Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007069.1 Hibiscus syriacus cultivar Beakdansim tig00018397_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: 253108
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:14451 original size:2 final size:2
Alignment explanation
Indices: 14444--14470 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14434 TGTGAGATCC
14444 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 A
14471 GGGTGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15884 original size:17 final size:18
Alignment explanation
Indices: 15862--15896 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15852 CTCGGCCGCA
15862 CTCTT-CTTTATCTTTTC
1 CTCTTCCTTTATCTTTTC
*
15879 CTCTTCCTTTTTCTTTTC
1 CTCTTCCTTTATCTTTTC
15897 TTTTTGACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (18 bp):
CTCTTCCTTTATCTTTTC
Found at i:20474 original size:92 final size:92
Alignment explanation
Indices: 20371--20556 Score: 354
Period size: 92 Copynumber: 2.0 Consensus size: 92
20361 TCATGTCATT
* *
20371 ATTTTTTGCTGACGTGGCATGTTCATATTATAGTAGATGATGACGTGACAGATTTACGTAGACTA
1 ATTTTTTGCTGACGTGGCATGTTCATATCATAGTAGATGATGACGTGACAGATCTACGTAGACTA
20436 AATATTGACGTGGTATGTACACGTGTG
66 AATATTGACGTGGTATGTACACGTGTG
20463 ATTTTTTGCTGACGTGGCATGTTCATATCATAGTAGATGATGACGTGACAGATCTACGTAGACTA
1 ATTTTTTGCTGACGTGGCATGTTCATATCATAGTAGATGATGACGTGACAGATCTACGTAGACTA
20528 AATATTGACGTGGTATGTACACGTGTG
66 AATATTGACGTGGTATGTACACGTGTG
20555 AT
1 AT
20557 GCCATGTCAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (92 bp):
ATTTTTTGCTGACGTGGCATGTTCATATCATAGTAGATGATGACGTGACAGATCTACGTAGACTA
AATATTGACGTGGTATGTACACGTGTG
Found at i:24475 original size:44 final size:45
Alignment explanation
Indices: 24412--24502 Score: 166
Period size: 44 Copynumber: 2.0 Consensus size: 45
24402 AACGAAGGAC
*
24412 GTGCAATTGTTCTTGGTCACTTTTC-TTTTGCTGAGGGAGACTTT
1 GTGCAATTGTTCTTCGTCACTTTTCTTTTTGCTGAGGGAGACTTT
24456 GTGCAATTGTTCTTCGTCACTTTTCTTTTTGCTGAGGGAGACTTT
1 GTGCAATTGTTCTTCGTCACTTTTCTTTTTGCTGAGGGAGACTTT
24501 GT
1 GT
24503 ACTCAATAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 24 0.53
45 21 0.47
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.46
Consensus pattern (45 bp):
GTGCAATTGTTCTTCGTCACTTTTCTTTTTGCTGAGGGAGACTTT
Found at i:32736 original size:57 final size:58
Alignment explanation
Indices: 32594--32754 Score: 173
Period size: 57 Copynumber: 2.8 Consensus size: 58
32584 ATGAATTTGG
* * *
32594 GGATGAAATTGGAATATTCAAAAGTTTAGGGATCAATTTAGAAAGTGGATCATAGTCTGA
1 GGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTA-AAA-TGGATCATAGTCTGA
* * * **
32654 GGATGAAATTAAAATGTTTAAAAGTTTAAGGATTAATTTAAAAT-GAGTCATAGT-TTT
1 GGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATGGA-TCATAGTCTGA
* * * *
32711 GGATGAAATTGTAACATTTAGAAGTTTAAGGACCAATTTAAAAT
1 GGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAAT
32755 AAGGGTTATA
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 40 0.47
58 8 0.09
59 3 0.04
60 34 0.40
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (58 bp):
GGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATGGATCATAGTCTGA
Found at i:33844 original size:35 final size:34
Alignment explanation
Indices: 33805--33873 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
33795 AAAATGTATA
* *
33805 TTACGAGGTATATTCATTTTTTATAGTTTAAAATC
1 TTACG-GGTATATTCATATTTTATAATTTAAAATC
* *
33840 TTACGTGTATATTTATATTTTATAATTTAAAATC
1 TTACGGGTATATTCATATTTTATAATTTAAAATC
33874 ATGTATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 25 0.83
35 5 0.17
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (34 bp):
TTACGGGTATATTCATATTTTATAATTTAAAATC
Found at i:34208 original size:36 final size:36
Alignment explanation
Indices: 34168--34238 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
34158 AATGGTTAAG
*
34168 TTAACAATAACAGATTAATTTAAACACCCTTAAAAA
1 TTAACAATAACAAATTAATTTAAACACCCTTAAAAA
* * *
34204 TTAACGATAACAAATTAATTTAAATACTCTTAAAA
1 TTAACAATAACAAATTAATTTAAACACCCTTAAAA
34239 TTACGTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (36 bp):
TTAACAATAACAAATTAATTTAAACACCCTTAAAAA
Found at i:40901 original size:17 final size:17
Alignment explanation
Indices: 40879--40914 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40869 TATTCGACAC
40879 AACCAAAATTTTATTAT
1 AACCAAAATTTTATTAT
40896 AACCAAAATTTTATTAT
1 AACCAAAATTTTATTAT
40913 AA
1 AA
40915 TTTGATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
AACCAAAATTTTATTAT
Found at i:41168 original size:60 final size:60
Alignment explanation
Indices: 41093--41232 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 60
41083 TCCTTATTTC
* **
41093 AAATTGGTCCCTAAACTTTTAAATATTAT-AATTTCATCCTTAAACTATGA-CTATCATTCT
1 AAATTAGTCCCTAAACTTTTAAATATT-TCAATTTCATCCCCAAACTATGATCT-TCATTCT
* *
41153 AAATTAGTCCTTAAACTTTTGAATATTTCAATTTCATCCCCAAACTATGATCTTCATTCT
1 AAATTAGTCCCTAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGATCTTCATTCT
*
41213 AAATTGGTTCCC-AAACTTTT
1 AAATTAG-TCCCTAAACTTTT
41233 TGAACATTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
59 1 0.01
60 64 0.91
61 5 0.07
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (60 bp):
AAATTAGTCCCTAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGATCTTCATTCT
Found at i:41243 original size:60 final size:61
Alignment explanation
Indices: 41122--41253 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 61
41112 TAAATATTAT
** * *
41122 AATTTCATCCTTAAACTATGACTATCATTCTAAATTAGTCCTTAAACTTTTGAATATTTC-
1 AATTTCATCCCCAAACTATGACTATCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCA
*
41182 AATTTCATCCCCAAACTATGATCT-TCATTCTAAATTGGTTCC-CAAACTTTTTGAACA-TTCA
1 AATTTCATCCCCAAACTATGA-CTATCATTCTAAATTAG-TCCTCAAAC-TTTTGAACATTTCA
*
41243 AATCTCATCCC
1 AATTTCATCCC
41254 AAATTATACG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
60 39 0.63
61 23 0.37
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.39
Consensus pattern (61 bp):
AATTTCATCCCCAAACTATGACTATCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCA
Found at i:46057 original size:158 final size:159
Alignment explanation
Indices: 45866--46162 Score: 526
Period size: 158 Copynumber: 1.9 Consensus size: 159
45856 CATTCTCCCC
45866 CAAAAAAAAATATCAAAATAATATTGGTTTCTTTATTTGTTGGATAATATTTGGTGATGAAAATT
1 CAAAAAAAAATATCAAAATAATATTGGTTTCTTTATTTGTTGGATAATATTTGGTGATGAAAATT
* *
45931 TATTTAGTAAATTATCATTGAATGTAGACCTGGTCGTTTTGAAGTCTATATTGAGATGCCCTTAC
66 TATTTAGTAAATTATCATTGAATGTAGACATGGTCGTTTTGAAGTCCATATTGAGATGCCCTTAC
45996 CGAAAATCCAAGAAAGATTGGAGATTTTG
131 CGAAAATCCAAGAAAGATTGGAGATTTTG
* *
46025 CAAAAAATAAA-AT-AAAATAATTTTGGTTTCTTTATTTGTTGGATAGTATTTGGTGATGAAAAT
1 CAAAAAA-AAATATCAAAATAATATTGGTTTCTTTATTTGTTGGATAATATTTGGTGATGAAAAT
*
46088 TTATTTAGTAAATTATCATTGAATGTAGATATGGTCGTTTTGAAGTCCATATTGAGATGCCCTTA
65 TTATTTAGTAAATTATCATTGAATGTAGACATGGTCGTTTTGAAGTCCATATTGAGATGCCCTTA
46153 CCGAAAATCC
130 CCGAAAATCC
46163 CTTTTTATCA
Statistics
Matches: 132, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
158 120 0.91
159 9 0.07
160 3 0.02
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (159 bp):
CAAAAAAAAATATCAAAATAATATTGGTTTCTTTATTTGTTGGATAATATTTGGTGATGAAAATT
TATTTAGTAAATTATCATTGAATGTAGACATGGTCGTTTTGAAGTCCATATTGAGATGCCCTTAC
CGAAAATCCAAGAAAGATTGGAGATTTTG
Found at i:48214 original size:14 final size:14
Alignment explanation
Indices: 48171--48205 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
48161 CCATTTAAAT
* *
48171 AATGAACAAATACA
1 AATGAACGAATATA
48185 AATGAACGAATATA
1 AATGAACGAATATA
48199 AATGAAC
1 AATGAAC
48206 TGATGTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (14 bp):
AATGAACGAATATA
Found at i:59227 original size:2 final size:2
Alignment explanation
Indices: 59220--59294 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
59210 ATCGTTTTAT
59220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59295 GCTTCCTCGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65675 original size:2 final size:2
Alignment explanation
Indices: 65670--65700 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
65660 GTTTAGTTCC
65670 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
65701 AGTTTAGTTT
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:66180 original size:8 final size:9
Alignment explanation
Indices: 66159--66188 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
66149 GTATATTTAT
*
66159 AAAAATGAG
1 AAAAATTAG
66168 AAAAATTAG
1 AAAAATTAG
66177 AAAAATTAG
1 AAAAATTAG
66186 AAA
1 AAA
66189 GCTTTTGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (9 bp):
AAAAATTAG
Found at i:69452 original size:19 final size:19
Alignment explanation
Indices: 69410--69452 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
69400 TTTTATTTGA
*
69410 TTTACTTTTTTATATTTTT
1 TTTAATTTTTTATATTTTT
*
69429 ATTAATTTTTT-TATTTTCT
1 TTTAATTTTTTATATTTT-T
69448 TTTAA
1 TTTAA
69453 AATTTTATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTAATTTTTTATATTTTT
Found at i:73065 original size:3 final size:3
Alignment explanation
Indices: 73059--73083 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
73049 TTTTCCTTTT
73059 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
73084 CAAATTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:73948 original size:31 final size:31
Alignment explanation
Indices: 73913--73979 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
73903 ATATTCTTTC
73913 AATTTGATCATAGTTTTAATAAATTAAAATA
1 AATTTGATCATAGTTTTAATAAATTAAAATA
*
73944 AATTTGATCCTAGTTTTAATAAATTAAAATA
1 AATTTGATCATAGTTTTAATAAATTAAAATA
73975 AATTT
1 AATTT
73980 ACCTACAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (31 bp):
AATTTGATCATAGTTTTAATAAATTAAAATA
Found at i:74067 original size:11 final size:11
Alignment explanation
Indices: 74046--74074 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
74036 TGGAAGACTA
74046 AATTT-ATTTT
1 AATTTAATTTT
74056 AATTTAATTTT
1 AATTTAATTTT
74067 AATTTAAT
1 AATTTAAT
74075 AGATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTAATTTT
Found at i:74334 original size:30 final size:30
Alignment explanation
Indices: 74250--74337 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 30
74240 AAGTTATATA
*
74250 TCTTAAATT-TTAAAATTATCTTTATTTTTG
1 TCTTAAATTATTAAATTTAT-TTTATTTTTG
* * *
74280 TTTTAACTTATTAAATAT-TTTTATTTTTG
1 TCTTAAATTATTAAATTTATTTTATTTTTG
*
74309 TCTTAATTTATTAAATTTATTTTATTTTT
1 TCTTAAATTATTAAATTTATTTTATTTTT
74338 ATTTTAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
29 25 0.51
30 18 0.37
31 6 0.12
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (30 bp):
TCTTAAATTATTAAATTTATTTTATTTTTG
Found at i:74507 original size:29 final size:27
Alignment explanation
Indices: 74462--74531 Score: 63
Period size: 29 Copynumber: 2.5 Consensus size: 27
74452 ATACATTTTA
*
74462 ATTTTATT-TTAAATTTA-AAATATATAAT
1 ATTTTATTCTTATATTTATAAA-A-AT-AT
*
74490 ATTTTATTCTTATCTTTACTTAAAAATAT
1 ATTTTATTCTTATATTTA--TAAAAATAT
74519 ATTTTATTCTTAT
1 ATTTTATTCTTAT
74532 TTCAAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 8 0.22
29 22 0.61
30 2 0.06
31 1 0.03
32 3 0.08
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTTATTCTTATATTTATAAAAATAT
Found at i:74574 original size:30 final size:29
Alignment explanation
Indices: 74488--74580 Score: 118
Period size: 29 Copynumber: 3.2 Consensus size: 29
74478 AAAATATATA
*
74488 ATATTTTATTCTTATCTTTACTTAAAAAT
1 ATATTTTATTCTTATCTTAACTTAAAAAT
*
74517 ATATTTTATTCTTAT-TTCAAATTAAAAAT
1 ATATTTTATTCTTATCTT-AACTTAAAAAT
*
74546 ATATTTT-TTATTATCTTAACTTTTAAAAAT
1 ATATTTTATTCTTATCTTAAC--TTAAAAAT
74576 ATATT
1 ATATT
74581 AAAATATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.18
29 33 0.59
30 13 0.23
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTTTATTCTTATCTTAACTTAAAAAT
Found at i:74623 original size:30 final size:31
Alignment explanation
Indices: 74589--74653 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
74579 TTAAAATATT
74589 ATATATATTTTAAT-TTAAAATAAGAGTAAA
1 ATATATATTTTAATATTAAAATAAGAGTAAA
* * *
74619 ATATATATTTTTATATTAAATTAATAGTAAA
1 ATATATATTTTAATATTAAAATAAGAGTAAA
74650 ATAT
1 ATAT
74654 TTAAATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (31 bp):
ATATATATTTTAATATTAAAATAAGAGTAAA
Found at i:74799 original size:28 final size:28
Alignment explanation
Indices: 74750--74803 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
74740 AAACAAAATT
*
74750 TATTTAATAAATTAAGATAAAATAAAAA
1 TATTTAATAAATTAAGAAAAAATAAAAA
*
74778 TATTTAATAAGTTAA-ACAAAAATAAA
1 TATTTAATAAATTAAGA-AAAAATAAA
74804 TATAGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (28 bp):
TATTTAATAAATTAAGAAAAAATAAAAA
Found at i:79643 original size:21 final size:21
Alignment explanation
Indices: 79598--79643 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
79588 ATTTCTTACG
** *
79598 AAAATATTGATATTTTGAACT
1 AAAATATTGATACGTTGAACC
*
79619 AAAATATTGATACGTTGAGCC
1 AAAATATTGATACGTTGAACC
79640 AAAA
1 AAAA
79644 GCATGATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (21 bp):
AAAATATTGATACGTTGAACC
Found at i:85045 original size:59 final size:59
Alignment explanation
Indices: 84946--85058 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
84936 TTGTTATACC
* ** *
84946 TTGAGCTCCCAGTTTCGAGTACCGGGTATGTAGAGATATGAGTGTTTATTATCATATAG
1 TTGAGCTCCCAGGTTCGAGTACCACGTATGTAGAGATATGAGCGTTTATTATCATATAG
* * *
85005 TTGAGCTCTCAGGTTCGAGTATCACGTATGTA-AGGGTATGAGCGTTTATTATCA
1 TTGAGCTCCCAGGTTCGAGTACCACGTATGTAGA-GATATGAGCGTTTATTATCA
85059 AGTAGTCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 1 0.02
59 45 0.98
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (59 bp):
TTGAGCTCCCAGGTTCGAGTACCACGTATGTAGAGATATGAGCGTTTATTATCATATAG
Found at i:86574 original size:12 final size:12
Alignment explanation
Indices: 86557--86584 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
86547 TCTTCAGATA
86557 ATTACTTATTTT
1 ATTACTTATTTT
86569 ATTACTTATTTT
1 ATTACTTATTTT
86581 ATTA
1 ATTA
86585 GTTGTGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTACTTATTTT
Found at i:92909 original size:14 final size:14
Alignment explanation
Indices: 92874--92931 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
92864 TCACATAATC
* *
92874 AGATTTATGGTTTG
1 AGATTTAGGGTTTT
*
92888 AGAATTAGGGTTTT
1 AGATTTAGGGTTTT
92902 AGATTTAGGGTTTT
1 AGATTTAGGGTTTT
*
92916 AAAATTTA-GGTTTT
1 -AGATTTAGGGTTTT
92930 AG
1 AG
92932 GGTTTTGGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 1 0.03
14 30 0.81
15 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (14 bp):
AGATTTAGGGTTTT
Found at i:92914 original size:28 final size:28
Alignment explanation
Indices: 92874--92931 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
92864 TCACATAATC
* *
92874 AGATTTATGGTTTGAGAA-TTAGGGTTTT
1 AGATTTAGGGTTTGAAAATTTA-GGTTTT
*
92902 AGATTTAGGGTTTTAAAATTTAGGTTTT
1 AGATTTAGGGTTTGAAAATTTAGGTTTT
92930 AG
1 AG
92932 GGTTTTGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (28 bp):
AGATTTAGGGTTTGAAAATTTAGGTTTT
Found at i:92965 original size:7 final size:7
Alignment explanation
Indices: 92955--93018 Score: 62
Period size: 7 Copynumber: 9.4 Consensus size: 7
92945 GAATTTAGGA
92955 TTTATGG
1 TTTATGG
*
92962 TTTAAGG
1 TTTATGG
*
92969 TTTATTG
1 TTTATGG
92976 TTTATGG
1 TTTATGG
92983 TTTA-GAG
1 TTTATG-G
92990 TTTA-GG
1 TTTATGG
*
92996 TTTAAGG
1 TTTATGG
*
93003 TTTATGA
1 TTTATGG
93010 TTTA-GG
1 TTTATGG
93016 TTT
1 TTT
93019 TATGATTAGG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
6 10 0.21
7 38 0.79
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (7 bp):
TTTATGG
Found at i:92972 original size:21 final size:20
Alignment explanation
Indices: 92948--93018 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
92938 GGGTATCGAA
92948 TTTAGGATTTATGGTTTAAGG
1 TTTAGG-TTTATGGTTTAAGG
*
92969 TTTATTGTTTATGGTTT-AGAG
1 TTTA-GGTTTATGGTTTAAG-G
* * *
92990 TTTAGGTTTAAGGTTTATGA
1 TTTAGGTTTATGGTTTAAGG
93010 TTTAGGTTT
1 TTTAGGTTT
93019 TATGATTAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 21 0.50
21 20 0.48
22 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (20 bp):
TTTAGGTTTATGGTTTAAGG
Found at i:93186 original size:22 final size:25
Alignment explanation
Indices: 93160--93214 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
93150 ATATTTTTAA
93160 AATTTTA-TA-ATTATCAATAATGT
1 AATTTTATTATATTATCAATAATGT
* * *
93183 ATTTTTATTATATTTTTAATAATGT
1 AATTTTATTATATTATCAATAATGT
93208 AATTTTA
1 AATTTTA
93215 AAAAATCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 6 0.23
24 2 0.08
25 18 0.69
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
AATTTTATTATATTATCAATAATGT
Found at i:93579 original size:23 final size:23
Alignment explanation
Indices: 93551--93596 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
93541 TTTTTTAGGG
*
93551 TAATATAATAATACAGGTG-GGAA
1 TAATAT-AGAATACAGGTGTGGAA
*
93574 TAATATGGAATACAGGTGTGGAA
1 TAATATAGAATACAGGTGTGGAA
93597 GAAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.26
Consensus pattern (23 bp):
TAATATAGAATACAGGTGTGGAA
Found at i:93730 original size:19 final size:17
Alignment explanation
Indices: 93674--93730 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 17
93664 TTTCTAAGAT
93674 ATTATTATTTTAATTAAAAA
1 ATTATT-TTTTAATT--AAA
93694 ATTATTTTTTAATT-AA
1 ATTATTTTTTAATTAAA
*
93710 ATTCATATTTTTAGTTAAA
1 ATT-AT-TTTTTAATTAAA
93729 AT
1 AT
93731 AAAAGAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
18 8 0.24
19 12 0.36
20 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTATTTTTTAATTAAA
Found at i:98675 original size:87 final size:86
Alignment explanation
Indices: 98529--98778 Score: 446
Period size: 87 Copynumber: 2.9 Consensus size: 86
98519 TATGTTATAT
98529 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAA-CGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
98594 AGCGCTTATATAATAAAATAGG
65 AGCGCTTATATAATAAAATAGG
98616 TATTTAACGAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACG-GAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
98681 AGCGCTTATATAATAAAATAGG
65 AGCGCTTATATAATAAAATAGG
* * *
98703 TATTTAACGGGAAATATTATCAAGAACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAAC-GGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
98768 AGCGCTTATAT
65 AGCGCTTATAT
98779 TGACCTATTT
Statistics
Matches: 158, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
86 2 0.01
87 155 0.98
88 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (86 bp):
TATTTAACGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATA
GCGCTTATATAATAAAATAGG
Found at i:102500 original size:120 final size:120
Alignment explanation
Indices: 102287--102533 Score: 422
Period size: 120 Copynumber: 2.1 Consensus size: 120
102277 TTTTTCTTCC
**
102287 ATTCTGGACATAAAGTACCGACACAATTTTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
102352 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
* *
102407 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
* * * *
102472 CATAAAACCGGTATATTTATACTGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
102527 ATTCTGG
1 ATTCTGG
102534 GTTCCAATGT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTATCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:102683 original size:303 final size:303
Alignment explanation
Indices: 102122--102716 Score: 1082
Period size: 303 Copynumber: 2.0 Consensus size: 303
102112 TTAAAATTAG
*
102122 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
102187 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCAATGTGTAAATGTCGA
*
102252 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATTTT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* *
102317 AAAAAGTATCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTATCGACATAAGTTGTAGACCTATTCGCTAATAAAACCAGTATACTTATACCGGTTATA
102382 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
102425 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
102490 ATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCAATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCAATGTGTAAATGTCGA
102555 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* * * * *
102620 AAAAAGTGTCGATATAAGTTGTAGACCTATTCGCTCATAAAACCAGTATATTTATATCGGTTATA
196 AAAAAGTATCGACATAAGTTGTAGACCTATTCGCTAATAAAACCAGTATACTTATACCGGTTATA
*
102685 TTACAAAATTATCTATTACATTATAATTCTGG
261 TTACAAAATTATCTAGTACATTATAATTCTGG
102717 GTTCCGATGT
Statistics
Matches: 280, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
303 280 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCAATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAGTATCGACATAAGTTGTAGACCTATTCGCTAATAAAACCAGTATACTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:102715 original size:183 final size:183
Alignment explanation
Indices: 102407--102995 Score: 1022
Period size: 183 Copynumber: 3.2 Consensus size: 183
102397 GTACATTATA
*
102407 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
102472 CATAAAACCGGTATATTTATA-CTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGT
66 CATAAAACCGGTATATTTATATC-GGTTATATTACAAAATTATCTATTACATTATAATTCTGGGT
*
102536 TCCAATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
130 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
102590 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAAGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
102655 CATAAAACCAGTATATTTATATCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATATCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
102720 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
102773 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATGGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* * *
102838 CATAAAACTGGTATATTTATATCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATATCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* * *
102903 CCGATGTTTTTTCAA--TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
102957 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
102996 GAAAACTTTG
Statistics
Matches: 389, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
183 307 0.79
184 78 0.20
186 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATATCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:104216 original size:6 final size:6
Alignment explanation
Indices: 104205--104263 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
104195 ACTTGTTTGG
* * *
104205 ATCATC ATCATC ATCATC ATCATC TTCATC ATCATC TTCATC GTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* *
104253 TTCATC TTCAT
1 ATCATC ATCAT
104264 TGACTGCTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (6 bp):
ATCATC
Found at i:104222 original size:12 final size:12
Alignment explanation
Indices: 104206--104263 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
104196 CTTGTTTGGA
*
104206 TCATCATCATCA
1 TCATCATCATCT
104218 TCATCATCATCT
1 TCATCATCATCT
104230 TCATCATCATCT
1 TCATCATCATCT
*
104242 TCATCGTCATCT
1 TCATCATCATCT
*
104254 TCATCTTCAT
1 TCATCATCAT
104264 TGACTGCTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.24, C:0.33, G:0.02, T:0.41
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:106087 original size:200 final size:200
Alignment explanation
Indices: 105715--106476 Score: 1278
Period size: 200 Copynumber: 3.8 Consensus size: 200
105705 CATTAAACAC
* *
105715 TGTCGATACA-TATTATATA-CTAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGA
1 TGTCGATACATTATT-TAGACCT-ATTCTCTCATAAAACCGGTATACTTATACCGGTTAGATTGA
* * *
105778 AAAATTACCTAATACATTATACTTTTGGGTTTAGATGTTTATGGGATCGACACTTTTTATATATG
64 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
105843 GATCGACACTTTATGATTCCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
129 GATCGACACTTTATGATTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
105908 ACAAAAG
194 ACAAAAG
* *
105915 TGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTATATCGGTTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
* *
105980 AATTACCTATTACATTATACTTATGGGTTTTGATGTTTATGGGATCGACATTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
*
106045 TCGACACTTTATTG-TTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTA
131 TCGACACTTTA-TGATTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA
106109 CAAAAG
195 CAAAAG
* *
106115 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCAGTTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
*
106180 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
* *
106245 TCGACACTTTATTATTGCACCCTGTTTGCCATTCATTCTGGACCAAAACTATCGACACAAACTAC
131 TCGACACTTTATGATTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
106310 AAAAG
196 AAAAG
* *
106315 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAA
1 TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
* *
106380 AATTACCTATTACATTATACTTTTAGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
66 AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
* *
106445 TTGACACTTTATGATTGCACCTTGTTTGCCAT
131 TCGACACTTTATGATTGCACCCTGTTTGCCAT
106477 ATTGTAAATT
Statistics
Matches: 530, Mismatches: 28, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
199 1 0.00
200 521 0.98
201 8 0.02
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (200 bp):
TGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTATACCGGTTAGATTGAAA
AATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGA
TCGACACTTTATGATTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
AAAAG
Found at i:106734 original size:19 final size:19
Alignment explanation
Indices: 106710--106758 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
106700 TTATATTCAA
106710 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
106729 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
106748 ATACAAAATTA
1 ATACAAAATTA
106759 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:107347 original size:4 final size:4
Alignment explanation
Indices: 107338--107362 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
107328 AATGTCCTTT
107338 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
107363 CAATCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:108674 original size:21 final size:21
Alignment explanation
Indices: 108661--108713 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
108651 CTCAAATGTA
108661 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTCTCAAGTTTC
*
108682 TCTTCGACTCTATCAAGTTTC
1 TCTTCGACTCTCTCAAGTTTC
108703 TCTTCGACTCT
1 TCTTCGACTCT
108714 TGATTGTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.32, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTTCGACTCTCTCAAGTTTC
Found at i:113159 original size:21 final size:22
Alignment explanation
Indices: 113110--113172 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
113100 TCCCCTGTGA
*
113110 GGGGGAATCAGTTCCCATTCAAAG
1 GGGGGAATCGGTTCCC--TCAAAG
*
113134 GGGGGAATCGGTTCCCTC-ATG
1 GGGGGAATCGGTTCCCTCAAAG
* *
113155 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
113173 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.51
22 2 0.06
24 15 0.43
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTCAAAG
Found at i:120744 original size:20 final size:19
Alignment explanation
Indices: 120698--120744 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
120688 TCCGGTAACG
120698 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
120717 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
120738 TTTTACC
1 TTTTACC
120745 TGGTATATCG
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:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:120788 original size:181 final size:182
Alignment explanation
Indices: 120484--120947 Score: 723
Period size: 181 Copynumber: 2.6 Consensus size: 182
120474 CGTACTTACG
* *
120484 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
120549 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
120614 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATATT
120665 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
120730 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
120795 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATATT
* * * * * **
120847 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
120912 TGTCATAGTTTTACCTGTTATAACGTTTTGGATCGA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGA
120948 CGCATTTTCC
Statistics
Matches: 259, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
181 168 0.65
182 91 0.35
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATCCTTATATT
Found at i:124237 original size:12 final size:12
Alignment explanation
Indices: 124222--124285 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
124212 CCGACCTGAA
124222 TTCTGTTTTGAT
1 TTCTGTTTTGAT
* *
124234 TTCTGATCTGGA-
1 TTCTG-TTTTGAT
*
124246 TTCTGTTCTGAT
1 TTCTGTTTTGAT
* * *
124258 ATCTGTTCTGAA
1 TTCTGTTTTGAT
124270 TTCTGTTTTGAT
1 TTCTGTTTTGAT
124282 TTCT
1 TTCT
124286 TATATCTCCG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
11 3 0.08
12 33 0.82
13 4 0.10
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.56
Consensus pattern (12 bp):
TTCTGTTTTGAT
Found at i:124248 original size:24 final size:24
Alignment explanation
Indices: 124206--124285 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
124196 ATATTTTATC
* *
124206 TGATTTCCGACCTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTT
* *
124230 TGATTTCTGATCTGGATTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTT
* *
124254 TGATATCTGTTCTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTT
124278 TGATTTCT
1 TGATTTCT
124286 TATATCTCCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.15, C:0.16, G:0.17, T:0.51
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTT
Found at i:126316 original size:66 final size:66
Alignment explanation
Indices: 126210--126368 Score: 318
Period size: 66 Copynumber: 2.4 Consensus size: 66
126200 GACCATAACC
126210 TAGATAATAAACATGAGAGAGTTAGTAGTGCCTATCCGTGTATAGTATTAACTCTAGACTTGTCC
1 TAGATAATAAACATGAGAGAGTTAGTAGTGCCTATCCGTGTATAGTATTAACTCTAGACTTGTCC
126275 T
66 T
126276 TAGATAATAAACATGAGAGAGTTAGTAGTGCCTATCCGTGTATAGTATTAACTCTAGACTTGTCC
1 TAGATAATAAACATGAGAGAGTTAGTAGTGCCTATCCGTGTATAGTATTAACTCTAGACTTGTCC
126341 T
66 T
126342 TAGATAATAAACATGAGAGAGTTAGTA
1 TAGATAATAAACATGAGAGAGTTAGTA
126369 TCTATAGCTA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 93 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (66 bp):
TAGATAATAAACATGAGAGAGTTAGTAGTGCCTATCCGTGTATAGTATTAACTCTAGACTTGTCC
T
Found at i:130361 original size:61 final size:61
Alignment explanation
Indices: 130281--130403 Score: 194
Period size: 61 Copynumber: 2.0 Consensus size: 61
130271 CTTACACTTA
* *
130281 ATGTCAAACTTTTAGTTTTACATC-TTTTTGAAATCGTTAGATAAGTAACAATAAACGGTTG
1 ATGTAAAACTTTTAGTTTTACA-CATTTTTGAAATCGTTAGATAAGTAACAATAAACAGTTG
* *
130342 ATGTAAAACTTTTAGTTTTACACATTTTTGAAATCGTTAGATGAGTAACAATAGACAGTTG
1 ATGTAAAACTTTTAGTTTTACACATTTTTGAAATCGTTAGATAAGTAACAATAAACAGTTG
130403 A
1 A
130404 GATTATCTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 1 0.02
61 56 0.98
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (61 bp):
ATGTAAAACTTTTAGTTTTACACATTTTTGAAATCGTTAGATAAGTAACAATAAACAGTTG
Found at i:136112 original size:13 final size:13
Alignment explanation
Indices: 136108--136183 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
136098 CCGTTTACCC
136108 GACCCGACCCGTT
1 GACCCGACCCGTT
*
136121 TACCCGACCCGTT
1 GACCCGACCCGTT
136134 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
136152 GACCCGACCCGTT
1 GACCCGACCCGTT
*
136165 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
136180 GACC
1 GACC
136184 GTTGACTACT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 26 0.49
14 1 0.02
15 13 0.25
16 1 0.02
17 1 0.02
18 11 0.21
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:136131 original size:18 final size:18
Alignment explanation
Indices: 136086--136131 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
136076 ACCGGTCACA
*
136086 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
136104 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
136122 ACCCGACCCG
1 ACCCGACCCG
136132 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:136131 original size:31 final size:31
Alignment explanation
Indices: 136090--136168 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
136080 GTCACAACCC
* *
136090 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
136121 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
136152 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
136169 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:136137 original size:8 final size:8
Alignment explanation
Indices: 136126--136189 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
136116 CCGTTTACCC
136126 GACCCGTT
1 GACCCGTT
*
136134 GACCCGACTC
1 GACCCG--TT
*
136144 GACTCGTT
1 GACCCGTT
136152 GACCC---
1 GACCCGTT
136157 GACCCGTT
1 GACCCGTT
136165 GA-CCGTT
1 GACCCGTT
136172 GACCCGTT
1 GACCCGTT
136180 GA-CCGTT
1 GACCCGTT
136187 GAC
1 GAC
136190 TACTGTTGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
5 5 0.11
7 14 0.31
8 20 0.44
10 6 0.13
ACGTcount: A:0.16, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:136146 original size:18 final size:18
Alignment explanation
Indices: 136125--136159 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
136115 CCCGTTTACC
136125 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
136143 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
136160 CCGTTGACCG
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:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:136172 original size:7 final size:7
Alignment explanation
Indices: 136160--136189 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
136150 TTGACCCGAC
136160 CCGTTGA
1 CCGTTGA
136167 CCGTTGA
1 CCGTTGA
136174 CCCGTTGA
1 -CCGTTGA
136182 CCGTTGA
1 CCGTTGA
136189 C
1 C
136190 TACTGTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.33, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:136177 original size:15 final size:15
Alignment explanation
Indices: 136157--136189 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
136147 TCGTTGACCC
136157 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
136172 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
136187 GAC
1 GAC
136190 TACTGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.33, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:137512 original size:18 final size:18
Alignment explanation
Indices: 137486--137520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
137476 TCGAAAGGAC
*
137486 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
137504 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
137521 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:141189 original size:13 final size:13
Alignment explanation
Indices: 141185--141260 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
141175 CCGTTTACCC
141185 GACCCGACCCGTT
1 GACCCGACCCGTT
*
141198 TACCCGACCCGTT
1 GACCCGACCCGTT
141211 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
141229 GACCCGACCCGTT
1 GACCCGACCCGTT
*
141242 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
141257 GACC
1 GACC
141261 GTTGACTACT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 26 0.49
14 1 0.02
15 13 0.25
16 1 0.02
17 1 0.02
18 11 0.21
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:141208 original size:18 final size:18
Alignment explanation
Indices: 141163--141208 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
141153 ACCGGTCACA
*
141163 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
141181 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
141199 ACCCGACCCG
1 ACCCGACCCG
141209 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:141208 original size:31 final size:31
Alignment explanation
Indices: 141167--141245 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
141157 GTCACAACCC
* *
141167 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
141198 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
141229 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
141246 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:141214 original size:8 final size:8
Alignment explanation
Indices: 141203--141266 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
141193 CCGTTTACCC
141203 GACCCGTT
1 GACCCGTT
*
141211 GACCCGACTC
1 GACCCG--TT
*
141221 GACTCGTT
1 GACCCGTT
141229 GACCC---
1 GACCCGTT
141234 GACCCGTT
1 GACCCGTT
141242 GA-CCGTT
1 GACCCGTT
141249 GACCCGTT
1 GACCCGTT
141257 GA-CCGTT
1 GACCCGTT
141264 GAC
1 GAC
141267 TACTGTTGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
5 5 0.11
7 14 0.31
8 20 0.44
10 6 0.13
ACGTcount: A:0.16, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:141223 original size:18 final size:18
Alignment explanation
Indices: 141202--141236 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
141192 CCCGTTTACC
141202 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
141220 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
141237 CCGTTGACCG
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:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:141249 original size:7 final size:7
Alignment explanation
Indices: 141237--141266 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
141227 TTGACCCGAC
141237 CCGTTGA
1 CCGTTGA
141244 CCGTTGA
1 CCGTTGA
141251 CCCGTTGA
1 -CCGTTGA
141259 CCGTTGA
1 CCGTTGA
141266 C
1 C
141267 TACTGTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.33, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:141254 original size:15 final size:15
Alignment explanation
Indices: 141234--141266 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
141224 TCGTTGACCC
141234 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
141249 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
141264 GAC
1 GAC
141267 TACTGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.33, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:142589 original size:18 final size:18
Alignment explanation
Indices: 142563--142597 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
142553 TCGAAAGGAC
*
142563 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
142581 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
142598 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:146198 original size:9 final size:9
Alignment explanation
Indices: 146184--146229 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
146174 AAGGGAAAAG
146184 TGACCGGTT
1 TGACCGGTT
146193 TGACCGGTT
1 TGACCGGTT
* *
146202 TGGAACTGTTT
1 T-G-ACCGGTT
146213 TGACCGGTT
1 TGACCGGTT
146222 TGACCGGT
1 TGACCGGT
146230 CACAACCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 23 0.74
10 2 0.06
11 6 0.19
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.35
Consensus pattern (9 bp):
TGACCGGTT
Found at i:146260 original size:13 final size:13
Alignment explanation
Indices: 146256--146331 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
146246 CCGTTTACCC
146256 GACCCGACCCGTT
1 GACCCGACCCGTT
*
146269 TACCCGACCCGTT
1 GACCCGACCCGTT
146282 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
146300 GACCCGACCCGTT
1 GACCCGACCCGTT
*
146313 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
146328 GACC
1 GACC
146332 GTTGACTACT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 26 0.49
14 1 0.02
15 13 0.25
16 1 0.02
17 1 0.02
18 11 0.21
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:146279 original size:18 final size:18
Alignment explanation
Indices: 146234--146279 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
146224 ACCGGTCACA
*
146234 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
146252 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
146270 ACCCGACCCG
1 ACCCGACCCG
146280 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:146279 original size:31 final size:31
Alignment explanation
Indices: 146238--146316 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
146228 GTCACAACCC
* *
146238 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
146269 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
146300 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
146317 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:146285 original size:8 final size:8
Alignment explanation
Indices: 146274--146337 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
146264 CCGTTTACCC
146274 GACCCGTT
1 GACCCGTT
*
146282 GACCCGACTC
1 GACCCG--TT
*
146292 GACTCGTT
1 GACCCGTT
146300 GACCC---
1 GACCCGTT
146305 GACCCGTT
1 GACCCGTT
146313 GA-CCGTT
1 GACCCGTT
146320 GACCCGTT
1 GACCCGTT
146328 GA-CCGTT
1 GACCCGTT
146335 GAC
1 GAC
146338 TACTGTTGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
5 5 0.11
7 14 0.31
8 20 0.44
10 6 0.13
ACGTcount: A:0.16, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:146294 original size:18 final size:18
Alignment explanation
Indices: 146273--146307 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
146263 CCCGTTTACC
146273 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
146291 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
146308 CCGTTGACCG
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:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:146320 original size:7 final size:7
Alignment explanation
Indices: 146308--146337 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
146298 TTGACCCGAC
146308 CCGTTGA
1 CCGTTGA
146315 CCGTTGA
1 CCGTTGA
146322 CCCGTTGA
1 -CCGTTGA
146330 CCGTTGA
1 CCGTTGA
146337 C
1 C
146338 TACTGTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.33, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:146325 original size:15 final size:15
Alignment explanation
Indices: 146305--146337 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
146295 TCGTTGACCC
146305 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
146320 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
146335 GAC
1 GAC
146338 TACTGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.33, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:147655 original size:18 final size:18
Alignment explanation
Indices: 147629--147663 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
147619 TCGAAAGGAC
*
147629 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
147647 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
147664 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:149228 original size:32 final size:31
Alignment explanation
Indices: 149181--149267 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 31
149171 ATCATTCTCG
** *
149181 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA
1 GGTAGGCCCCACGGCCCTAAGATGT-ATCTTA
* * *
149213 GGTAGGCCCCACGGCCCGAA-ATCTATCTTG
1 GGTAGGCCCCACGGCCCTAAGATGTATCTTA
*
149243 GGTAGGCTCTCA-GGCCCTAAGATGT
1 GGTAGGC-CCCACGGCCCTAAGATGT
149268 TCCCTTAGGT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
30 18 0.41
31 9 0.20
32 17 0.39
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.24
Consensus pattern (31 bp):
GGTAGGCCCCACGGCCCTAAGATGTATCTTA
Found at i:151330 original size:13 final size:13
Alignment explanation
Indices: 151326--151400 Score: 78
Period size: 13 Copynumber: 5.3 Consensus size: 13
151316 CCGTTTACCC
151326 GACCCGACCCGTT
1 GACCCGACCCGTT
*
151339 TACCCGACCCGTT
1 GACCCGACCCGTT
151352 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
151370 GACCCGACCCGTT
1 GACCCGACCCGTT
*
151383 GACCGTGACCCGTT
1 GACC-CGACCCGTT
151397 GACC
1 GACC
151401 GTTGACTACT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
13 26 0.49
14 13 0.25
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.21
ACGTcount: A:0.16, C:0.43, G:0.23, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:151349 original size:18 final size:18
Alignment explanation
Indices: 151304--151349 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
151294 ACCGGTCACA
*
151304 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
151322 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
151340 ACCCGACCCG
1 ACCCGACCCG
151350 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:151349 original size:31 final size:31
Alignment explanation
Indices: 151308--151386 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
151298 GTCACAACCC
* *
151308 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
151339 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
151370 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
151387 GTGACCCGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:151364 original size:18 final size:18
Alignment explanation
Indices: 151343--151377 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
151333 CCCGTTTACC
151343 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
151361 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
151378 CCGTTGACCG
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:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:151394 original size:14 final size:14
Alignment explanation
Indices: 151366--151402 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
151356 CGACTCGACT
*
151366 CGTTGACC-CGACC
1 CGTTGACCGTGACC
151379 CGTTGACCGTGACC
1 CGTTGACCGTGACC
151393 CGTTGACCGT
1 CGTTGACCGT
151403 TGACTACTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.14, C:0.38, G:0.27, T:0.22
Consensus pattern (14 bp):
CGTTGACCGTGACC
Found at i:161968 original size:7 final size:7
Alignment explanation
Indices: 161947--162100 Score: 73
Period size: 7 Copynumber: 22.1 Consensus size: 7
161937 GGTTTGGGAA
161947 TTAGGGTT
1 TTAGGG-T
161955 TTA-GGT
1 TTAGGGT
161961 TTAGGGTT
1 TTAGGG-T
***
161969 TTAAAAT
1 TTAGGGT
*
161976 TTAGGTT
1 TTAGGGT
*
161983 TTAGGTT
1 TTAGGGT
161990 TTAGGGT
1 TTAGGGT
*
161997 TTTGGGT
1 TTAGGGT
**
162004 ATT-GAAT
1 -TTAGGGT
*
162011 TTAGGAT
1 TTAGGGT
*
162018 TTAGGAT
1 TTAGGGT
*
162025 TTATGGT
1 TTAGGGT
*
162032 TTAAGGT
1 TTAGGGT
***
162039 TTATTAT
1 TTAGGGT
*
162046 TTATGGT
1 TTAGGGT
*
162053 TTAGAGT
1 TTAGGGT
162060 TTA-GGT
1 TTAGGGT
162066 TTAGGGT
1 TTAGGGT
* *
162073 TTATGAT
1 TTAGGGT
*
162080 TTAGGTT
1 TTAGGGT
162087 TTAGGG-
1 TTAGGGT
162093 TTAGGGT
1 TTAGGGT
162100 T
1 T
162101 CATCACAAAT
Statistics
Matches: 113, Mismatches: 27, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
6 17 0.15
7 87 0.77
8 9 0.08
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:162068 original size:13 final size:14
Alignment explanation
Indices: 162045--162087 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
162035 AGGTTTATTA
162045 TTTATGGTTTAGAG
1 TTTATGGTTTAGAG
*
162059 TTTA-GGTTTAGGG
1 TTTATGGTTTAGAG
*
162072 TTTATGATTTAG-G
1 TTTATGGTTTAGAG
162085 TTT
1 TTT
162088 TAGGGTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (14 bp):
TTTATGGTTTAGAG
Found at i:162075 original size:27 final size:27
Alignment explanation
Indices: 162045--162100 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
162035 AGGTTTATTA
* *
162045 TTTATGGTTTAGAG-TTTAGGTTTAGGG
1 TTTATGATTTAG-GTTTTAGGGTTAGGG
162072 TTTATGATTTAGGTTTTAGGGTTAGGG
1 TTTATGATTTAGGTTTTAGGGTTAGGG
162099 TT
1 TT
162101 CATCACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (27 bp):
TTTATGATTTAGGTTTTAGGGTTAGGG
Found at i:162637 original size:23 final size:23
Alignment explanation
Indices: 162609--162654 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
162599 TTTTTTAGGG
*
162609 TAATATAATAATACAGGTG-GGAA
1 TAATAT-AGAATACAGGTGCGGAA
*
162632 TAATATGGAATACAGGTGCGGAA
1 TAATATAGAATACAGGTGCGGAA
162655 GAAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (23 bp):
TAATATAGAATACAGGTGCGGAA
Found at i:173287 original size:59 final size:59
Alignment explanation
Indices: 173188--173309 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 59
173178 TTGTTATATC
* * ** * * *
173188 TTGAGCTCCCAGTTTCGAGTCCCGGGTATGCAGTGATATGAGTGTTTATTATCATATAA
1 TTGAGCTCCCAGGTTCGAGTACCACGTATGCAGGGATATGAGCGTTTATTATCAAATAA
* * * *
173247 TTGAGCTCTCAGGTTCGAGTACCACGTATGTAGGGGTATGAGCGTTTATTATCAAATAG
1 TTGAGCTCCCAGGTTCGAGTACCACGTATGCAGGGATATGAGCGTTTATTATCAAATAA
173306 TTGA
1 TTGA
173310 AAATTATTGA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (59 bp):
TTGAGCTCCCAGGTTCGAGTACCACGTATGCAGGGATATGAGCGTTTATTATCAAATAA
Found at i:178051 original size:37 final size:37
Alignment explanation
Indices: 177923--178061 Score: 169
Period size: 37 Copynumber: 3.8 Consensus size: 37
177913 ATTTTTCGTC
*
177923 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
177960 -T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATT
* * *
177994 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
178031 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
178062 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
33 1 0.01
34 30 0.34
35 1 0.01
36 1 0.01
37 55 0.62
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:178444 original size:32 final size:32
Alignment explanation
Indices: 178408--178479 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
178398 ATTATTCTTG
*
178408 TTATATATGCATAT-TACTTTCTATTAATTTTA
1 TTATATATGCATATAT-CTTTCTATTAATGTTA
* * * *
178440 TTATATATGTATATATGTTTTTATTAGTGTTA
1 TTATATATGCATATATCTTTCTATTAATGTTA
178472 TTATATAT
1 TTATATAT
178480 ATATATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (32 bp):
TTATATATGCATATATCTTTCTATTAATGTTA
Found at i:178582 original size:20 final size:20
Alignment explanation
Indices: 178557--178594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
178547 ATTATTATTA
178557 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
178577 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
178595 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:178623 original size:37 final size:36
Alignment explanation
Indices: 178543--178628 Score: 88
Period size: 37 Copynumber: 2.4 Consensus size: 36
178533 GATTTTCTTT
* *
178543 TTTTA-TTATTAT-TATTTTACTTATATATATATGC
1 TTTTACTTTTTATATATTTTACTCATATATATATGC
* *
178577 TTTTACTTTTTTATATATTTTACTCATTTATTTAT-C
1 TTTTAC-TTTTTATATATTTTACTCATATATATATGC
*
178613 TATTTTCTTTTTATAT
1 T-TTTACTTTTTATAT
178629 TTATCCTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.12
36 17 0.40
37 21 0.49
ACGTcount: A:0.24, C:0.08, G:0.01, T:0.66
Consensus pattern (36 bp):
TTTTACTTTTTATATATTTTACTCATATATATATGC
Found at i:179024 original size:106 final size:105
Alignment explanation
Indices: 178838--179032 Score: 302
Period size: 106 Copynumber: 1.8 Consensus size: 105
178828 TCTTCTAACC
*
178838 CAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAA
1 CAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAA
178903 CTTCACGACGAAGGATATTGGACTCGAGACAACACAAGTT
66 CTTCACGACGAAGGATATTGGACTCGAGACAACACAAGTT
* * * **
178943 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGT-TCCAGAGCCAATTTC
1 CAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCAATTTC
*
179007 AACTTCACGACGGAGGATATTGGACT
64 AACTTCACGACGAAGGATATTGGACT
179033 TTGAACAATG
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 32 0.40
106 49 0.60
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (105 bp):
CAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAA
CTTCACGACGAAGGATATTGGACTCGAGACAACACAAGTT
Found at i:179705 original size:37 final size:37
Alignment explanation
Indices: 179577--179715 Score: 169
Period size: 37 Copynumber: 3.8 Consensus size: 37
179567 ATTTTTCGTC
*
179577 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
179614 -T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATT
* * *
179648 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
179685 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
179716 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
33 1 0.01
34 30 0.34
35 1 0.01
36 1 0.01
37 55 0.62
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:180239 original size:20 final size:20
Alignment explanation
Indices: 180214--180251 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
180204 ATTATTATTA
180214 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
180234 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
180252 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:180256 original size:17 final size:17
Alignment explanation
Indices: 180234--180278 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
180224 ATATATATGC
180234 TTTTACTTTTTTATATA
1 TTTTACTTTTTTATATA
*
180251 TTTTACTCATTTTTATCTA
1 TTTTACT--TTTTTATATA
180270 TTTT-CTTTT
1 TTTTACTTTT
180279 ATATTATCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 3 0.12
17 7 0.28
18 2 0.08
19 13 0.52
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTACTTTTTTATATA
Found at i:181007 original size:22 final size:22
Alignment explanation
Indices: 180982--181029 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
180972 CTAGCCGCTT
180982 AAGATCACACAATGACCATGCA
1 AAGATCACACAATGACCATGCA
181004 AAGATCACACAATGACCATGCA
1 AAGATCACACAATGACCATGCA
181026 AAGA
1 AAGA
181030 AAAGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.25, G:0.15, T:0.12
Consensus pattern (22 bp):
AAGATCACACAATGACCATGCA
Found at i:183904 original size:15 final size:15
Alignment explanation
Indices: 183865--183907 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
183855 TCAATTTCTG
*
183865 CCTTTAAATTTTA-A
1 CCTTTAAATTTCAGA
* *
183879 CATTTACATTTCAGA
1 CCTTTAAATTTCAGA
183894 CCTTTAAATTTCAG
1 CCTTTAAATTTCAG
183908 CTTTTAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (15 bp):
CCTTTAAATTTCAGA
Found at i:184466 original size:139 final size:139
Alignment explanation
Indices: 184209--184459 Score: 328
Period size: 139 Copynumber: 1.8 Consensus size: 139
184199 TACTAATCCT
* * * *
184209 TTAAATTAGGAGAATTCTTAATTTGGTCATCGCTTTTGCTCGAGGTTTCGAATTAATTATTTGAT
1 TTAAACTAGGAGAATTATTAATTTGGTCATCGCTTTTGCTCGAGGTTTCCAATTAATTATTCGAT
* * * * * * * *
184274 ATGCCATAATTTATTTAAATTAATTTGGATTAATATTGGAGCCTATATCTTAGGCCTAATTTCAT
66 ATGCCACAATTGATTAAAATTAATTTAGATTAATATTGAAACATACATCTTAGGCCTAATTTCAT
184339 ATTTAGTCA
131 ATTTAGTCA
*
184348 TTAAACTAGGAGAATTATTAATTTGGTCCTCGCTTTTGCTCGAGG-TTCCAATTTAATTATTCGA
1 TTAAACTAGGAGAATTATTAATTTGGTCATCGCTTTTGCTCGAGGTTTCCAA-TTAATTATTCGA
**
184412 -ATTTCACAATTGATTAAAATTAATTTA-AGTTAATATTGAAACATACAT
65 TATGCCACAATTGATTAAAATTAATTTAGA-TTAATATTGAAACATACAT
184460 TTTTAGGTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
137 1 0.01
138 41 0.43
139 53 0.56
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (139 bp):
TTAAACTAGGAGAATTATTAATTTGGTCATCGCTTTTGCTCGAGGTTTCCAATTAATTATTCGAT
ATGCCACAATTGATTAAAATTAATTTAGATTAATATTGAAACATACATCTTAGGCCTAATTTCAT
ATTTAGTCA
Found at i:184592 original size:26 final size:26
Alignment explanation
Indices: 184543--184595 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
184533 TGCATTATAA
*
184543 TTAGGAAGGGAGGAATTATTAAAATT
1 TTAGGAAGGGAGGAATTATCAAAATT
*
184569 TTAGGAATGGAGGAATT-TACAAAATT
1 TTAGGAAGGGAGGAATTAT-CAAAATT
184595 T
1 T
184596 CAAAGGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (26 bp):
TTAGGAAGGGAGGAATTATCAAAATT
Found at i:188231 original size:23 final size:23
Alignment explanation
Indices: 188201--188265 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
188191 ATTCGTATAT
188201 ATATATTCGTTTAATATTTGTGA
1 ATATATTCGTTTAATATTTGTGA
* *
188224 ATATATTCATTTAATATTCGTGA
1 ATATATTCGTTTAATATTTGTGA
*
188247 ATGTATTCGTTTAATATTT
1 ATATATTCGTTTAATATTT
188266 ATAACATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (23 bp):
ATATATTCGTTTAATATTTGTGA
Found at i:197487 original size:11 final size:12
Alignment explanation
Indices: 197461--197491 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
197451 AGTAAAAAAT
197461 ATAGATTTACAA
1 ATAGATTTACAA
197473 ATAGATTTA-AA
1 ATAGATTTACAA
197484 ATAGATTT
1 ATAGATTT
197492 GCAATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (12 bp):
ATAGATTTACAA
Found at i:200784 original size:2 final size:2
Alignment explanation
Indices: 200777--200802 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
200767 TATTACATTA
200777 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
200803 TAATAATCAA
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:202787 original size:31 final size:31
Alignment explanation
Indices: 202752--202825 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
202742 GACTCCAATA
202752 TTCAATTTGGTACTTGAACTTCTCCTATTAG
1 TTCAATTTGGTACTTGAACTTCTCCTATTAG
*
202783 TTCAATCTGGTACTTGAACTTCTCCTATTAG
1 TTCAATTTGGTACTTGAACTTCTCCTATTAG
202814 TTCAATTTGGTA
1 TTCAATTTGGTA
202826 AAGTATACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.45
Consensus pattern (31 bp):
TTCAATTTGGTACTTGAACTTCTCCTATTAG
Found at i:203150 original size:32 final size:31
Alignment explanation
Indices: 203111--203184 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
203101 GTTTAAAGAC
*
203111 TATTTTATAATAGTTTAATAA-GTTGAATAAT
1 TATTTTATAATAATTTAA-AATGTTGAATAAT
* *
203142 TATTTTTATAATAATTTAAAATTTTTAATAAT
1 TA-TTTTATAATAATTTAAAATGTTGAATAAT
203174 TATTTTATAAT
1 TATTTTATAAT
203185 GACTTGACCG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 13 0.34
32 25 0.66
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (31 bp):
TATTTTATAATAATTTAAAATGTTGAATAAT
Found at i:219228 original size:6 final size:6
Alignment explanation
Indices: 219200--219242 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
219190 GTATCTGCCC
* *
219200 CCCTCT CCCTCT CCCTTT CCCTTT CCCTTT --CTTT CCCTTT CCC
1 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT CCC
219243 GGAGGACGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
4 4 0.12
6 30 0.88
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (6 bp):
CCCTTT
Found at i:225790 original size:32 final size:30
Alignment explanation
Indices: 225754--225826 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 30
225744 TTTAAGGGTA
* * *
225754 AAATTAATATTTTATCTAAAATTTTAATGAAT
1 AAATTAATATTTTATC-AAAAATTTAAAG-AC
*
225786 AAATTATTATTTTATCAAAAATTTAAAGAC
1 AAATTAATATTTTATCAAAAATTTAAAGAC
225816 AAATTAATATT
1 AAATTAATATT
225827 ATTTTTAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 11 0.31
31 10 0.28
32 15 0.42
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTAATATTTTATCAAAAATTTAAAGAC
Found at i:226079 original size:22 final size:21
Alignment explanation
Indices: 226030--226184 Score: 95
Period size: 21 Copynumber: 7.4 Consensus size: 21
226020 TTGCATTTCG
* * **
226030 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTTACAATTT
*
226051 CGTTGCGATAGTTTACAGTTGT
1 CGTTGCGATAGTTTACAATT-T
* *
226073 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTTTACAATTT
*
226092 CGTTGCGAT--TTTTCAAATTT
1 CGTTGCGATAGTTTAC-AATTT
* * *
226112 -GTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTTTACAATT-T
* * *
226133 TGTTGCGATAGTTTATAAATT
1 CGTTGCGATAGTTTACAATTT
* *
226154 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTTACAATT-T
226176 CGTTGCGAT
1 CGTTGCGAT
226185 TTTCCAAATT
Statistics
Matches: 105, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
19 22 0.21
20 13 0.12
21 35 0.33
22 35 0.33
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (21 bp):
CGTTGCGATAGTTTACAATTT
Found at i:226096 original size:19 final size:19
Alignment explanation
Indices: 226072--226119 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
226062 TTTACAGTTG
226072 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
226091 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
*
226110 TTGTTGCGAT
1 TCGTTGCGAT
226120 AGTCTATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:230365 original size:168 final size:168
Alignment explanation
Indices: 230081--230924 Score: 1429
Period size: 168 Copynumber: 5.0 Consensus size: 168
230071 CAATCTGAGG
*
230081 AAGAGGCTTCTGAGTCCAAGGAGGAAGAAGCTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
1 AAGAGGCTTCTGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
* *
230146 AAGGTGATTTATCTGCAAGAAGCTCTAGAGGAAGTCAAGACTGAAAGCATGAAATTAAAGGATAG
66 AAGGTGATTTATCTGCAAGAAGCTCTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGAGAG
230211 TTTGTTGGATAAAGAAAAC-GAGTTGCAGAGTGTCATTC
131 TTTGTTGGATAAAG-AAACTGAGTTGCAGAGTGTCATTC
* *
230249 AAGAGGCTTATGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCTTAAAGGAAGTTGAATCT
1 AAGAGGCTTCTGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
* * *
230314 AAGGTGATTTATCGGCAAGAAGCTCTAGAGGAAGTCGAGACCGAGAGCATGAAATTAAAGGAGAG
66 AAGGTGATTTATCTGCAAGAAGCTCTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGAGAG
*
230379 TTTGTTGAATAAAGAAACTGAGTTGCAGAGTGTCATTC
131 TTTGTTGGATAAAGAAACTGAGTTGCAGAGTGTCATTC
* * * * *
230417 AGGAGGCTTCTGAATCGAAGGGGGAAGAAACGCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
1 AAGAGGCTTCTGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
* * *
230482 AAAGTGATTTATCTGCAAGAAGCACTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGGGAG
66 AAGGTGATTTATCTGCAAGAAGCTCTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGAGAG
230547 TTTGTTGGATAAAGAAACTGAGTTGCAGAGTGTCATTC
131 TTTGTTGGATAAAGAAACTGAGTTGCAGAGTGTCATTC
* *
230585 AGGAGGCTTCTGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCC
1 AAGAGGCTTCTGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
* * * *
230650 AAGGTGATTTATCTGCAAGAAGCTCTAGAGAAAGTCAAGGCTGAGAGCATGAAACTAGAGGAGAG
66 AAGGTGATTTATCTGCAAGAAGCTCTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGAGAG
*
230715 TTTGTTGGCTAAAGAAACTGAGTTGCAGAGTGTCATTC
131 TTTGTTGGATAAAGAAACTGAGTTGCAGAGTGTCATTC
* *
230753 AAGAGGCTTCTGAGTTCAAGGAGGAAGAAACTCGGTTGAAGGATGGCCTAAAGGAAGTTGAATCT
1 AAGAGGCTTCTGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
*
230818 AAGGTGATTTATCTGCAAGAATCTCTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGAGAG
66 AAGGTGATTTATCTGCAAGAAGCTCTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGAGAG
230883 TTTGTTGGATAAAGAAACTGAGTTGCAGAGTGTCATTC
131 TTTGTTGGATAAAGAAACTGAGTTGCAGAGTGTCATTC
230921 AAGA
1 AAGA
230925 AAACAATGAA
Statistics
Matches: 629, Mismatches: 46, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
167 4 0.01
168 625 0.99
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.23
Consensus pattern (168 bp):
AAGAGGCTTCTGAGTCCAAGGAGGAAGAAACTCGGTTGAAGGATAGCCTAAAGGAAGTTGAATCT
AAGGTGATTTATCTGCAAGAAGCTCTAGAGGAAGTCAAGACTGAGAGCATGAAATTAAAGGAGAG
TTTGTTGGATAAAGAAACTGAGTTGCAGAGTGTCATTC
Found at i:235927 original size:24 final size:24
Alignment explanation
Indices: 235888--235981 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
235878 TAATGAGCAA
** *
235888 ACTCATTTATTGGCTCGTTTATCG
1 ACTCATTTATAAGCTCGTTTATAG
* * *
235912 ACACATTTATAAGCTCGTTTGTTG
1 ACTCATTTATAAGCTCGTTTATAG
** * *
235936 GGTCATTTATAAGTTTGTTTATAG
1 ACTCATTTATAAGCTCGTTTATAG
* *
235960 ACTCATTTATAAACTCATTTAT
1 ACTCATTTATAAGCTCGTTTAT
235982 TCAATTCTCA
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (24 bp):
ACTCATTTATAAGCTCGTTTATAG
Done.