Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008317.1 Hibiscus syriacus cultivar Beakdansim tig00111014_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: 312147
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:653 original size:21 final size:21
Alignment explanation
Indices: 627--669 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
617 TTTATGGGTT
* *
627 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
648 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
669 A
1 A
670 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:785 original size:67 final size:67
Alignment explanation
Indices: 649--797 Score: 189
Period size: 66 Copynumber: 2.2 Consensus size: 67
639 ACCCATTCAA
* *
649 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGTATGCTAGAGGGGAATCGGTACCCCCAG
1 GGGGAACCGATACCCCTTCAACGAATATGAATTCCAGTATGCTAGAGGGGAATCGATACCCCCAG
714 GG
66 GG
* **
716 GGGGAACCGATACCCC-TCATCGTTTATGAATTCCAG-ATTGCTTA-AGGGGAATCGATA-CCCC
1 GGGGAACCGATACCCCTTCAACGAATATGAATTCCAGTA-TGC-TAGAGGGGAATCGATACCCCC
777 AGGGG
64 A-GGG
*
782 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
798 CATGAGAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
65 6 0.08
66 49 0.67
67 18 0.25
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (67 bp):
GGGGAACCGATACCCCTTCAACGAATATGAATTCCAGTATGCTAGAGGGGAATCGATACCCCCAG
GG
Found at i:1136 original size:29 final size:29
Alignment explanation
Indices: 1102--1173 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1092 CATATTATGA
**
1102 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
1131 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
1160 TACATGACATGAAT
1 TACATGACATGAAT
1174 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1228 original size:30 final size:31
Alignment explanation
Indices: 1188--1246 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1178 AGAAAAGTTC
*
1188 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
1219 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
1247 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:7038 original size:20 final size:21
Alignment explanation
Indices: 7001--7043 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
6991 CAGAACCTCC
7001 CATTTCTTCTCCTTCTTC-CT
1 CATTTCTTCTCCTTCTTCTCT
7021 CATTTCTTCT-CTTCCTTCTCT
1 CATTTCTTCTCCTT-CTTCTCT
7042 CA
1 CA
7044 ACGTTGGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (21 bp):
CATTTCTTCTCCTTCTTCTCT
Found at i:7520 original size:21 final size:21
Alignment explanation
Indices: 7494--7536 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7484 TTTATGGGTT
* *
7494 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
7515 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
7536 A
1 A
7537 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:7612 original size:67 final size:66
Alignment explanation
Indices: 7516--7665 Score: 196
Period size: 67 Copynumber: 2.3 Consensus size: 66
7506 ACCCATTCAA
* * *
7516 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAG-TATGC-TAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAT-TGCTTA-AGGGGAATCGATA-CCCC
7579 AGGG
63 AGGG
* **
7583 GGGGAACCGATACCCCCTCATCGTTTATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
7648 G
66 G
*
7649 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
7666 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
66 24 0.32
67 47 0.64
68 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
G
Found at i:8004 original size:29 final size:29
Alignment explanation
Indices: 7970--8041 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
7960 CATATTATGA
**
7970 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
7999 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
8028 TACATGACATGAAT
1 TACATGACATGAAT
8042 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:8096 original size:30 final size:31
Alignment explanation
Indices: 8056--8114 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
8046 AGAAAAGTTC
*
8056 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
8087 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
8115 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:8408 original size:22 final size:22
Alignment explanation
Indices: 8334--8400 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
8324 TTATGGACAA
8334 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
8356 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
8378 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
8400 A
1 A
8401 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:10068 original size:25 final size:25
Alignment explanation
Indices: 10040--10087 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
10030 ATAACATTTT
* *
10040 TTATTATAATGACGAAAAGTAATAC
1 TTATTATAATGACAAAAAATAATAC
10065 TTATTATAATGACAAAAAATAAT
1 TTATTATAATGACAAAAAATAAT
10088 GATACTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (25 bp):
TTATTATAATGACAAAAAATAATAC
Found at i:10233 original size:27 final size:26
Alignment explanation
Indices: 10184--10234 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
10174 TGTTGACGCT
* *
10184 ATATTTAATTAATATGATTAATATCA
1 ATATTTAATGAATATGATGAATATCA
*
10210 ATATTTGAATGAATGTGATGAATAT
1 ATATTT-AATGAATATGATGAATAT
10235 TAATTCAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (26 bp):
ATATTTAATGAATATGATGAATATCA
Found at i:10890 original size:101 final size:102
Alignment explanation
Indices: 10692--10903 Score: 297
Period size: 101 Copynumber: 2.1 Consensus size: 102
10682 AAAATATGTT
*
10692 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAATAAAACATTAAAATTTAAAC
1 AAATCAAAATAAATAGTCCAATTAATTTATATTTACAATAAAAAATAAAACATTAAAATTTAAAC
* * * *
10757 TAAATTTACCAAACCACTCAAATACTATTTAATCTGTA
66 TAAACTTACCAAACCACTCAAATACAACTTAATATG-A
*
10795 AAATCAAAATAAATAGTCCAA-TAATTTATA-TTACCCAATAAAAAATAAAA-A-TATAATTTAA
1 AAATCAAAATAAATAGTCCAATTAATTTATATTTA--CAATAAAAAATAAAACATTAAAATTTAA
*
10856 ACTAAACTTACCAAACTACTCAAATACAACTTAATATGA
64 ACTAAACTTACCAAACCACTCAAATACAACTTAATATGA
10895 ATAATCAAA
1 A-AATCAAA
10904 TGGGGAAAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
100 2 0.02
101 52 0.53
102 10 0.10
103 35 0.35
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (102 bp):
AAATCAAAATAAATAGTCCAATTAATTTATATTTACAATAAAAAATAAAACATTAAAATTTAAAC
TAAACTTACCAAACCACTCAAATACAACTTAATATGA
Found at i:12186 original size:14 final size:14
Alignment explanation
Indices: 12167--12201 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
12157 GAGGAGGGAC
12167 CACAGCTGGACATG
1 CACAGCTGGACATG
12181 CACAGCTGGACATG
1 CACAGCTGGACATG
12195 CACAGCT
1 CACAGCT
12202 TCGCTGCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (14 bp):
CACAGCTGGACATG
Found at i:14017 original size:15 final size:16
Alignment explanation
Indices: 13934--14031 Score: 85
Period size: 16 Copynumber: 6.2 Consensus size: 16
13924 AATTTTTGTT
* * *
13934 GAACCGAAAACCATCC
1 GAACCGAAATCAACCC
*
13950 GAACCGAAAGT-AACAC
1 GAACCGAAA-TCAACCC
*
13966 GAACC-AATAGCAACCC
1 GAACCGAA-ATCAACCC
*
13982 GAACCAAAATCAACCC
1 GAACCGAAATCAACCC
13998 GAACCGAAATC-ACCC
1 GAACCGAAATCAACCC
* *
14013 AAACCGAAAACAACCC
1 GAACCGAAATCAACCC
14029 GAA
1 GAA
14032 TTTAATTTAC
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
15 15 0.23
16 49 0.74
17 2 0.03
ACGTcount: A:0.48, C:0.35, G:0.12, T:0.05
Consensus pattern (16 bp):
GAACCGAAATCAACCC
Found at i:17269 original size:3 final size:3
Alignment explanation
Indices: 17261--17328 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
17251 TGCATTGATC
17261 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
17309 TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TC
17329 CTTTTCCTGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:20630 original size:71 final size:71
Alignment explanation
Indices: 20514--20657 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
20504 TACGTACTCC
20514 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
1 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
20579 AGTAGA
66 AGTAGA
20585 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
1 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
20650 AGTAGA
66 AGTAGA
20656 AA
1 AA
20658 ATAGCTTAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (71 bp):
AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
AGTAGA
Found at i:33660 original size:146 final size:148
Alignment explanation
Indices: 33488--33782 Score: 535
Period size: 149 Copynumber: 2.0 Consensus size: 148
33478 TGGCAAGCCC
33488 ATCAACTCGAATCAATTGAAAATACAAAAATATAAAAAAAATTAT-AAATA-TTTTA-CTTTAAA
1 ATCAACTCGAATCAATTGAAAATACAAAAATATAAAAAAAATTATAAAATATTTTTACCTTTAAA
33550 AATGTTTTTTTATCTAATT-AAATGGTATTTAATTAATTTTATTTGTGATACCAAACTCAATCAA
66 AATGTTTTTTTATCTAATTAAAATGGTATTTAATTAA--TTATTTGTGATACCAAACTCAATCAA
33614 AAATTTTAAGGGACCATGTT
129 AAATTTTAAGGGACCATGTT
33634 ATCAACTCGAATCAATTGAAAATACAAAAATATAAAAAAAATTATAAAAATATTTTTACCTTTAA
1 ATCAACTCGAATCAATTGAAAATACAAAAATATAAAAAAAATTAT-AAAATATTTTTACCTTTAA
33699 AAATGTTTTTTTATCTAATTAAAATGGTATTTAATTAATTATTTGTGATACCAAACTCAATCAAA
65 AAATGTTTTTTTATCTAATTAAAATGGTATTTAATTAATTATTTGTGATACCAAACTCAATCAAA
33764 AATTTTAAGGGACCATGTT
130 AATTTTAAGGGACCATGTT
33783 GCTTTCTCTA
Statistics
Matches: 144, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
146 45 0.31
148 5 0.03
149 51 0.35
150 26 0.18
151 17 0.12
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (148 bp):
ATCAACTCGAATCAATTGAAAATACAAAAATATAAAAAAAATTATAAAATATTTTTACCTTTAAA
AATGTTTTTTTATCTAATTAAAATGGTATTTAATTAATTATTTGTGATACCAAACTCAATCAAAA
ATTTTAAGGGACCATGTT
Found at i:39505 original size:20 final size:22
Alignment explanation
Indices: 39466--39506 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
39456 ATAATATATT
*
39466 AATAATATTACTACATTTTATA
1 AATAATATTACTAAATTTTATA
39488 AATAATA-TA-TAAATTTTAT
1 AATAATATTACTAAATTTTAT
39507 TTAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATATTACTAAATTTTATA
Found at i:40607 original size:32 final size:31
Alignment explanation
Indices: 40571--40657 Score: 84
Period size: 37 Copynumber: 2.6 Consensus size: 31
40561 AACATTTTTT
40571 ATATTTTTAATTTTGTAAAAAAAATTATATAA
1 ATATTTTTAATTTTGTAAAAAAAA-TATATAA
* *
40603 ATATTATGAATTTAATTTTTTAAATAAAATATATAA
1 ATA-T-T---TTTAATTTTGTAAAAAAAATATATAA
*
40639 ATATTTTTAAAATTTGTAA
1 ATATTTTT-AATTTTGTAA
40658 TATTATACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
31 3 0.07
32 11 0.24
33 1 0.02
34 2 0.04
35 1 0.02
36 10 0.22
37 17 0.38
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (31 bp):
ATATTTTTAATTTTGTAAAAAAAATATATAA
Found at i:40824 original size:20 final size:20
Alignment explanation
Indices: 40799--40856 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
40789 ATCATATTCC
**
40799 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
40819 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
40839 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
40857 GTGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:42029 original size:160 final size:159
Alignment explanation
Indices: 41805--42121 Score: 519
Period size: 160 Copynumber: 2.0 Consensus size: 159
41795 TTCGTCCTGA
* * *
41805 TGATAGATAATATTATGTGAGCATCGAACGTGTATTATTATACAGAATGTCACGTCAGTATTATT
1 TGATAGATAATATTATGTGAGCATCGAACGTGTATTATTATACAAAATGTCACATCAATATTATT
* * *
41870 AAAAGTTAAAATTTTAATC-TACTTTCATTTAAAAGATAATTTTATCATTTCTATGTTGATGGTC
66 AAAAGTT-AAACTTTAATCATACTTTCATTTAAAAAATAATTTTATAATTTCTATGTTGAT-GTC
41934 AAAATTTAGGTAAAAATTAAGAACTATATGT
129 AAAATTTAGGTAAAAATTAAGAACTATATGT
41965 TGATAGATAATATTATGTGAGCATCGAACGTGTATTATTATACAAAATGTCACATCAATATTATT
1 TGATAGATAATATTATGTGAGCATCGAACGTGTATTATTATACAAAATGTCACATCAATATTATT
* *
42030 AAAAGTTAAACTTTAATCAATACTTTTATTTAAAAAATAATTTTATAATTTCTATGTTTATGTCA
66 AAAAGTTAAACTTTAATC-ATACTTTCATTTAAAAAATAATTTTATAATTTCTATGTTGATGTCA
*
42095 AAATTTAGGTAAAAATTAATAACTATA
130 AAATTTAGGTAAAAATTAAGAACTATA
42122 AAAATATAAA
Statistics
Matches: 146, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
159 10 0.07
160 99 0.68
161 37 0.25
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (159 bp):
TGATAGATAATATTATGTGAGCATCGAACGTGTATTATTATACAAAATGTCACATCAATATTATT
AAAAGTTAAACTTTAATCATACTTTCATTTAAAAAATAATTTTATAATTTCTATGTTGATGTCAA
AATTTAGGTAAAAATTAAGAACTATATGT
Found at i:48439 original size:67 final size:67
Alignment explanation
Indices: 48359--48493 Score: 209
Period size: 67 Copynumber: 2.0 Consensus size: 67
48349 CTCTATAATA
* * **
48359 ACATTTGTATTACTCTAGATCTCTTGAA-TAAATAGAAGAGTTTGAAAGTTGTGAATATAACAAA
1 ACATTTGTATTACTCTAAATCTC-TCAACTAAATAGAAGAGTTTGAAAGTTAAGAATATAACAAA
48423 TTG
65 TTG
*
48426 ACATTTGTATTACTCTAAATCTCTCAACTAAATAGAAGAGTTTGAAAGTTAAGAATATAATAAAT
1 ACATTTGTATTACTCTAAATCTCTCAACTAAATAGAAGAGTTTGAAAGTTAAGAATATAACAAAT
48491 TG
66 TG
48493 A
1 A
48494 GCGAAAAGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 3 0.05
67 59 0.95
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (67 bp):
ACATTTGTATTACTCTAAATCTCTCAACTAAATAGAAGAGTTTGAAAGTTAAGAATATAACAAAT
TG
Found at i:55063 original size:26 final size:26
Alignment explanation
Indices: 55033--55105 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
55023 ATTATATTTG
55033 TATTTACTTTATTTTGTTTAATTGTAA
1 TATTTACTTTATTTTGTTTAATT-TAA
*
55060 -ATTT--TTT-TTATT-TTTCATTTAA
1 TATTTACTTTATT-TTGTTTAATTTAA
* *
55082 TACTTACTTTATTTTGTTAAATTT
1 TATTTACTTTATTTTGTTTAATTT
55106 GTTGGACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
22 3 0.08
23 11 0.31
24 5 0.14
25 5 0.14
26 12 0.33
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (26 bp):
TATTTACTTTATTTTGTTTAATTTAA
Found at i:58007 original size:17 final size:17
Alignment explanation
Indices: 57985--58018 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
57975 TTGTTTATAC
57985 TTGAAGAGGAATGATAT
1 TTGAAGAGGAATGATAT
58002 TTGAAGAGGAATGATAT
1 TTGAAGAGGAATGATAT
58019 ATGCATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (17 bp):
TTGAAGAGGAATGATAT
Found at i:69093 original size:21 final size:20
Alignment explanation
Indices: 69006--69488 Score: 179
Period size: 20 Copynumber: 23.7 Consensus size: 20
68996 AAAATGACCA
**
69006 ACAAAATCGCAACGCGAAAT
1 ACAAAATCGCAACGCGATTT
**
69026 A-AAAATCGCAACGCGATCC
1 ACAAAATCGCAACGCGATTT
* * **
69045 CCAGAATCGCAAATC-AGTTT
1 ACAAAATCGCAACGCGA-TTT
*
69065 CCAAAATCGCAACGCGATTCT
1 ACAAAATCGCAACGCGATT-T
** * *
69086 TGAAAATCGCAATGCGATAGT
1 ACAAAATCGCAACGCGAT-TT
* * **
69107 ACAAATTTGCATTGCGATTTT
1 ACAAAATCGCAACGCGA-TTT
* *
69128 CCAAAATCGCAACGCGA-AT
1 ACAAAATCGCAACGCGATTT
** **
69147 ATGTAAATCGCAACGCGA-AC
1 A-CAAAATCGCAACGCGATTT
*
69167 ACATAAATCGCAACGCG-TAT
1 ACA-AAATCGCAACGCGATTT
69187 ATCAAAATCGCAACGCGATTT
1 A-CAAAATCGCAACGCGATTT
* ** ***
69208 AGAAAATCGCAACGTTAAAA
1 ACAAAATCGCAACGCGATTT
* **
69228 AGAAAATCGCAACG-G-TCAAA
1 ACAAAATCGCAACGCGAT--TT
* *
69248 AGAAAATCGCAACGCGAGCTT
1 ACAAAATCGCAACGCGA-TTT
* **
69269 CCAAGTTCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* * *
69289 AGAAGAAAATCGCAATGCGATTG
1 ---ACAAAATCGCAACGCGATTT
*** *
69312 ATTGAATCGCAATGCGATTT
1 ACAAAATCGCAACGCGATTT
* * * *
69332 ATAGAATCGCAATGCGATTG
1 ACAAAATCGCAACGCGATTT
* * *
69352 AGAGAGTCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* * * *
69372 AGAAGAGAATCGCAATGCGACTG
1 A-CA-A-AATCGCAACGCGATTT
* *
69395 AGAGAATCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* *
69415 AGAGAATCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* *
69435 AGAGAATCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* *
69455 AGAGAATCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* *
69475 AGAGAATCGCAACG
1 ACAAAATCGCAACG
69489 TTAAAAAGAA
Statistics
Matches: 362, Mismatches: 79, Indels: 44
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.05
20 253 0.70
21 63 0.17
22 2 0.01
23 27 0.07
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
ACAAAATCGCAACGCGATTT
Found at i:69213 original size:20 final size:20
Alignment explanation
Indices: 69067--69488 Score: 233
Period size: 20 Copynumber: 20.6 Consensus size: 20
69057 ATCAGTTTCC
*
69067 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TAG
* * *
69088 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTAG
* * ** **
69109 AAATTTGCATTGCGATTTTCC
1 AAAATCGCAACGCGA-TTTAG
*
69130 AAAATCGCAACGCGA-ATATG
1 AAAATCGCAACGCGATTTA-G
* ** *
69150 TAAATCGCAACGCGA-ACAC
1 AAAATCGCAACGCGATTTAG
* *
69169 ATAAATCGCAACGCG-TATATC
1 A-AAATCGCAACGCGATTTA-G
69190 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
69210 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
69230 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
69250 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
69271 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
69294 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
69314 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
69334 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
69354 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
69374 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
*
69397 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
69417 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
69437 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
69457 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
69477 AGAATCGCAACG
1 AAAATCGCAACG
69489 TTAAAAAGAA
Statistics
Matches: 320, Mismatches: 63, Indels: 37
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.00
20 228 0.71
21 61 0.19
22 2 0.01
23 28 0.09
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:69386 original size:83 final size:83
Alignment explanation
Indices: 69275--69488 Score: 308
Period size: 83 Copynumber: 2.6 Consensus size: 83
69265 GCTTCCAAGT
* ** * *
69275 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAGAATC
* *
69340 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAGAA
*
69358 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAGAATC
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAGAATC
*
69423 GCAACGCGATTTAGAGAA
66 GCAACGCGATTGAGAGAA
* *
69441 TCGCAACGCGATTT---AGAGAATCGCAACGCGATTTAGAGAATCGCAACG
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAACG
69489 TTAAAAAGAA
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 31 0.26
83 88 0.74
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAGAATC
GCAACGCGATTGAGAGAA
Found at i:69473 original size:40 final size:40
Alignment explanation
Indices: 69275--69488 Score: 284
Period size: 40 Copynumber: 5.2 Consensus size: 40
69265 GCTTCCAAGT
**
69275 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
69318 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
69358 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTT---AGAGAATCGCAATGCGATTGAGAGAA
* *
69401 TCGCAACGCGATTTAGAGAATCGCAACGCGATTTAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
69441 TCGCAACGCGATTTAGAGAATCGCAACGCGATTTAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
69481 TCGCAACG
1 TCGCAACG
69489 TTAAAAAGAA
Statistics
Matches: 156, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
40 103 0.66
42 2 0.01
43 51 0.33
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:69502 original size:20 final size:20
Alignment explanation
Indices: 69479--69518 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
69469 CGATTTAGAG
*
69479 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
69499 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
69519 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:69607 original size:6 final size:6
Alignment explanation
Indices: 69596--69703 Score: 195
Period size: 6 Copynumber: 18.5 Consensus size: 6
69586 GACACGTATT
69596 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
69644 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
69691 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
69704 CGAGACGAGA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.15
6 87 0.85
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:70418 original size:6 final size:6
Alignment explanation
Indices: 70392--70445 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
70382 TCTCGTCTCG
70392 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
70437 GGTCGT GGT
1 GGTCGT GGT
70446 AATACGTGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:70548 original size:20 final size:20
Alignment explanation
Indices: 70523--70566 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
70513 TTTTTAACTA
*
70523 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
70543 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
70563 TTCT
1 TTCT
70567 AAATCGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:70578 original size:20 final size:20
Alignment explanation
Indices: 70555--70705 Score: 185
Period size: 20 Copynumber: 7.4 Consensus size: 20
70545 CTTTTTAACG
* *
70555 TTGCGATTTTCTAAATCGCA
1 TTGCGATTCTCTCAATCGCA
70575 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
70595 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
*
70615 TTGCGATTCTCTTCTAAATCGCG
1 TTGCGATTCTC-TC--AATCGCA
*
70638 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
70658 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
***
70678 TTGCGATTGAATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
70698 TTGCGATT
1 TTGCGATT
70706 TTCTTCTAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 96 0.83
21 2 0.02
22 2 0.02
23 15 0.13
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:70642 original size:63 final size:63
Alignment explanation
Indices: 70563--70685 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
70553 CGTTGCGATT
* * * *
70563 TTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTC
1 TTCTAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTC
*
70626 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATT
1 TTCTAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATT
70686 GAATCAATCG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (63 bp):
TTCTAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTC
Found at i:70659 original size:83 final size:83
Alignment explanation
Indices: 70553--70726 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
70543 TTCTTTTTAA
* * * * ** *
70553 CGTTGCGATTTTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCATTG
70618 CGATTCTCTTCTAAATCG
66 CGATTCTCTTCTAAATCG
* *
70636 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTGAATCAATCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCATTG
*
70701 CGATTTTCTTCTAAATCG
66 CGATTCTCTTCTAAATCG
70719 CGTTGCGA
1 CGTTGCGA
70727 ACTTGGAAGC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (83 bp):
CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCATTG
CGATTCTCTTCTAAATCG
Found at i:70719 original size:63 final size:62
Alignment explanation
Indices: 70567--70705 Score: 183
Period size: 63 Copynumber: 2.3 Consensus size: 62
70557 GCGATTTTCT
* * * ***
70567 AAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTTC
1 AAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCGAATC
* *
70629 TAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATT-GAATC
1 -AAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCGAATC
70691 -AATCGCATTGCGATT
1 AAATCGCATTGCGATT
70706 TTCTTCTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
60 13 0.20
62 2 0.03
63 51 0.77
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (62 bp):
AAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCGAATC
Found at i:70803 original size:20 final size:20
Alignment explanation
Indices: 70553--70830 Score: 146
Period size: 20 Copynumber: 13.6 Consensus size: 20
70543 TTCTTTTTAA
70553 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
70573 CATTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
70593 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
70613 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
70636 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
70656 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
70676 CATTGCGATTGAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
70696 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
70719 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* ***
70740 TGTTGCGATTTTCTTTTGTC-
1 CGTTGCGATTTTC-TAAATCG
*** **
70760 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
70780 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
70800 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
70819 CGTTGCGATTTT
1 CGTTGCGATTTT
70831 ATTGGTCATT
Statistics
Matches: 203, Mismatches: 46, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
19 21 0.10
20 136 0.67
21 16 0.08
22 3 0.01
23 27 0.13
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:70820 original size:19 final size:20
Alignment explanation
Indices: 70780--70830 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
70770 TTCTTTTTAA
*
70780 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
70800 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
70819 CGTTGCGATTTT
1 CGTTGCGATTTT
70831 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:83206 original size:16 final size:16
Alignment explanation
Indices: 83182--83212 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
83172 ATCGAAAATC
83182 AATCCAAAAAATCGAT
1 AATCCAAAAAATCGAT
*
83198 AATCGAAAAAATCGA
1 AATCCAAAAAATCGA
83213 AACTGATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (16 bp):
AATCCAAAAAATCGAT
Found at i:83394 original size:19 final size:19
Alignment explanation
Indices: 83366--83411 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
83356 ACAAAATCTC
* *
83366 ACAAAATCCATATATAAAT
1 ACAAATTCCATATACAAAT
83385 ACAAATTCCATATACAAAT
1 ACAAATTCCATATACAAAT
*
83404 ATAAATTC
1 ACAAATTC
83412 AGCTTTCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.28
Consensus pattern (19 bp):
ACAAATTCCATATACAAAT
Found at i:83785 original size:17 final size:17
Alignment explanation
Indices: 83763--83799 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
83753 TTTAGAATAA
83763 AAAAACCGCACAAATCC
1 AAAAACCGCACAAATCC
*
83780 AAAAACTGCACAAATCC
1 AAAAACCGCACAAATCC
83797 AAA
1 AAA
83800 TCGAATCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.57, C:0.30, G:0.05, T:0.08
Consensus pattern (17 bp):
AAAAACCGCACAAATCC
Found at i:85634 original size:21 final size:21
Alignment explanation
Indices: 85585--85648 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
85575 CATATGAAAT
*
85585 TTGTCCCAAAGGACCTGTGAA
1 TTGTCCCAAAGGACCTATGAA
* *
85606 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCAAAGGACCTATGAA
85628 TTGTCCCAAAGGACCTATGAA
1 TTGTCCCAAAGGACCTATGAA
85649 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
TTGTCCCAAAGGACCTATGAA
Found at i:91698 original size:31 final size:32
Alignment explanation
Indices: 91636--91698 Score: 110
Period size: 33 Copynumber: 2.0 Consensus size: 32
91626 CCTCGAACCC
91636 GACCCGAATATCACACTTAAAAAAACCCGACCT
1 GACCCGAATATCACACTTAAAAAAA-CCGACCT
91669 GACCCGAATATCACACTTAAAAAAA-CGACC
1 GACCCGAATATCACACTTAAAAAAACCGACC
91699 CGAACAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 5 0.17
33 25 0.83
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14
Consensus pattern (32 bp):
GACCCGAATATCACACTTAAAAAAACCGACCT
Found at i:94481 original size:30 final size:29
Alignment explanation
Indices: 94415--94511 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
94405 GTTAATTTTT
*
94415 ATTTGACCTCTGAGTTTTAGATAGAATA-CTA
1 ATTTGACCT-TGAATTTTAGATA-AATATC-A
94446 ATTTGACCTTGAATTTTAGATGAAATATCA
1 ATTTGACCTTGAATTTTAGAT-AAATATCA
* * * *
94476 TTTTGACCGTAAACTTTAGATAAAATATCA
1 ATTTGACCTTGAATTTTAGAT-AAATATCA
*
94506 AATTGA
1 ATTTGA
94512 TCCATAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 45 0.80
31 11 0.20
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (29 bp):
ATTTGACCTTGAATTTTAGATAAATATCA
Found at i:95242 original size:2 final size:2
Alignment explanation
Indices: 95196--95229 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
95186 TTAAAGGAAG
95196 TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
95230 TTCAAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:106192 original size:27 final size:27
Alignment explanation
Indices: 106142--106194 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
106132 AATAAAACTT
* *
106142 TTATTTTCTAATAAGATCATATATATA
1 TTATTTTATAATAAGATCAGATATATA
*
106169 TTATTTTATAATAAGATCGGATATAT
1 TTATTTTATAATAAGATCAGATATAT
106195 TAAATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (27 bp):
TTATTTTATAATAAGATCAGATATATA
Found at i:107106 original size:11 final size:11
Alignment explanation
Indices: 107090--107114 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
107080 TACGGACACG
107090 CTGGGTCGGAT
1 CTGGGTCGGAT
107101 CTGGGTCGGAT
1 CTGGGTCGGAT
107112 CTG
1 CTG
107115 ACACGGGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.20, G:0.44, T:0.28
Consensus pattern (11 bp):
CTGGGTCGGAT
Found at i:109686 original size:60 final size:58
Alignment explanation
Indices: 109559--109689 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 58
109549 TATAGTCTTA
* **
109559 CGACTATTAAAAGGTATAAATTATTCTCTGATTATAAGGTGTTATCTTATTGAGTCAT
1 CGACTATTAAAAAGTATAAATTATTCTCTGATTATAAGACGTTATCTTATTGAGTCAT
* * *
109617 CATATTATTAAAAAGTATGAAATTTTATT-T-TGATTATATGACGTTA-CTTTATTGGAGTCAT
1 C-GACTATTAAAAAGTAT-AAA--TTATTCTCTGATTATAAGACGTTATC-TTATT-GAGTCAT
109678 CGACTATTAAAA
1 CGACTATTAAAA
109690 GTTACTATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
58 1 0.02
59 14 0.24
60 30 0.51
61 9 0.15
62 5 0.08
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (58 bp):
CGACTATTAAAAAGTATAAATTATTCTCTGATTATAAGACGTTATCTTATTGAGTCAT
Found at i:112616 original size:2 final size:2
Alignment explanation
Indices: 112609--112649 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
112599 TTATCTTATT
112609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
112650 ATACTTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:123346 original size:26 final size:28
Alignment explanation
Indices: 123283--123348 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
123273 TTTTTTTTTT
* *
123283 AATAATGACAACTGAATTTTATTACTAAA
1 AATAATGA-AACTGAATTTCATTACGAAA
123312 AATAATGAAA-TGAATTTCATTACGAAA
1 AATAATGAAACTGAATTTCATTACGAAA
123339 AA-AATGAAAC
1 AATAATGAAAC
123349 ATTCCCTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 7 0.21
27 17 0.50
28 2 0.06
29 8 0.24
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (28 bp):
AATAATGAAACTGAATTTCATTACGAAA
Found at i:124486 original size:23 final size:25
Alignment explanation
Indices: 124435--124486 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
124425 GAAACATATC
*
124435 AAAAGACAGACGAAAATGTATCATA
1 AAAAGACAGACGAAAATGTACCATA
124460 AAAA-ACAGA-GAAAATTGTACCATA
1 AAAAGACAGACGAAAA-TGTACCATA
124484 AAA
1 AAA
124487 GCAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 4 0.16
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.15
Consensus pattern (25 bp):
AAAAGACAGACGAAAATGTACCATA
Found at i:125794 original size:20 final size:20
Alignment explanation
Indices: 125771--125809 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
125761 TAAACTACGT
*
125771 TTTTTATTATTTAATTTTTG
1 TTTTGATTATTTAATTTTTG
*
125791 TTTTGATTATTTGATTTTT
1 TTTTGATTATTTAATTTTT
125810 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTGATTATTTAATTTTTG
Found at i:127299 original size:12 final size:12
Alignment explanation
Indices: 127282--127308 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
127272 GTTTAAGACT
127282 TATTATAAAAAA
1 TATTATAAAAAA
127294 TATTATAAAAAA
1 TATTATAAAAAA
127306 TAT
1 TAT
127309 AACATTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TATTATAAAAAA
Found at i:127633 original size:2 final size:2
Alignment explanation
Indices: 127626--127655 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
127616 TCCTTTAATC
127626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
127656 ATAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:131644 original size:42 final size:42
Alignment explanation
Indices: 131585--131704 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
131575 TTTCCCCGAA
*
131585 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
*
131627 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
131669 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
131705 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
Found at i:131938 original size:22 final size:22
Alignment explanation
Indices: 131913--131993 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
131903 ATATATTTAT
131913 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
131935 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATA--ATATAATA
* *
131959 TAATCAATTAT-ATTATAATAATA
1 TAAT-ATTTATAATAAT-ATAATA
*
131982 TAAGATATTATA
1 TAATAT-TTATA
131994 TTTTTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 16 0.36
23 12 0.27
24 13 0.29
25 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:131961 original size:34 final size:34
Alignment explanation
Indices: 131885--131962 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 34
131875 CAAAATATTA
*
131885 ATTAT-TAAAAT-ATTTAAAATATATTTATTAAT
1 ATTATATAAAATAATATAAAATATATTTATTAAT
*
131917 ATT-TAT--AATAATATAATATAATATTT-TTAAT
1 ATTATATAAAATAATATAAAAT-ATATTTATTAAT
131948 ATTATATAAAATAAT
1 ATTATATAAAATAAT
131963 CAATTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 3 0.08
31 16 0.42
32 13 0.34
34 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTATATAAAATAATATAAAATATATTTATTAAT
Found at i:132029 original size:54 final size:52
Alignment explanation
Indices: 131918--132029 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 52
131908 TTTATTAATA
*
131918 TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATCAATTAT
1 TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATAAATTAT
* * * *
131970 ATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATTTT
1 TTTATAATAATAT-A-ATATAATATTTTTAATATTATATAA-A-ATAATAAATTAT
132024 TTTATA
1 TTTATA
132030 TATTTAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
52 16 0.32
53 7 0.14
54 27 0.54
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (52 bp):
TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATAAATTAT
Found at i:132049 original size:19 final size:19
Alignment explanation
Indices: 132027--132079 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
132017 AAATTTTTTT
*
132027 ATATATTTAATAATGAATA
1 ATATATTTAATAATCAATA
*
132046 ATATTATTTATATATTTCAATA
1 ATA-TATTTA-ATA-ATCAATA
132068 ATAT-TTTAATAA
1 ATATATTTAATAA
132080 AGATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATCAATA
Found at i:132295 original size:20 final size:20
Alignment explanation
Indices: 132238--132287 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
132228 TTTCCAGATG
132238 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
132258 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
132278 TTTTCCAGAA
1 TTTTCCAGAA
132288 TTCAAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:132304 original size:15 final size:15
Alignment explanation
Indices: 132270--132351 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
132260 TTCCAGAAAT
**
132270 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
132285 G-AATTCAAATTTCA
1 GTAATTCAAATTCCA
**
132299 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
132314 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
132329 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
132344 GTAATTCA
1 GTAATTCA
132352 TTTTCTGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.19
15 47 0.81
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:132322 original size:30 final size:30
Alignment explanation
Indices: 132270--132351 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
132260 TTCCAGAAAT
*
132270 GTAATTCATTTTCCAG-AATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
132299 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
132329 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
132352 TTTTCTGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:132347 original size:45 final size:44
Alignment explanation
Indices: 132270--132356 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
132260 TTCCAGAAAT
** *
132270 GTAATTCATTTTCCAGAATTCAAATTTCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
132314 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
132357 TGAAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:132415 original size:17 final size:17
Alignment explanation
Indices: 132390--132432 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
132380 AAACAGACCC
*
132390 TAAGTGATTTCAGTGAT
1 TAAGGGATTTCAGTGAT
132407 TAAGGGATTTCAGTGAT
1 TAAGGGATTTCAGTGAT
132424 TAAGGGATT
1 TAAGGGATT
132433 GTTGTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (17 bp):
TAAGGGATTTCAGTGAT
Found at i:142166 original size:301 final size:301
Alignment explanation
Indices: 141623--142227 Score: 1138
Period size: 301 Copynumber: 2.0 Consensus size: 301
141613 TGGCCAAGTC
*
141623 GATGAGCTCTAGCCATTGCTTGTAAATCAGTATGAGGATTCCAATCACTGTAGAGACAGGACCCA
1 GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGACAGGACCCA
*
141688 TATTTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGTAATATACCTAAACCTTAAAATATT
66 TATTTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATT
141753 ACACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGG
131 ACACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGG
141818 CAATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTG
196 CAATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTG
141883 ACACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
261 ACACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
*
141924 GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGGCAGGACCCA
1 GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGACAGGACCCA
141989 TATTTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATT
66 TATTTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATT
*
142054 ACACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATTACATCAGCAAACGGG
131 ACACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGG
* *
142119 CAATAGTTCGTGATATTGTAACCTTTATACCATTCGCTCTGCAATATGAGAAACCTAATATTCTG
196 CAATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTG
* *
142184 TCACATGGTACTGTAAAGGCAATATCAGGTTTGTGCTTCTT
261 ACACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
142225 GAT
1 GAT
142228 CATTCGGGTT
Statistics
Matches: 296, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
301 296 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (301 bp):
GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGACAGGACCCA
TATTTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATT
ACACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGG
CAATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTG
ACACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
Found at i:150763 original size:7 final size:7
Alignment explanation
Indices: 150745--150774 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
150735 TCATTTGAGG
150745 ATTAATAT
1 ATTAA-AT
150753 ATTAAAT
1 ATTAAAT
150760 ATTAAAT
1 ATTAAAT
150767 ATTAAAT
1 ATTAAAT
150774 A
1 A
150775 AAATGGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTAAAT
Found at i:152335 original size:58 final size:56
Alignment explanation
Indices: 152208--152340 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 56
152198 TTTTGAACTT
*
152208 ATTTT-GGACCCCTA-TTTTTTGGAGCTTCTTAATGACAACTAATAGATATATTCG
1 ATTTTCGGACCCCTATTTTTTTGGAGCTTCTTAATGACAACTAATAGATATACTCG
* * *
152262 ATTTTTGGACCCCTATTTTTTTGGA-TTTCTTAATGACAACAACTGATAGATATACTCG
1 ATTTTCGGACCCCTATTTTTTTGGAGCTTCTTAATG---ACAACTAATAGATATACTCG
* *
152320 A-TTTCGAGGCTCCTATTTTTT
1 ATTTTCG-GACCCCTATTTTTT
152341 GAGCCCCTGC
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
54 5 0.07
55 18 0.27
56 9 0.13
57 4 0.06
58 31 0.46
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (56 bp):
ATTTTCGGACCCCTATTTTTTTGGAGCTTCTTAATGACAACTAATAGATATACTCG
Found at i:159685 original size:13 final size:13
Alignment explanation
Indices: 159667--159711 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
159657 GCCATAAATC
159667 TATGACGCGCATT
1 TATGACGCGCATT
* *
159680 TATGACACGTATT
1 TATGACGCGCATT
159693 TATGACGCGCATT
1 TATGACGCGCATT
159706 TATGAC
1 TATGAC
159712 TTACATTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:167246 original size:14 final size:14
Alignment explanation
Indices: 167221--167263 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
167211 TTTTTAGGTA
167221 TGTTTATTATTAATT
1 TGTTT-TTATTAATT
167236 TGTTTTTATTAA-T
1 TGTTTTTATTAATT
* *
167249 TATTTTTATTTATT
1 TGTTTTTATTAATT
167263 T
1 T
167264 ATTTATACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.44
14 9 0.36
15 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (14 bp):
TGTTTTTATTAATT
Found at i:167257 original size:27 final size:27
Alignment explanation
Indices: 167227--167281 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
167217 GGTATGTTTA
* *
167227 TTATTAATTTGTTTTTA-TTAATTATTT
1 TTATTAATTTATTTATACTT-ATTATTT
*
167254 TTATTTATTTATTTATACTTATTATTT
1 TTATTAATTTATTTATACTTATTATTT
167281 T
1 T
167282 ATTCATGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (27 bp):
TTATTAATTTATTTATACTTATTATTT
Found at i:167265 original size:14 final size:14
Alignment explanation
Indices: 167227--167281 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
167217 GGTATGTTTA
* *
167227 TTATTAATTTGTTT
1 TTATTTATTTATTT
*
167241 TTA-TTAATTATTT
1 TTATTTATTTATTT
167254 TTATTTATTTATTT
1 TTATTTATTTATTT
* *
167268 ATACTTA-TTATTT
1 TTATTTATTTATTT
167281 T
1 T
167282 ATTCATGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
13 16 0.48
14 17 0.52
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:168965 original size:18 final size:18
Alignment explanation
Indices: 168942--168986 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
168932 TATATTTTTA
168942 ATTTTTAATTTTAAAT-AT
1 ATTTTTAATTTT-AATGAT
*
168960 ATTTTT--TTTTCATGAT
1 ATTTTTAATTTTAATGAT
168976 ATTTTTAATTT
1 ATTTTTAATTT
168987 AGTTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
18 9 0.39
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTTAATTTTAATGAT
Found at i:170587 original size:42 final size:43
Alignment explanation
Indices: 170528--170608 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
170518 TCGAATAAAT
*
170528 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTTTTAA
1 GCATGCGAACTAGATATCATGCAGTTAGGATTTATTTTTTTAA
*
170570 GCATGCGAATTAGATATCATGCAGTTAGGATTTATTTTT
1 GCATGCGAACTAGATATCATGCAGTTAGGATTTATTTTT
170609 GTGAATAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 27 0.75
43 9 0.25
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (43 bp):
GCATGCGAACTAGATATCATGCAGTTAGGATTTATTTTTTTAA
Found at i:180293 original size:16 final size:15
Alignment explanation
Indices: 180272--180438 Score: 88
Period size: 16 Copynumber: 10.3 Consensus size: 15
180262 TAAAAGAGAA
180272 AAAAAAACGAAAAATG
1 AAAAAAA-GAAAAATG
* *
180288 AAAAAAATAATAAT-
1 AAAAAAAGAAAAATG
*
180302 AAAAATGAGAAAAA-G
1 AAAAA-AAGAAAAATG
180317 AAAAAGAAGAAAAGAAAAAATG
1 ---AA-AA-AA-AGAA-AAATG
*
180339 AGAAAAAATAAAAATG
1 A-AAAAAAGAAAAATG
*
180355 AGAAAAAATAAAAATG
1 A-AAAAAAGAAAAATG
*
180371 AGAAAAAATAAAAATG
1 A-AAAAAAGAAAAATG
**
180387 AAAAAAAAGAAAGAAAA
1 -AAAAAAAGAAA-AATG
180404 ATAAAAAGAGAAAAATG
1 A-AAAAA-AGAAAAATG
*
180421 AAAAAAAGAGAAAT-
1 AAAAAAAGAAAAATG
180435 AAAA
1 AAAA
180439 GGAGGGTTCA
Statistics
Matches: 123, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.07
15 17 0.14
16 59 0.48
17 14 0.11
18 9 0.07
19 5 0.04
20 6 0.05
21 3 0.02
22 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.09
Consensus pattern (15 bp):
AAAAAAAGAAAAATG
Found at i:180314 original size:30 final size:29
Alignment explanation
Indices: 180280--180425 Score: 117
Period size: 30 Copynumber: 4.9 Consensus size: 29
180270 AAAAAAAAAC
180280 GAAAAATGAAAAA-AATAATAATAAAAATGA
1 GAAAAATGAAAAAGAA-AA-AATAAAAATGA
*
180310 GAAAAA-GAAAAAGAAGAAAAGAAAAAATGA
1 GAAAAATGAAAAAGAA-AAAA-TAAAAATGA
*
180340 GAAAAAATAAAAATGAGAAAAAATAAAAATGA
1 G-AAAAATGAAAA--AGAAAAAATAAAAATGA
*
180372 GAAAAAAT-AAAAATGAAAAAA-AAGAA--A
1 G-AAAAATGAAAAA-GAAAAAATAAAAATGA
180399 GAAAAAT-AAAAAGAGAAAAATGAAAAA
1 GAAAAATGAAAAAGA-AAAAAT-AAAAA
180426 AAGAGAAATA
Statistics
Matches: 100, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
25 2 0.02
26 16 0.16
27 2 0.02
28 4 0.04
29 13 0.13
30 26 0.26
31 9 0.09
32 20 0.20
33 4 0.04
34 4 0.04
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.10
Consensus pattern (29 bp):
GAAAAATGAAAAAGAAAAAATAAAAATGA
Found at i:180320 original size:15 final size:15
Alignment explanation
Indices: 180299--180438 Score: 134
Period size: 16 Copynumber: 9.5 Consensus size: 15
180289 AAAAAATAAT
180299 AATAAAAATGAGAAA
1 AATAAAAATGAGAAA
*
180314 AAGAAAAA-GAAGAAA
1 AATAAAAATG-AGAAA
180329 AGA-AAAAATGAGAAAA
1 A-ATAAAAATGAG-AAA
180345 AATAAAAATGAGAAAA
1 AATAAAAATGAG-AAA
180361 AATAAAAATGAGAAAA
1 AATAAAAATGAG-AAA
180377 AATAAAAATGA-AAA
1 AATAAAAATGAGAAA
*
180391 AA-AAGAA--AGAAA
1 AATAAAAATGAGAAA
180403 AATAAAAA-GAGAAA
1 AATAAAAATGAGAAA
* *
180417 AATGAAAAA-AAGAGA
1 AAT-AAAAATGAGAAA
180432 AATAAAA
1 AATAAAA
180439 GGAGGGTTCA
Statistics
Matches: 111, Mismatches: 5, Indels: 19
0.82 0.04 0.14
Matches are distributed among these distances:
11 1 0.01
12 5 0.05
13 8 0.07
14 18 0.16
15 33 0.30
16 46 0.41
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (15 bp):
AATAAAAATGAGAAA
Found at i:180375 original size:42 final size:40
Alignment explanation
Indices: 180313--180427 Score: 121
Period size: 41 Copynumber: 2.8 Consensus size: 40
180303 AAAATGAGAA
* *
180313 AAAGAAAAAGAAGAAA-AGAAAAAATGAGAAAAAATAAAAATG
1 AAAGAAAAATAA-AAAGAGAAAAAATGA-AAAAAA-AAAAAAG
*
180355 AGA-AAAAATAAAAATGAGAAAAAAT-AAAAATGAAAAAAAAG
1 AAAGAAAAATAAAAA-GAGAAAAAATGAAAAA--AAAAAAAAG
180396 AAAGAAAAATAAAAAGAG-AAAAATGAAAAAAA
1 AAAGAAAAATAAAAAGAGAAAAAATGAAAAAAA
180428 GAGAAATAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
39 2 0.03
40 13 0.21
41 24 0.38
42 24 0.38
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (40 bp):
AAAGAAAAATAAAAAGAGAAAAAATGAAAAAAAAAAAAAG
Found at i:182139 original size:51 final size:51
Alignment explanation
Indices: 181416--182284 Score: 1100
Period size: 51 Copynumber: 16.6 Consensus size: 51
181406 TCAGACGAAA
*
181416 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
*
181467 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAAG-TCGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC-AAGTTTGTTGAAG
* * *
181518 ATTGAGTCATATACTATCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAA
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
*
181569 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAAG-TCGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC-AAGTTTGTTGAAG
*
181620 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTATTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
181671 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
181722 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
*
181773 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTATTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
*
181824 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
* * *
181875 ATTGAGTCCTATACTCTCTGAATGAATAGGGATCGGACAAGTTCGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
*
181926 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
* * * **
181977 ATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAACGGACCCGTTT-TATGAAG
1 A---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGT-TGAAG
* * * *
182032 ATTGCTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAG
1 A-T--T-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
* * * ** *
182087 ATTGAGTCCTATACTCTCTGAAAGAATAGAGAGCGGGCCTGTTTATTGAAG
1 ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
* * * * ** *
182138 ATTTTCCGAGTTCTATACTCTCTGAAGGAGTAGAGAGCAGACCTGTTTTATTGAAG
1 A--TT--GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTTGTTGAAG
* * * * *
182194 ATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTT-TATGAAG
1 ATTG----AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGT-TGAAG
*
182249 ATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGA
1 A---TT-GAGTCCTATACTCT-CTGAAGGAATAGGGA
182285 ACAGACTCGT
Statistics
Matches: 739, Mismatches: 52, Indels: 50
0.88 0.06 0.06
Matches are distributed among these distances:
50 6 0.01
51 517 0.70
52 8 0.01
53 3 0.00
54 8 0.01
55 151 0.20
56 43 0.06
58 2 0.00
59 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (51 bp):
ATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTTGTTGAAG
Found at i:184978 original size:14 final size:15
Alignment explanation
Indices: 184940--184979 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
184930 ATGAATAGTC
184940 CATCTTTTAAAAGTA
1 CATCTTTTAAAAGTA
184955 CATCTTTTAAAAGTA
1 CATCTTTTAAAAGTA
184970 CAT-TTTTAAA
1 CATCTTTTAAA
184980 GACGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (15 bp):
CATCTTTTAAAAGTA
Found at i:191366 original size:19 final size:21
Alignment explanation
Indices: 191322--191366 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
191312 AAGGAAATCA
191322 GTGGCCCAGGAAATACCACCAG
1 GTGGCCCAGGAAATACCA-CAG
*
191344 GTGGCCCCGGAAAT-CCA-AG
1 GTGGCCCAGGAAATACCACAG
191363 GTGG
1 GTGG
191367 ATTGAAGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
21 3 0.14
22 13 0.59
ACGTcount: A:0.27, C:0.29, G:0.33, T:0.11
Consensus pattern (21 bp):
GTGGCCCAGGAAATACCACAG
Found at i:200537 original size:13 final size:13
Alignment explanation
Indices: 200519--200543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200509 CTCCTAATAG
200519 TTTTATCAATTTT
1 TTTTATCAATTTT
200532 TTTTATCAATTT
1 TTTTATCAATTT
200544 AGCACTTAAT
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:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTATCAATTTT
Found at i:208157 original size:35 final size:38
Alignment explanation
Indices: 208065--208164 Score: 118
Period size: 35 Copynumber: 2.7 Consensus size: 38
208055 TTTTAAAAGT
*
208065 AATTTA-AATATTAGGGTGAAATAATTTAAGAAAATAA
1 AATTTAGAATATTATGGTGAAATAATTTAAGAAAATAA
* * * *
208102 AATTTAGAATTTTATAGTGAAATAATTTAAG-CAAT-T
1 AATTTAGAATATTATGGTGAAATAATTTAAGAAAATAA
*
208138 GA-TTAGAATATTATGGTGAAATAATTT
1 AATTTAGAATATTATGGTGAAATAATTT
208165 TGAAAATTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 23 0.43
36 1 0.02
37 9 0.17
38 21 0.39
ACGTcount: A:0.47, C:0.01, G:0.14, T:0.38
Consensus pattern (38 bp):
AATTTAGAATATTATGGTGAAATAATTTAAGAAAATAA
Found at i:208173 original size:35 final size:35
Alignment explanation
Indices: 208050--208172 Score: 108
Period size: 35 Copynumber: 3.4 Consensus size: 35
208040 AAATTAAAAG
* *
208050 AATAATTTTAAAAGTAATTTA-AATATTAGGGTGA
1 AATAATTTTAAAATTAATTTAGAATATTATGGTGA
* * * *
208084 AATAATTTAAGAAAATAAAATTTAGAATTTTATAGTGA
1 AATAATTT--TAAAAT-TAATTTAGAATATTATGGTGA
*
208122 AATAA-TTTAAGCAATTGA-TTAGAATATTATGGTGA
1 AATAATTTTAA--AATTAATTTAGAATATTATGGTGA
208157 AATAATTTTGAAAATT
1 AATAATTTT-AAAATT
208173 GGGTGTGGAA
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
34 8 0.11
35 26 0.37
36 8 0.11
37 13 0.19
38 15 0.21
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (35 bp):
AATAATTTTAAAATTAATTTAGAATATTATGGTGA
Found at i:210300 original size:2 final size:2
Alignment explanation
Indices: 210293--210322 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
210283 ATTGATTTTA
210293 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
210323 TTCTTCGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215361 original size:18 final size:17
Alignment explanation
Indices: 215338--215380 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
215328 CAGAGCTAAA
215338 CATTCAAAGTCTCTGAAT
1 CATTCAAA-TCTCTGAAT
*
215356 CATTCAGCATCTCTGAAT
1 CATTCA-AATCTCTGAAT
*
215374 TATTCAA
1 CATTCAA
215381 CGCTTAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (17 bp):
CATTCAAATCTCTGAAT
Found at i:219239 original size:172 final size:169
Alignment explanation
Indices: 218919--219264 Score: 482
Period size: 172 Copynumber: 2.0 Consensus size: 169
218909 CACATCCAAG
* * *
218919 GCACTAAACCAGATCCTCGTCCATACTATTGTCCTTAGCACCACAATGATAAACTGATTCAGTTC
1 GCACTAAACCAGATCCTCCTCCATACTATTGTCCTTAGCACCACAATGATAAACTGATCCAGTTA
* * *
218984 TGAGAAGTTGCTGTCAAGAGAAGATACTTTTAAGGACAAGTTATGGGGTAAAATCCAAGCTTGTT
66 TGAGAAGTTGCTGTCAAGAGAAGATACTTTTAAGGACAAGTTATGGGCTAAAATCAAAGCTTGCT
219049 CCTTCTTGGGAGATGGGAAATATGCCTGATGCTAGGTGGAACAT
131 CCTTCTTGGGAGATGGGAAATA-----GATGCTAGGTGGAACAT
* * *
219093 GCACTAAACCAGATCCCTCCTGCATACTCTTGTCC-TAGCACCACGATGATAAACTGATCCAGTT
1 GCACTAAACCAGAT-CCTCCTCCATACTATTGTCCTTAGCACCACAATGATAAACTGATCCAGTT
* * * *
219157 ATGAGAAG-TGCTGTCAGGTGAAGGTAC-TTTAAGGACATGTTATGGGCTAAAATCAAAGCTTGC
65 ATGAGAAGTTGCTGTCAAGAGAAGATACTTTTAAGGACAAGTTATGGGCTAAAATCAAAGCTTGC
* *
219220 TCCTTGTTGGGAGATGGGAAATAGATGCTTGGTGGAACAT
130 TCCTTCTTGGGAGATGGGAAATAGATGCTAGGTGGAACAT
219260 GCACT
1 GCACT
219265 TGTTTACAGG
Statistics
Matches: 156, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
167 21 0.13
172 54 0.35
173 16 0.10
174 48 0.31
175 17 0.11
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (169 bp):
GCACTAAACCAGATCCTCCTCCATACTATTGTCCTTAGCACCACAATGATAAACTGATCCAGTTA
TGAGAAGTTGCTGTCAAGAGAAGATACTTTTAAGGACAAGTTATGGGCTAAAATCAAAGCTTGCT
CCTTCTTGGGAGATGGGAAATAGATGCTAGGTGGAACAT
Found at i:223117 original size:14 final size:15
Alignment explanation
Indices: 223086--223118 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
223076 ATGAAGAATG
223086 TGGAGAAGAGATAGAA
1 TGGAGAAGAGA-AGAA
223102 TGGAGAAGAG-AGAA
1 TGGAGAAGAGAAGAA
223116 TGG
1 TGG
223119 CCGTGAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.12
Consensus pattern (15 bp):
TGGAGAAGAGAAGAA
Found at i:225222 original size:45 final size:45
Alignment explanation
Indices: 225153--225303 Score: 239
Period size: 45 Copynumber: 3.3 Consensus size: 45
225143 TTTATTTTCG
*
225153 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAAT-AA-GCATGCGAACTAGATATCATGCGGTTAGGTTTA
225200 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
* *
225245 TTTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTATGATTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTA-GGTTTA
225291 TTTTTGTGAATAA
1 TTTTT-TGAATAA
225304 CAAAGCATGG
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
45 71 0.72
46 12 0.12
47 16 0.16
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (45 bp):
TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
Found at i:230180 original size:21 final size:21
Alignment explanation
Indices: 230138--230180 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
230128 TTTCTGGGTT
* * *
230138 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
230159 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
230180 A
1 A
230181 TGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:230250 original size:71 final size:72
Alignment explanation
Indices: 230160--230303 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
230150 ACCCATTCAA
* *
230160 GGGGAACCGATACCCCCTCAAT-G-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
230223 AGGGGGGG
65 AGGGGGGG
* * *
230231 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
230296 GGGGGGG
66 GGGGGGG
230303 G
1 G
230304 AACCGATTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
70 2 0.03
71 20 0.30
72 44 0.67
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.17
Consensus pattern (72 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGGGGGG
Found at i:230718 original size:30 final size:31
Alignment explanation
Indices: 230676--230735 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
230666 AGAAAAAGTT
*
230676 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
230707 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
230736 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:231029 original size:22 final size:22
Alignment explanation
Indices: 230955--231021 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
230945 TTATGGACAT
230955 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
230977 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
230999 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
231021 A
1 A
231022 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:235246 original size:19 final size:19
Alignment explanation
Indices: 235222--235262 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
235212 TTCCATCAGG
235222 ATTATTGCAACCGCTGTTC
1 ATTATTGCAACCGCTGTTC
235241 ATTATTGCAACCGCTGTTC
1 ATTATTGCAACCGCTGTTC
235260 ATT
1 ATT
235263 CCTCAATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (19 bp):
ATTATTGCAACCGCTGTTC
Found at i:237122 original size:21 final size:21
Alignment explanation
Indices: 237080--237122 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
237070 TTTCTGGGTT
* * *
237080 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
237101 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
237122 A
1 A
237123 TGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:237188 original size:68 final size:70
Alignment explanation
Indices: 237102--237256 Score: 226
Period size: 69 Copynumber: 2.2 Consensus size: 70
237092 ACCCATTCAA
* *
237102 GGGGAACCGATACCCCCTCAAT-G-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
237165 A-GGGG
65 AGGGGG
* * *
237170 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
237235 GGGGG
66 GGGGG
*
237240 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
237257 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
67 2 0.03
68 20 0.26
69 36 0.46
70 20 0.26
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.17
Consensus pattern (70 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGGGG
Found at i:237654 original size:30 final size:31
Alignment explanation
Indices: 237612--237671 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
237602 AGAAAAAGTT
*
237612 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
237643 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
237672 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:237965 original size:22 final size:22
Alignment explanation
Indices: 237891--237957 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
237881 TTATGGACAT
237891 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
237913 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
237935 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
237957 A
1 A
237958 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:243766 original size:64 final size:63
Alignment explanation
Indices: 243662--243780 Score: 141
Period size: 64 Copynumber: 1.9 Consensus size: 63
243652 TTGTTTAAGG
* **
243662 TGCATCGATGCACATGAAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGCCATCGA
1 TGCATCGATGCACAAGAAGTGCATCGATGCACCAATTTAAAAA-AAAACATCGAATGCCATCGA
* * * * *
243726 TGCATCGATGCATAAGGAGTGCATCGATGCACCCCA-TTAAATACAAACATCGAAT
1 TGCATCGATGCACAAGAAGTGCATCGATGCA-CCAATTTAAAAAAAAACATCGAAT
243781 AAGATTTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 11 0.24
64 34 0.74
65 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (63 bp):
TGCATCGATGCACAAGAAGTGCATCGATGCACCAATTTAAAAAAAAACATCGAATGCCATCGA
Found at i:251123 original size:23 final size:22
Alignment explanation
Indices: 251097--251160 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
251087 CAGCTCATAT
251097 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
251120 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
*
251143 AATTACACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
251161 TATAATAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:251297 original size:103 final size:103
Alignment explanation
Indices: 251176--251393 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
251166 TAATGTCCAT
*
251176 AAGGACAACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
* *
251241 GACCTCACACCTGTTCTAAAGAATACATATATGTCCCG
66 GACCTCACACCTATTCCAAAGAATACATATATGTCCCG
*
251279 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
251344 GACCTCACACCTATTCCAAAGAATACATATATGTCCCG
66 GACCTCACACCTATTCCAAAGAATACATATATGTCCCG
251382 AAGGACCACATA
1 AAGGACCACATA
251394 GACCCTCTAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
GACCTCACACCTATTCCAAAGAATACATATATGTCCCG
Found at i:259036 original size:19 final size:19
Alignment explanation
Indices: 259012--259048 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
259002 AACTTCAAAT
**
259012 AATTCAAATCTTATTTTAA
1 AATTCAAAAATTATTTTAA
259031 AATTCAAAAATTATTTTA
1 AATTCAAAAATTATTTTA
259049 CTTTTAATTA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTCAAAAATTATTTTAA
Found at i:261732 original size:2 final size:2
Alignment explanation
Indices: 261725--261750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
261715 GAATATTTAA
261725 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
261751 TCTTATCATG
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:271837 original size:24 final size:24
Alignment explanation
Indices: 271809--271862 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
271799 ATAAACAATG
*
271809 TTAAACAAAAAATGTTCATGAACA
1 TTAAACAAAAAATGTTCACGAACA
* *
271833 TTAAA-TAAATATGTTCACGAACA
1 TTAAACAAAAAATGTTCACGAACA
271856 TATAAAC
1 T-TAAAC
271863 GAACATGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (24 bp):
TTAAACAAAAAATGTTCACGAACA
Found at i:271870 original size:24 final size:23
Alignment explanation
Indices: 271809--271872 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
271799 ATAAACAATG
* *
271809 TTAAACAAAAAATGTTCATGAACA
1 TTAAAC-AAACATGTTCACGAACA
* *
271833 TTAAATAAATATGTTCACGAACA
1 TTAAACAAACATGTTCACGAACA
*
271856 TATAAACGAACATGTTC
1 T-TAAACAAACATGTTC
271873 GTAAATGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.28
Consensus pattern (23 bp):
TTAAACAAACATGTTCACGAACA
Found at i:275098 original size:21 final size:21
Alignment explanation
Indices: 275074--275160 Score: 113
Period size: 21 Copynumber: 4.2 Consensus size: 21
275064 TATTCGCATT
275074 GCGAATTGGGAAAATCGCAAC
1 GCGAATTGGGAAAATCGCAAC
* *
275095 GCGAATTGGGAAATTCGCAAT
1 GCGAATTGGGAAAATCGCAAC
** *
275116 GCGAA-TAAGTAAATCGCAAC
1 GCGAATTGGGAAAATCGCAAC
*
275136 GCGAATTGGGAAAATCGCAAT
1 GCGAATTGGGAAAATCGCAAC
275157 GCGA
1 GCGA
275161 TACTGACTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.28
21 39 0.72
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTGGGAAAATCGCAAC
Found at i:275174 original size:20 final size:20
Alignment explanation
Indices: 275149--275242 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
275139 AATTGGGAAA
*
275149 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
275169 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
275190 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
275210 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
275230 TTCGCAACGCGAT
1 ATCGCAACGCGAT
275243 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:275192 original size:62 final size:61
Alignment explanation
Indices: 275074--275198 Score: 148
Period size: 62 Copynumber: 2.0 Consensus size: 61
275064 TATTCGCATT
* *
275074 GCGAATTGGGAAAATCGCAACGCGAATTGGGAAATTCGCAATGCGAATAAGTAAATCGCAAC
1 GCGAATTGGGAAAATCGCAACGCGAACT-GGAAATTCGCAATGCGAATAAGAAAATCGCAAC
* *
275136 GCGAATTGGGAAAATCGCAATGCGATACT-G-ACTATCGCAATGCGATAATAA-AAAATCGCAAC
1 GCGAATTGGGAAAATCGCAACGCGA-ACTGGAAAT-TCGCAATGCG--AATAAGAAAATCGCAAC
275198 G
1 G
275199 AGATACTTAC
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
60 2 0.04
61 11 0.20
62 35 0.64
63 7 0.13
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (61 bp):
GCGAATTGGGAAAATCGCAACGCGAACTGGAAATTCGCAATGCGAATAAGAAAATCGCAAC
Found at i:275223 original size:41 final size:41
Alignment explanation
Indices: 275146--275223 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
275136 GCGAATTGGG
* * **
275146 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
275187 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
275224 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:275851 original size:20 final size:19
Alignment explanation
Indices: 275803--275954 Score: 152
Period size: 20 Copynumber: 8.1 Consensus size: 19
275793 GAAACCAAAA
*
275803 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
275822 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
275841 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
275861 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
275877 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
275894 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
275913 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
275933 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
275953 TC
1 TC
275955 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 49 0.43
20 50 0.44
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:278013 original size:42 final size:42
Alignment explanation
Indices: 277953--278075 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
277943 GCTCGACTCG
* * *
277953 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
277995 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
278037 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
278076 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:278033 original size:21 final size:21
Alignment explanation
Indices: 278009--278075 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
277999 TCATTCCTCG
278009 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
278030 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
278051 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
278072 AGAG
1 AGAG
278076 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:279453 original size:14 final size:14
Alignment explanation
Indices: 279434--279469 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
279424 ATTGTTTAAT
279434 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
279448 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
279462 TGATTTGT
1 TGATTTGT
279470 TTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:279680 original size:19 final size:19
Alignment explanation
Indices: 279648--279745 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
279638 CGAAATTAAA
* *
279648 TTCGCGTTGTGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
279667 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
279683 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
279700 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
279716 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
279733 TTCGCATTGCGAT
1 TTCGCATTGCGAT
279746 AGTAATTTCC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 12 0.20
16 13 0.21
17 13 0.21
19 23 0.38
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:279695 original size:33 final size:33
Alignment explanation
Indices: 279652--279745 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
279642 ATTAAATTCG
*
279652 CGTTGTGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
279685 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
279718 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
279746 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:283551 original size:14 final size:15
Alignment explanation
Indices: 283532--283569 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
283522 CATCAATTAA
283532 ACAAATCAA-CATTT
1 ACAAATCAATCATTT
*
283546 ACAAAT-AATCTTTT
1 ACAAATCAATCATTT
283560 ACAAATCAAT
1 ACAAATCAAT
283570 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 16 0.76
15 3 0.14
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:283957 original size:20 final size:20
Alignment explanation
Indices: 283932--283982 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
283922 ATTCATTTGA
*
283932 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
283952 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
283972 TTATCGCAACG
1 CTATCGCAACG
283983 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:284032 original size:14 final size:15
Alignment explanation
Indices: 284012--284084 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
284002 TGACAATCGC
284012 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
284027 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
284044 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
284062 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
284078 -TTGCGAT
1 ATTGCGAT
284085 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:284049 original size:19 final size:19
Alignment explanation
Indices: 284008--284074 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
283998 GAAATGACAA
284008 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
284024 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
284041 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
284059 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
284075 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:284210 original size:14 final size:14
Alignment explanation
Indices: 284191--284227 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
284181 CATCAATTAA
284191 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
284205 ACAAATCATCTTTT
1 ACAAATCAACATTT
284219 ACAAATCAA
1 ACAAATCAA
284228 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.