAAGTTCGCATAGCGATAGT-
1 CAAGTTCGCATTGCGATAGTC
* * * *
166275 CGACTATCGCATTGCGAT-TTA
1 CAAGT-TCGCATTGCGATAGTC
166296 CATA-TTCGCATTGCGATAGTC
1 CA-AGTTCGCATTGCGATAGTC
166317 CAAGTTCGCATTGCGATAGTC
1 CAAGTTCGCATTGCGATAGTC
*
166338 AAAGTTCGCATTGCGA
1 CAAGTTCGCATTGCGA
166354 ATCTGGAAAC
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
20 17 0.26
21 48 0.73
22 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
CAAGTTCGCATTGCGATAGTC
Found at i:182295 original size:23 final size:22
Alignment explanation
Indices: 182253--182333 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 22
182243 ATAGGGCAGA
182253 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
182275 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
* * *
182298 GGGAACCAATTCCCCC-T--AG
1 GGGAATCGATACCCCCTTGAAG
182317 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
182334 GGGGTTCTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
19 15 0.29
21 1 0.02
22 15 0.29
23 20 0.39
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:183866 original size:14 final size:14
Alignment explanation
Indices: 183847--183882 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
183837 CAGCCCCTTT
*
183847 GTTTGACTTTACAA
1 GTTTGACCTTACAA
183861 GTTTGACCTTACAA
1 GTTTGACCTTACAA
183875 GTTTGACC
1 GTTTGACC
183883 AATCAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (14 bp):
GTTTGACCTTACAA
Found at i:188592 original size:20 final size:20
Alignment explanation
Indices: 188575--188613 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
188565 TGAAACTTGT
188575 AATACAATCATCAAACTTTC
1 AATACAATCATCAAACTTTC
*
188595 AATACAGTCATCAAACTTT
1 AATACAATCATCAAACTTT
188614 TAGTTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (20 bp):
AATACAATCATCAAACTTTC
Found at i:189477 original size:12 final size:12
Alignment explanation
Indices: 189453--189486 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
189443 TAAAAGACAA
189453 AAGAAGAAAGAAT
1 AAGAAG-AAGAAT
*
189466 GAGAAGAAGAAT
1 AAGAAGAAGAAT
189478 AAGAAGAAG
1 AAGAAGAAG
189487 GTGAATGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (12 bp):
AAGAAGAAGAAT
Found at i:195375 original size:229 final size:229
Alignment explanation
Indices: 194975--195693 Score: 1352
Period size: 229 Copynumber: 3.1 Consensus size: 229
194965 GTTATATTGT
* *
194975 AAAGTATCTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
*
195039 ATCTTTGGTTAATATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
* *
195104 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAATATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
195169 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
195203 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
*
195268 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
195333 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
195398 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
*
195432 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCAATGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
*
195497 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
195562 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
195626 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
195660 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
195694 GTATAAAAGT
Statistics
Matches: 481, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
228 114 0.24
229 367 0.76
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:195765 original size:20 final size:19
Alignment explanation
Indices: 195742--195788 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
195732 CGATATACCA
195742 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
195762 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
195782 GGTAAAA
1 GGTAAAA
195789 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:195937 original size:20 final size:19
Alignment explanation
Indices: 195923--195969 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
195913 CGATATAACA
195923 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
195943 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
195963 GGTAAAA
1 GGTAAAA
195970 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:195971 original size:17 final size:19
Alignment explanation
Indices: 195932--195974 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
195922 AGGTAAAAAT
195932 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
195952 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
195969 ATGATA
1 ATGATA
195975 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:198301 original size:33 final size:33
Alignment explanation
Indices: 198259--198324 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
198249 AAATAGATGG
*
198259 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
198292 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
198325 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:200139 original size:19 final size:19
Alignment explanation
Indices: 200115--200163 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
200105 AATGTAGGGT
200115 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
200134 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
200153 TATTTTTGTAT
1 TAATTTTGTAT
200164 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:200937 original size:198 final size:198
Alignment explanation
Indices: 200282--201425 Score: 2067
Period size: 198 Copynumber: 5.8 Consensus size: 198
200272 CAATATGGCC
* * * *
200282 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATTCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* *
200347 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* **
200412 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTATTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
200477 TGGAA
194 TGGAA
*
200482 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
200547 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACGGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
200612 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
200677 GGAA
195 GGAA
200681 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
200746 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
200811 AATATGTCTAAATAATGTGTCGACGCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
200876 GAA
196 GAA
* *
200879 AACAGGGTGCACCCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
200944 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
201009 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGAT-TTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
201073 GAA
196 GAA
*
201076 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
201140 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
201205 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
201270 GAA
196 GAA
*
201273 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
201338 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
201403 AATATGTCTAAATAATGTGTCGA
131 AATATGTCTAAATAATGTGTCGA
201426 TACTAATTTA
Statistics
Matches: 926, Mismatches: 16, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
196 137 0.15
197 115 0.12
198 327 0.35
199 288 0.31
200 59 0.06
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
GAA
Found at i:201280 original size:394 final size:397
Alignment explanation
Indices: 200282--201435 Score: 2089
Period size: 394 Copynumber: 2.9 Consensus size: 397
200272 CAATATGGCC
* * * *
200282 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATTCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* *
200347 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* **
200412 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTATTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
* *
200477 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
194 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
* *
200542 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACGGGTACAAGTTTACCGGTTTTAT
259 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
*
200607 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
324 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGGTCCAGAA
200672 TGAATGGAA
389 TGAATGGAA
200681 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
200746 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
200811 AATATGTCTAAATAATGTGTCGACGCTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
*
200876 GAAAACAGGGTGCACCCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAATCATCGA
196 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
200941 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
*
201006 GAGAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGAT-TTTTTGGTCCAGAATG
326 GAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
201069 AATGGAA
391 AATGGAA
*
201076 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
201140 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
201205 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
201270 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
196 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
201335 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
*
201400 GAGAATATGTCTAAATAATGTGTCGATACTAATTTA
326 GAGAATATGTCTAAATAATGTGTCGACACTAATTTA
201436 AATATCAAGT
Statistics
Matches: 731, Mismatches: 23, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
394 315 0.43
395 60 0.08
396 16 0.02
397 190 0.26
398 92 0.13
399 58 0.08
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (397 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
GAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
AATGGAA
Found at i:202914 original size:6 final size:6
Alignment explanation
Indices: 202890--202993 Score: 91
Period size: 6 Copynumber: 17.3 Consensus size: 6
202880 AGCGGTCGCA
* * * * *
202890 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GAAGAT GACGAT GATGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * * * *
202938 GACGAT GAAGCT GACGAT GAAGAT GATGAC GATGAT GATGAT GATGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
202986 GAAGAT GA
1 GAAGAT GA
202994 TGATCTAAAC
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:202997 original size:12 final size:12
Alignment explanation
Indices: 202893--202993 Score: 121
Period size: 12 Copynumber: 8.4 Consensus size: 12
202883 GGTCGCAGAA
*
202893 GATGAAGCTGAC
1 GATGAAGATGAC
202905 GATGAAGATGAC
1 GATGAAGATGAC
202917 GATGAAGATGAC
1 GATGAAGATGAC
*
202929 GATGATGATGAC
1 GATGAAGATGAC
*
202941 GATGAAGCTGAC
1 GATGAAGATGAC
*
202953 GATGAAGATGAT
1 GATGAAGATGAC
* * *
202965 GACGATGATGAT
1 GATGAAGATGAC
* *
202977 GATGATGATGAA
1 GATGAAGATGAC
202989 GATGA
1 GATGA
202994 TGATCTAAAC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 79 1.00
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:204772 original size:183 final size:182
Alignment explanation
Indices: 204497--204989 Score: 869
Period size: 183 Copynumber: 2.7 Consensus size: 182
204487 GCAATGCTAT
*
204497 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
204562 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACA
*
204627 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
* *
204680 CGGTATAAATATACCGGTTTTATGCGTGAATAGGTCTACAACCTATATTGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
204745 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACA
*
204810 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
* * *
204863 CGGTATAAATATACCTGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
204928 GTGTCGGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
204990 GTAATTTTAA
Statistics
Matches: 296, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
183 292 0.99
184 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACAT
TTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:207315 original size:23 final size:23
Alignment explanation
Indices: 207284--207356 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
207274 ATAGGTAAAA
*
207284 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
207307 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
207330 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
207353 ATAT
1 ATAT
207357 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:207746 original size:23 final size:23
Alignment explanation
Indices: 207715--207787 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
207705 ATAGGTAAAA
*
207715 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
207738 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
207761 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
207784 ATAT
1 ATAT
207788 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:208075 original size:431 final size:431
Alignment explanation
Indices: 207272--208138 Score: 1689
Period size: 431 Copynumber: 2.0 Consensus size: 431
207262 AAAAATTTTG
207272 TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAAT
1 TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAAT
207337 GTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCA
66 GTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCA
* *
207402 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
131 CTGTAGAAAACATTAATTTAAGGTTATCTTTTGAATGAGTTTTAAGATATTAATTTAGTAATTAT
207467 AGGCATCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
196 AGGCATCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
207532 ATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATAT
261 ATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATAT
207597 TGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGA
326 TGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGA
*
207662 AGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATA
391 AGTATCGATCATTTTTATAAAAAGTATGAACACTTTCAATA
207703 TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAAT
1 TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAAT
207768 GTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCA
66 GTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCA
207833 CTGTAGAAAACATTAATTTAAGGTTATCTTTTGAATGAGTTTTAAGATATTAATTTAGTAATTAT
131 CTGTAGAAAACATTAATTTAAGGTTATCTTTTGAATGAGTTTTAAGATATTAATTTAGTAATTAT
*
207898 AGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
196 AGGCATCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
207963 ATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATAT
261 ATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATAT
208028 TGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGA
326 TGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGA
*
208093 AGTATCGATCTTTTTTATAAAAAGTATGAACACTTTCAATA
391 AGTATCGATCATTTTTATAAAAAGTATGAACACTTTCAATA
208134 TAATA
1 TAATA
208139 TAATGTAATA
Statistics
Matches: 431, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
431 431 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (431 bp):
TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAAT
GTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCA
CTGTAGAAAACATTAATTTAAGGTTATCTTTTGAATGAGTTTTAAGATATTAATTTAGTAATTAT
AGGCATCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATA
ATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATAT
TGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGA
AGTATCGATCATTTTTATAAAAAGTATGAACACTTTCAATA
Found at i:209647 original size:50 final size:50
Alignment explanation
Indices: 209584--209685 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
209574 TTTATCCTAT
*
209584 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATATATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
209634 TTTAGTATATATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATATATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
209684 TT
1 TT
209686 CAATAATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (50 bp):
TTTAGTATATATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:213913 original size:41 final size:41
Alignment explanation
Indices: 213856--213944 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
213846 CTATCGCAAA
**
213856 TTCGCGTTGAGATAGTTGAAAATCGTGTTGCGATTTTCCAT
1 TTCGCGTTGAGATAGTTGAAAATCGCATTGCGATTTTCCAT
* *
213897 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCTAT
1 TTCGCGTTGAGATAGTTGAAAATCGCATTGCGATTTTCCAT
213938 TTCGCGT
1 TTCGCGT
213945 AGATTTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
TTCGCGTTGAGATAGTTGAAAATCGCATTGCGATTTTCCAT
Found at i:214027 original size:11 final size:11
Alignment explanation
Indices: 214000--214055 Score: 89
Period size: 10 Copynumber: 5.2 Consensus size: 11
213990 AGACACGTAT
214000 GACCACGACCAC
1 GACCACGACC-C
214012 GACCACGACCC
1 GACCACGACCC
214023 GACCACGACCC
1 GACCACGACCC
214034 GACC-CGACCC
1 GACCACGACCC
214044 GACC-CGACCC
1 GACCACGACCC
214054 GA
1 GA
214056 GACGAGACGG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.41
11 16 0.36
12 10 0.23
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (11 bp):
GACCACGACCC
Found at i:214036 original size:5 final size:5
Alignment explanation
Indices: 214000--214055 Score: 76
Period size: 5 Copynumber: 10.4 Consensus size: 5
213990 AGACACGTAT
214000 GACCAC GACCAC GACCAC GACCC GACCAC GACCC GACCC GACCC GACCC
1 GACC-C GACC-C GACC-C GACCC GACC-C GACCC GACCC GACCC GACCC
214049 GACCC GA
1 GACCC GA
214056 GACGAGACGG
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 28 0.57
6 21 0.43
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:214651 original size:19 final size:19
Alignment explanation
Indices: 214627--214695 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
214617 TCTTTTTTTT
214627 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
214646 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
*
214668 CAACGAATTTGAAAAATCG
1 CAACGAATTTGGAAAATCG
214687 CAACGAATT
1 CAACGAATT
214696 GCTTGAACTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 21 0.55
20 2 0.05
21 2 0.05
22 13 0.34
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:215032 original size:29 final size:29
Alignment explanation
Indices: 214986--215044 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
214976 GTTACCACTG
* *
214986 CCAGCCACCATAGTATTTTTCACGTCGAT
1 CCAGCCACCATAGCATTTTTCACATCGAT
215015 CCAGCCACCATAGCATTTTTCACATCGAT
1 CCAGCCACCATAGCATTTTTCACATCGAT
215044 C
1 C
215045 ACCGTCCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.34, G:0.12, T:0.29
Consensus pattern (29 bp):
CCAGCCACCATAGCATTTTTCACATCGAT
Found at i:217398 original size:28 final size:28
Alignment explanation
Indices: 217366--217478 Score: 111
Period size: 29 Copynumber: 4.0 Consensus size: 28
217356 TATTCTATCA
* *
217366 AAAATATATTTTAATTTTATTTTAGCTT
1 AAAATATATTTTAATTTTATCTTAACTT
* *
217394 AAAATATATTTTAATCTTATCATAACTT
1 AAAATATATTTTAATTTTATCTTAACTT
* *
217422 AAAAATATTTTTTATTTTTATCTTAACTTTT
1 -AAAATATATTTTAATTTTATCTTAAC--TT
* * *
217453 AAAATATA-TATATTTTTATTTTAACT
1 AAAATATATTTTAATTTTATCTTAACT
217479 AATTACATAT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.01
28 24 0.34
29 37 0.52
30 7 0.10
31 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (28 bp):
AAAATATATTTTAATTTTATCTTAACTT
Found at i:217442 original size:29 final size:29
Alignment explanation
Indices: 217365--217677 Score: 115
Period size: 30 Copynumber: 10.7 Consensus size: 29
217355 ATATTCTATC
* *
217365 AAAAATATATTTTAATTTTATTTTAGCTT
1 AAAAATATATTTTAATTTTATCTTAACTT
* *
217394 -AAAATATATTTTAATCTTATCATAACTT
1 AAAAATATATTTTAATTTTATCTTAACTT
* *
217422 AAAAATATTTTTTATTTTTATCTTAACTTT
1 AAAAATATATTTTAATTTTATCTTAAC-TT
* * * *
217452 TAAAATATA-TATATTTTTATTTTAAC-T
1 AAAAATATATTTTAATTTTATCTTAACTT
* * *
217479 AATTACATATATTAT-ATTCTTAAT-TTAAATT
1 AA--AAATATATTTTAATT-TT-ATCTTAACTT
* * * * *
217510 ATTAAATATATTATAATCTTACCTTAAATT
1 A-AAAATATATTTTAATTTTATCTTAACTT
* * * * * *
217540 ATTAAATAAAATTT-ATCCTTATTTTAACAT
1 A-AAAATATATTTTAAT-TTTATCTTAACTT
* *
217570 AAAATATATATTTT-ATTCTTGTTTTTAACTT
1 AAAA-ATATATTTTAATT-TT-ATCTTAACTT
** * * * *
217601 AACATGTATATTTTTATTTTATTTTTATTT
1 AA-AAATATATTTTAATTTTATCTTAACTT
* * *
217631 AAACATATTTATGTTAATTTT-T-TTAATTT
1 AAA-A-ATATATTTTAATTTTATCTTAACTT
217660 AAAAATATATTTT-ATTTT
1 AAAAATATATTTTAATTTT
217678 CTCCGCTCAC
Statistics
Matches: 219, Mismatches: 46, Indels: 41
0.72 0.15 0.13
Matches are distributed among these distances:
26 5 0.02
27 9 0.04
28 25 0.11
29 60 0.27
30 79 0.36
31 37 0.17
32 4 0.02
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (29 bp):
AAAAATATATTTTAATTTTATCTTAACTT
Found at i:217596 original size:31 final size:31
Alignment explanation
Indices: 217561--217627 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
217551 TTTATCCTTA
*
217561 TTTTAACATAAAATATATA-TTTTATTCTTGT
1 TTTTAACATAAAATATATATTTTTATT-TTAT
* * *
217592 TTTTAACTTAACATGTATATTTTTATTTTAT
1 TTTTAACATAAAATATATATTTTTATTTTAT
217623 TTTTA
1 TTTTA
217628 TTTAAACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTTAACATAAAATATATATTTTTATTTTAT
Done.