Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 26
Found at i:373 original size:28 final size:29
Alignment explanation
Indices: 333--389 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
323 CTCTCAAAAA
333 TGTAATATTATCT-AAGAAAATAAGAGGT
1 TGTAATATTATCTAAAGAAAATAAGAGGT
361 TGTAATATTATCTAAAGAAAATAAGAGGT
1 TGTAATATTATCTAAAGAAAATAAGAGGT
390 GATGAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.32
Consensus pattern (29 bp):
TGTAATATTATCTAAAGAAAATAAGAGGT
Found at i:1588 original size:31 final size:31
Alignment explanation
Indices: 1550--1649 Score: 159
Period size: 31 Copynumber: 3.3 Consensus size: 31
1540 TAATAAGTTC
*
1550 TGGTCACTTATATTATCATTTTATTAAATTT
1 TGGTCACTTACATTATCATTTTATTAAATTT
*
1581 TGGTCACTTACGTTATCA--TTATTAAATTT
1 TGGTCACTTACATTATCATTTTATTAAATTT
*
1610 TGGTCACTTACATTATTATTTTATTAAATTT
1 TGGTCACTTACATTATCATTTTATTAAATTT
1641 TGGTCACTT
1 TGGTCACTT
1650 GAACGTTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
29 27 0.43
31 36 0.57
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (31 bp):
TGGTCACTTACATTATCATTTTATTAAATTT
Found at i:1623 original size:23 final size:27
Alignment explanation
Indices: 1570--1644 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
1560 TATTATCATT
1570 TTATTAAATTTTGGTCACTTACGTTATCA
1 TTATTAAATTTTGGT-AC-TACGTTATCA
* *
1599 TTATTAAATTTTGGTCACTTACATTATTA
1 TTATTAAATTTTGGT-AC-TACGTTATCA
1628 TTTTATTAAATTTTGGT
1 --TTATTAAATTTTGGT
1645 CACTTGAACG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 27 0.64
31 15 0.36
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (27 bp):
TTATTAAATTTTGGTACTACGTTATCA
Found at i:2766 original size:31 final size:31
Alignment explanation
Indices: 2679--2776 Score: 153
Period size: 31 Copynumber: 3.2 Consensus size: 31
2669 TAATAAGTTC
* *
2679 TGGTCACTTATATTATCATTTTATTAAATTT
1 TGGTCACTTACATTATTATTTTATTAAATTT
* *
2710 TGGTCATTTACGTTATTA-TTTATTAAATTT
1 TGGTCACTTACATTATTATTTTATTAAATTT
2740 TGGTCACTTACATTATTATTTTATTAAATTT
1 TGGTCACTTACATTATTATTTTATTAAATTT
2771 TGGTCA
1 TGGTCA
2777 TTTGAACGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 28 0.47
31 32 0.53
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (31 bp):
TGGTCACTTACATTATTATTTTATTAAATTT
Found at i:4604 original size:31 final size:31
Alignment explanation
Indices: 4505--4617 Score: 156
Period size: 31 Copynumber: 3.7 Consensus size: 31
4495 TGAAATATTG
* *
4505 TTTAATAAGTTTTGGTCACTTACATTATCAT
1 TTTATTAAATTTTGGTCACTTACATTATCAT
* * ** *
4536 TTTATTAAATTTTAGTCATTTATGTTATTA-
1 TTTATTAAATTTTGGTCACTTACATTATCAT
4566 TTTATTAAATTTTGGTCACTTACATTATCAT
1 TTTATTAAATTTTGGTCACTTACATTATCAT
4597 TTTATTAAATTTTGGTCACTT
1 TTTATTAAATTTTGGTCACTT
4618 GAACGTTGAA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
30 25 0.36
31 44 0.64
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (31 bp):
TTTATTAAATTTTGGTCACTTACATTATCAT
Found at i:4609 original size:61 final size:61
Alignment explanation
Indices: 4500--4614 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 61
4490 CAAAATGAAA
* *
4500 TATTGTTTAATAAGTTTTGGTCACTTACATTATCATTTTATTAAATTTTAGTCATTTATGT
1 TATTATTTAATAAATTTTGGTCACTTACATTATCATTTTATTAAATTTTAGTCATTTATGT
* *
4561 TATTATTTATTAAATTTTGGTCACTTACATTATCATTTTATTAAATTTTGGTCA
1 TATTATTTAATAAATTTTGGTCACTTACATTATCATTTTATTAAATTTTAGTCA
4615 CTTGAACGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (61 bp):
TATTATTTAATAAATTTTGGTCACTTACATTATCATTTTATTAAATTTTAGTCATTTATGT
Found at i:6438 original size:26 final size:27
Alignment explanation
Indices: 6409--6463 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
6399 TTTTTCATCT
* *
6409 AAGTATCTAAA-ATATTTTTTTTGTCA
1 AAGTATCTAAATATATCTTTTTGGTCA
* *
6435 AAGTATTTAAATTTATCTTTTTGGTCA
1 AAGTATCTAAATATATCTTTTTGGTCA
6462 AA
1 AA
6464 ATATGCACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (27 bp):
AAGTATCTAAATATATCTTTTTGGTCA
Found at i:6489 original size:29 final size:29
Alignment explanation
Indices: 6455--6511 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
6445 ATTTATCTTT
*
6455 TTGGTCAAAATATGCACTTAAAATATTTG
1 TTGGTCAAAATAGGCACTTAAAATATTTG
* *
6484 TTGGTCAAATTAGGCACTTAAAGTATTT
1 TTGGTCAAAATAGGCACTTAAAATATTT
6512 AATCTTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (29 bp):
TTGGTCAAAATAGGCACTTAAAATATTTG
Found at i:9576 original size:18 final size:18
Alignment explanation
Indices: 9541--9578 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9531 TTGTAATTAA
* *
9541 TGGCATTTGGATCGATTT
1 TGGCATTTGGACCAATTT
9559 TGGCATTTGGACCAATTT
1 TGGCATTTGGACCAATTT
9577 TG
1 TG
9579 TATTAGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.42
Consensus pattern (18 bp):
TGGCATTTGGACCAATTT
Found at i:12074 original size:10 final size:10
Alignment explanation
Indices: 12043--12206 Score: 72
Period size: 10 Copynumber: 15.8 Consensus size: 10
12033 TTCAGTTTTC
12043 TTTTTTCT-T
1 TTTTTTCTCT
* *
12052 TCTTTTCCCCT
1 T-TTTTTCTCT
12063 TTTTTTCTCTT
1 TTTTTTCTC-T
*
12074 TTTCTTTTTCT
1 TTT-TTTCTCT
12085 TTTTTT-TCAT
1 TTTTTTCTC-T
* *
12095 TTTCTT-TCA
1 TTTTTTCTCT
*
12104 TTTTCTC-CTT
1 TTTTTTCTC-T
12114 TTTTTTCTCT
1 TTTTTTCTCT
*
12124 TTCTCTTTTTCT
1 TT-T-TTTCTCT
*
12136 CTTTTTCTCT
1 TTTTTTCTCT
12146 TTTTCTTCT-T
1 TTTT-TTCTCT
12156 TTTCTTTCT-T
1 TTT-TTTCTCT
*
12166 TTTCTTTCTTT
1 TTT-TTTCTCT
*
12177 TTTCTTTTTCT
1 TTT-TTTCTCT
12188 TTCTTTT-TCT
1 TT-TTTTCTCT
12198 TTTTCTTCT
1 TTTT-TTCT
12207 TCAGGTGTAA
Statistics
Matches: 122, Mismatches: 17, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
9 10 0.08
10 65 0.53
11 34 0.28
12 13 0.11
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:12080 original size:16 final size:17
Alignment explanation
Indices: 12038--12204 Score: 163
Period size: 17 Copynumber: 9.9 Consensus size: 17
12028 CTCATTTCAG
12038 TTTTCT-TTTTTCTTTC
1 TTTTCTCTTTTTCTTTC
*
12054 TTTTCCCCTTTTT-TTCTC
1 TTTT-CTCTTTTTCTT-TC
12072 TTTT-TCTTTTTCTTT-
1 TTTTCTCTTTTTCTTTC
*
12087 TTTT-TCATTTTCTTTC
1 TTTTCTCTTTTTCTTTC
12103 ATTTTCTCCTTTTT-TTTC
1 -TTTTCT-CTTTTTCTTTC
*
12121 TCTTTCTCTTTTTCTCT-
1 T-TTTCTCTTTTTCTTTC
12138 TTTTCTCTTTTTC-TTC
1 TTTTCTCTTTTTCTTTC
12154 TTTTTCTTTCTTTTTCTTTC
1 -TTTTC--TCTTTTTCTTTC
*
12174 TTTTTTCTTTTTCTTTC
1 TTTTCTCTTTTTCTTTC
12191 TTTT-TCTTTTTCTT
1 TTTTCTCTTTTTCTT
12205 CTTCAGGTGT
Statistics
Matches: 129, Mismatches: 7, Indels: 30
0.78 0.04 0.18
Matches are distributed among these distances:
15 15 0.12
16 33 0.26
17 38 0.29
18 23 0.18
19 17 0.13
20 3 0.02
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTCTTTTTCTTTC
Found at i:12081 original size:6 final size:6
Alignment explanation
Indices: 12038--12204 Score: 95
Period size: 6 Copynumber: 28.2 Consensus size: 6
12028 CTCATTTCAG
* * * *
12038 TTTTCT TTTT-T CTTTCT TTTCCCC TTTT-T TTCTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTT-TCT TTTTCT TTTTCT TTTTCT TTTTCT
* *
12085 TTTT-T TTCATT-T TCTTTCAT TTTCTCCT TTTT-T TTCTCT TTCTCT
1 TTTTCT TT--TTCT T-TTTC-T TTT-T-CT TTTTCT TTTTCT TTTTCT
* * *
12130 TTTTC- TCTT-T TTCTCT TTTTCT TCTTT-T TCTTTCT TTTTCT TTCT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT T-TTTCT TTTTCT TTTTCT
12176 TTTTCT TTTTC- -TTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
12205 CTTCAGGTGT
Statistics
Matches: 127, Mismatches: 16, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.03
5 23 0.18
6 75 0.59
7 16 0.13
8 8 0.06
9 1 0.01
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:13288 original size:14 final size:14
Alignment explanation
Indices: 13269--13295 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13259 AACACATTTA
13269 ATTTTTAAAAGATG
1 ATTTTTAAAAGATG
13283 ATTTTTAAAAGAT
1 ATTTTTAAAAGAT
13296 CCCATCTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
ATTTTTAAAAGATG
Found at i:14015 original size:131 final size:131
Alignment explanation
Indices: 13777--14135 Score: 520
Period size: 131 Copynumber: 2.7 Consensus size: 131
13767 ATAATTCTAA
* *
13777 GAGAGAAAACAATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATAGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
13842 GTCATTTATTACTCCGATCGAAATGAAGAGATATCACTATTTCCTCTTAAAATTCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACCATTTCATCTTAAAAATCAATATTGATT
*
13907 T
131 C
* * * * * * * *
13908 GATAGAAAACTATAACATCTAATTATTACCAATAAAAAATAAATGACTTTTCATGCCTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATAGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
13973 GTCATTTATTACTCCAATCAAAATGAAGGGATATCACCATTTCATCTTAAAAATCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACCATTTCATCTTAAAAATCAATATTGATT
14038 C
131 C
* * *
14039 GAGAGAAAACGATAATATCTAATTATTTCAAATAGAGAATAAATGACCTCTCATGCCTTATAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATAGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
14104 GTCATTTATTACTCCAACCGAAATGAAAAGAT
66 GTCATTTATTACTCCAATCGAAATGAAGAGAT
14136 TTTACTATTT
Statistics
Matches: 197, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
131 197 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (131 bp):
GAGAGAAAACAATAATATCTAATTATTTCCAATAGAGAATAAATGACCTCTCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAGATATCACCATTTCATCTTAAAAATCAATATTGATT
C
Found at i:16264 original size:26 final size:26
Alignment explanation
Indices: 16225--16284 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
16215 GGAACAATGC
* *
16225 CAGGGGACTGGTGCAGATGACGGTGG
1 CAGGGGATTAGTGCAGATGACGGTGG
* *
16251 CAGGGGATTAGTGCATATGAGGGTGG
1 CAGGGGATTAGTGCAGATGACGGTGG
*
16277 TAGGGGAT
1 CAGGGGAT
16285 GTTAGGGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.48, T:0.20
Consensus pattern (26 bp):
CAGGGGATTAGTGCAGATGACGGTGG
Found at i:16429 original size:3 final size:3
Alignment explanation
Indices: 16421--16473 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
16411 ATTTGGACCT
16421 ATA ATA ATA ATA A-A ATA A-A A-A ATA ATTA ATA ATA A-A CATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA -ATA ATA
16464 ATA ATA ATA A
1 ATA ATA ATA A
16474 CGGTCTCCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 7 0.16
3 34 0.76
4 4 0.09
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:16955 original size:133 final size:132
Alignment explanation
Indices: 16664--17116 Score: 500
Period size: 133 Copynumber: 3.4 Consensus size: 132
16654 GTCTGAGAAG
* * * * * *
16664 AGATATGGAAATGTTGATTTATTCTACTATTCTTCAGGGAATATTGAATCGAGGCATACTTGTTC
1 AGATATGGAAATGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAGGTAGATTTGTTC
* * * * * * * * *
16729 CACTCCTTCTTTAGAGG-AGACCAACTTTGGAAAGAGGGGATCTGTTCCGCTGTTTCTTTAGGGA
66 CACTGCTTC-TCAG-GGAAGATCAAATATGGAAA-AAGTGATCTGTTCCACAGTTTCTTTAGGGA
16793 AAATC
128 AAATC
* * * * * *
16798 AGATCTGGAAATATTAATTCATTCCA-TATTTCTTTAGGGAACATTGAATCGAGGTAGATTTGTT
1 AGATATGGAAATGTTGATTCATTCCACT-GTTCTTCAGGGAATATTGAATCGAGGTAGATTTGTT
* * * * *
16862 CTACTGTTTCTCAGGGAAGATCAAATCTAGAAAAAGATGATATGTTCCACAGTTT-TTTCAGGGA
65 CCACTGCTTCTCAGGGAAGATCAAATATGGAAAAAG-TGATCTGTTCCACAGTTTCTTT-AGGGA
* *
16926 AATTT
128 AAATC
*
16931 AGATATGGAAATGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATTGAGGTAGATTTGTTC
1 AGATATGGAAATGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAGGTAGATTTGTTC
*
16996 CACTGCTTCTCAGGGAAGATCAAATATGGAAAAAGTGTATCTGTTCCACTA-TTTCTTTAGGAAA
66 CACTGCTTCTCAGGGAAGATCAAATATGGAAAAAGTG-ATCTGTTCCAC-AGTTTCTTTAGGGAA
17060 AATC
129 AATC
* ** *
17064 AGATCTATAAATTTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAG
1 AGATATGGAAATGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAG
17117 TTTGATTCGC
Statistics
Matches: 265, Mismatches: 46, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
132 9 0.03
133 193 0.73
134 63 0.24
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (132 bp):
AGATATGGAAATGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCGAGGTAGATTTGTTC
CACTGCTTCTCAGGGAAGATCAAATATGGAAAAAGTGATCTGTTCCACAGTTTCTTTAGGGAAAA
TC
Found at i:17892 original size:240 final size:241
Alignment explanation
Indices: 17384--17933 Score: 742
Period size: 240 Copynumber: 2.3 Consensus size: 241
17374 AGATGGCCCG
* * *
17384 AAGGATTTAAGCATCATGCTTGCAAGACTTACTAATGGCCCGAAGGAC-T--T-AGTAAAAAACT
1 AAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACT
* * * *
17445 TTGGAAATCGTTTTCTTACTTTTCAAAAGAAACCAATTTTTAGAAAAGGTTTAAGTGATAAACTT
66 TTGGAAATCATTTTCTTACTTTTCAAAAGAAACCAATTTTAAGAAAAGGTTTAAATGAGAAACTT
*
17510 TGGAAATTACTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTACCTGAAGGTCTTATGGATA
131 TGGAAATTACTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTACCTAAAGGTCTTATGGATA
*
17575 GCCCAAAGGACTTATCATCTTGCTCGAAAGACATTCAGAAGACCTG
196 GCCCAAAGGACTTATCATCTTGCTCGAAAGACATTCAGAAGACCTA
* * *
17621 AAGGATTTTAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTACTAAGTAAGAAACT
1 AAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACT
* *
17686 TTGGAAATCATTTTCTTACTTTTCAAAAGAAACCAATTTTCAAG-AAAGGTTTAAATTAGAAAGT
66 TTGGAAATCATTTTCTTACTTTTCAAAAGAAACCAATTTT-AAGAAAAGGTTTAAATGAGAAACT
* * *
17750 TTGGAAATTATTTTCTTATTTTTT-AAAATCATGTGAAAACATCCTTTCC-AAAGGTCTTATGGA
130 TTGGAAATTACTTTCTCATTTTTTGAAAATCATGTGAAAACATCC-TACCTAAAGGTCTTATGGA
* * * * *
17813 TGGCCCGAAGGACTTATCATCTTGTTCGAAAGAC-TTACATATGA-CTCA
194 TAGCCCAAAGGACTTATCATCTTGCTCGAAAGACATT-CAGAAGACCT-A
* * * * *
17861 AAGGATCTAAACATAATGCTTGAAAGACTTACTGATGACCCGATA-GACTTACTAGGTAAGAAAC
1 AAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGA-AGGACTTACTAAGTAAGAAAC
17925 TTTGGAAAT
65 TTTGGAAAT
17934 GAAGCTTGGT
Statistics
Matches: 274, Mismatches: 30, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
237 43 0.16
238 1 0.00
239 4 0.01
240 133 0.49
241 91 0.33
242 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (241 bp):
AAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACT
TTGGAAATCATTTTCTTACTTTTCAAAAGAAACCAATTTTAAGAAAAGGTTTAAATGAGAAACTT
TGGAAATTACTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTACCTAAAGGTCTTATGGATA
GCCCAAAGGACTTATCATCTTGCTCGAAAGACATTCAGAAGACCTA
Found at i:20658 original size:46 final size:46
Alignment explanation
Indices: 20608--20713 Score: 212
Period size: 46 Copynumber: 2.3 Consensus size: 46
20598 TGCATGGCTG
20608 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA
20654 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA
20700 GTGCATCGATGCAT
1 GTGCATCGATGCAT
20714 GGTATGTGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA
Found at i:20681 original size:64 final size:63
Alignment explanation
Indices: 20545--20682 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 63
20535 GCACTAAGAG
* * * ***
20545 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCAT-GCAAA
20609 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT-CAGTGCATCGATGCAT-CAA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATA-CCTACAGTGCATCGATGCATGCAA
20671 A
63 A
20672 TGCATTCGATG
1 TGCA-TCGATG
20683 TTTTCATAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
63 5 0.08
64 33 0.52
65 21 0.33
66 5 0.08
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATGCAAA
Found at i:20738 original size:111 final size:110
Alignment explanation
Indices: 20543--20749 Score: 312
Period size: 111 Copynumber: 1.9 Consensus size: 110
20533 GTGCACTAAG
* * *
20543 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGGCTG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATGGCTG
20608 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
66 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
20653 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT-CAGTGCATCGATGCATGG
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATA-CCTACAGTGCATCGATGCATGG
* *
20716 -TATGTGCATCGATGCATGAAATGCATTCGATGTT
63 CT-GGTGCATCGATGCATCAAATGCATTCGATGTT
20750 CAATTTAATT
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
110 30 0.34
111 53 0.60
112 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (110 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATGGCTG
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
Found at i:20788 original size:65 final size:63
Alignment explanation
Indices: 20654--20799 Score: 163
Period size: 65 Copynumber: 2.3 Consensus size: 63
20644 AAAATCCTCA
*
20654 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCAATGCATGGTAT
* **
20719 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCAATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCAATGCATGGTA
20781 TT
63 -T
*
20783 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
20800 CTTTGAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.04
63 4 0.06
64 21 0.30
65 42 0.60
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCAATGCATGGTAT
Found at i:21167 original size:24 final size:25
Alignment explanation
Indices: 21139--21199 Score: 99
Period size: 24 Copynumber: 2.5 Consensus size: 25
21129 CCCCTTACTA
*
21139 TAACACTTCTCCCTTTTAA-AATTT
1 TAACACTTCTCCCTTCTAAGAATTT
21163 TAACACTTCTCCCTTCTAAGAATTT
1 TAACACTTCTCCCTTCTAAGAATTT
21188 T-ACACTTCTCCC
1 TAACACTTCTCCC
21200 CCTTTTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 29 0.83
25 6 0.17
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.41
Consensus pattern (25 bp):
TAACACTTCTCCCTTCTAAGAATTT
Found at i:23333 original size:23 final size:22
Alignment explanation
Indices: 23301--23382 Score: 94
Period size: 23 Copynumber: 3.7 Consensus size: 22
23291 AAAACCCGAC
23301 GGATGCATCGATGCACATTCAA
1 GGATGCATCGATGCACATTCAA
* * *
23323 GGCATGCATCGGTGCACCTTCAT
1 GG-ATGCATCGATGCACATTCAA
** *
23346 GG-TTTATTGATGCACATTCAA
1 GGATGCATCGATGCACATTCAA
23367 GGATGCATCGATGCAC
1 GGATGCATCGATGCAC
23383 TATTAGGTGT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
21 15 0.33
22 12 0.26
23 19 0.41
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (22 bp):
GGATGCATCGATGCACATTCAA
Found at i:29346 original size:65 final size:64
Alignment explanation
Indices: 29213--29335 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 64
29203 AGCCAGAGTA
* * *
29213 CATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGTATCGATGCGTGGTATGTG
1 CATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGGTATGTG
* ** * *
29278 CATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGG
1 CATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG
29336 ATTGGTGCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.06
64 21 0.43
65 25 0.51
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (64 bp):
CATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGGTATGTG
Found at i:33087 original size:31 final size:31
Alignment explanation
Indices: 33049--33107 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
33039 TCTACTTGAG
*
33049 AAGGTAAAAGTATGAATTTGGTGTCTCAAAA
1 AAGGTAAAAGTATGAATTTGGAGTCTCAAAA
* *
33080 AAGGTAAAGGTATGACTTTGGAGTCTCA
1 AAGGTAAAAGTATGAATTTGGAGTCTCA
33108 GATAAATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (31 bp):
AAGGTAAAAGTATGAATTTGGAGTCTCAAAA
Found at i:36121 original size:132 final size:132
Alignment explanation
Indices: 35748--36121 Score: 430
Period size: 132 Copynumber: 2.8 Consensus size: 132
35738 AATAATTCTA
* * *
35748 CGAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATAATCTCTCATGCCTTAAAGC
1 CGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * * * * *
35813 AAG-CATTTATTATTCCGATCAAAATGAAGAGATATCAATATTTT-GTCTTAAAAGTCAATATTG
66 -AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTTCATCTTAAAAATCAATATTA
*
35876 GTT
130 ATT
* * * * * * *
35879 TGATAGAAAACGATAACATCTAATTATTTCCAATAGAAAATAAAATGGCATCTCATGCCTTAAAG
1 CGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAAT-AAATGACCTCTCATGCCTTAAAG
* * * *
35944 CAGTCATTTATTACTCCAATCGAAATGAAGAGACAACACCA-TTTCATCTTAAAAATTAATATTA
65 CAGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTTCATCTTAAAAATCAATATTA
36008 ATT
130 ATT
* * *
36011 CGAGAGAAAACGATAATATCCAATTATTTCCAATCGCGAATAAATGACCTCTAATGCCTTAAAGC
1 CGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * * * *
36076 AGTCATTTATTACTCCAACCGTAATAAAAATATATTACTATTTTCA
66 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTTCA
36122 ATATGAATTC
Statistics
Matches: 198, Mismatches: 41, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
131 92 0.46
132 106 0.54
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (132 bp):
CGAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTTCATCTTAAAAATCAATATTAA
TT
Found at i:37916 original size:8 final size:8
Alignment explanation
Indices: 37903--37932 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
37893 AATCTGATTC
37903 TTGTTTGA
1 TTGTTTGA
37911 TTGTTT-A
1 TTGTTTGA
37918 TTGTTTGA
1 TTGTTTGA
37926 TTGTTTG
1 TTGTTTG
37933 GTGATGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.67
Consensus pattern (8 bp):
TTGTTTGA
Found at i:37923 original size:15 final size:15
Alignment explanation
Indices: 37903--37931 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37893 AATCTGATTC
37903 TTGTTTGATTGTTTA
1 TTGTTTGATTGTTTA
37918 TTGTTTGATTGTTT
1 TTGTTTGATTGTTT
37932 GGTGATGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (15 bp):
TTGTTTGATTGTTTA
Found at i:38074 original size:26 final size:26
Alignment explanation
Indices: 38045--38108 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
38035 ACAAATTACA
*
38045 GTGGCAGGGGACTGGTGCAGATGACG
1 GTGGCAGGGGACTGGTGCACATGACG
* * * * *
38071 GTGGCAGAGGATTGTTGTACATGATG
1 GTGGCAGGGGACTGGTGCACATGACG
38097 GTGGCAGGGGAC
1 GTGGCAGGGGAC
38109 GTTAGGATTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.12, G:0.47, T:0.20
Consensus pattern (26 bp):
GTGGCAGGGGACTGGTGCACATGACG
Found at i:54145 original size:14 final size:14
Alignment explanation
Indices: 54108--54172 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
54098 AGCCTAAACC
54108 GAGTCAACTCGGA-CT
1 GAGTCAACTC--ATCT
* *
54123 GATTCAACTCGTCT
1 GAGTCAACTCATCT
* *
54137 GAGTTAACTTATCT
1 GAGTCAACTCATCT
*
54151 GAGTCAACTCATCC
1 GAGTCAACTCATCT
54165 GAGTCAAC
1 GAGTCAAC
54173 CCATTGACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 31 0.77
15 9 0.22
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (14 bp):
GAGTCAACTCATCT
Found at i:56982 original size:2 final size:2
Alignment explanation
Indices: 56975--57011 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56965 AGCTAAAGTC
56975 AT AT AT 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 AT AT AT A
57012 AATCCAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57225 original size:13 final size:13
Alignment explanation
Indices: 57207--57232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57197 CCAATTCCCT
57207 GTGCCTTGATAAA
1 GTGCCTTGATAAA
57220 GTGCCTTGATAAA
1 GTGCCTTGATAAA
57233 TCTATTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGCCTTGATAAA
Found at i:70075 original size:81 final size:81
Alignment explanation
Indices: 69940--70339 Score: 507
Period size: 81 Copynumber: 4.9 Consensus size: 81
69930 TTTCCTTTAG
* ** * * * *
69940 TCTTTTACCCAAAGACATTTAGCCTTTTATCTAACTTG-CATGATTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAAC-TGACATAATTGACACCTTTCTGTCAAATG
*
70004 CACAGCTAGGCTATTAA
65 CACAGCTAGGCCATTAA
* * * * *
70021 TCTTTTACTCAAAGGTAGTTAACCTTTCATCTAGCTGACATAATTGACACCTTTCCGTTAAATGC
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
70086 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
70102 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTTTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
* *
70167 ACAGTTAGGCTATTAA
66 ACAGCTAGGCCATTAA
* *
70183 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATAATTGACACCTTTCAGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
70248 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * * **
70264 TATTTTACTCAAATGTACTTAACATTTCATCTAACTGGCA-AGATTGTCATTTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATA-ATTGACACCTTTCTGTCAAATG
*
70328 CACAGTTAGGCC
65 CACAGCTAGGCC
70340 TCAAAGGTAC
Statistics
Matches: 277, Mismatches: 40, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
80 3 0.01
81 274 0.99
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:70213 original size:162 final size:162
Alignment explanation
Indices: 69940--70338 Score: 559
Period size: 162 Copynumber: 2.5 Consensus size: 162
69930 TTTCCTTTAG
* ** * * * * * * *
69940 TCTTTTACCCAAAGACATTTAGCCTTTTATCTAACTTGCATGATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTTTGTCAAATGC
* * *
70005 ACAGCTAGGCTATTAATCTTTTACTCAAAGGTAGTTAACCTTTCATCTAGCTGACATAATTGACA
66 ACAGTTAGGCTATTAATCTTTTACTCAAAGGTAGTTAACATTTCATCTAACTGACATAATTGACA
* * *
70070 CCTTTCCGTTAAATGCACAGCTAGGCCATTAA
131 CCTTTCAGTCAAATACACAGCTAGGCCATTAA
*
70102 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTTTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTTTGTCAAATGC
*
70167 ACAGTTAGGCTATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATAATTGACA
66 ACAGTTAGGCTATTAATCTTTTACTCAAAGGTAGTTAACATTTCATCTAACTGACATAATTGACA
70232 CCTTTCAGTCAAATACACAGCTAGGCCATTAA
131 CCTTTCAGTCAAATACACAGCTAGGCCATTAA
* * * * *
70264 TATTTTACTCAAATGTACTTAACATTTCATCTAACTGGCA-AGATTGTCA-TTTTTCTGTCAAAT
1 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATA-ATTGACACATTTT-TGTCAAAT
70327 GCACAGTTAGGC
64 GCACAGTTAGGC
70339 CTCAAAGGTA
Statistics
Matches: 211, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
161 5 0.02
162 206 0.98
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (162 bp):
TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTTTGTCAAATGC
ACAGTTAGGCTATTAATCTTTTACTCAAAGGTAGTTAACATTTCATCTAACTGACATAATTGACA
CCTTTCAGTCAAATACACAGCTAGGCCATTAA
Found at i:70387 original size:68 final size:68
Alignment explanation
Indices: 70288--70498 Score: 316
Period size: 68 Copynumber: 3.1 Consensus size: 68
70278 GTACTTAACA
* * ** *
70288 TTTCATCTAACTGGCAAGATTGTCATTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGTACTTA
1 TTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
70353 GTC
66 GCC
* *
70356 TTTCATCTGACTGGCATGATTGACACCTTTCTTTCAAA-GACACAGTTAGGCCTCAAAGGCACTT
1 TTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATG-CACAGTTAGGCCTCAAAGGCACTT
70420 AGCC
65 AGCC
* *
70424 TTTTATCTAACTAGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
70489 GCC
66 GCC
70492 TTTCATC
1 TTTCATC
70499 CCATTTTAGC
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
67 1 0.01
68 126 0.98
69 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (68 bp):
TTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
GCC
Found at i:71033 original size:21 final size:21
Alignment explanation
Indices: 71004--71043 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
70994 ATTTTCCCCT
* *
71004 TTTTTTTTAATCCTATATAAC
1 TTTTCTTTAAGCCTATATAAC
*
71025 TTTTCTTTAAGCTTATATA
1 TTTTCTTTAAGCCTATATA
71044 TTACTTAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTCTTTAAGCCTATATAAC
Found at i:71129 original size:178 final size:178
Alignment explanation
Indices: 70830--71177 Score: 680
Period size: 178 Copynumber: 2.0 Consensus size: 178
70820 CATCTCATAG
70830 TTTTAATCCTATATAACTTTTCTTTAAGCTTATATATTACTTAAGGTTACAAGAACTAACCATAA
1 TTTTAATCCTATATAACTTTTCTTTAAGCTTATATATTACTTAAGGTTACAAGAACTAACCATAA
70895 TCAAAAGGAAAAATTGATCAATTCAAGTTTACCTTTGAAGCTACAGAGGAGAGCAAACCCACCGA
66 TCAAAAGGAAAAATTGATCAATTCAAGTTTACCTTTGAAGCTACAGAGGAGAGCAAACCCA-CGA
70960 -AAAGAAGAAGAGGAAGAGATAGTTTCTTTAACTTATTTTCCCCTTTTT
130 GAAAGAAGAAGAGGAAGAGATAGTTTCTTTAACTTATTTTCCCCTTTTT
71008 TTTTAATCCTATATAACTTTTCTTTAAGCTTATATATTACTTAAGGTTACAAGAACTAACCATAA
1 TTTTAATCCTATATAACTTTTCTTTAAGCTTATATATTACTTAAGGTTACAAGAACTAACCATAA
71073 TCAAAAGGAAAAATTGATCAATTCAAGTTTACCTTTGAAGCTACAGAGGAGAGCAAACCCACGAG
66 TCAAAAGGAAAAATTGATCAATTCAAGTTTACCTTTGAAGCTACAGAGGAGAGCAAACCCACGAG
71138 AAAGAAGAAGAGGAAGAGATAGTTTCTTTAACTTATTTTC
131 AAAGAAGAAGAGGAAGAGATAGTTTCTTTAACTTATTTTC
71178 TTAAATCCCT
Statistics
Matches: 169, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
177 3 0.02
178 166 0.98
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (178 bp):
TTTTAATCCTATATAACTTTTCTTTAAGCTTATATATTACTTAAGGTTACAAGAACTAACCATAA
TCAAAAGGAAAAATTGATCAATTCAAGTTTACCTTTGAAGCTACAGAGGAGAGCAAACCCACGAG
AAAGAAGAAGAGGAAGAGATAGTTTCTTTAACTTATTTTCCCCTTTTT
Found at i:72530 original size:31 final size:33
Alignment explanation
Indices: 72494--72579 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
72484 ACATGAATGG
*
72494 TTTTATGA-ACT-TGTGTTTTACTTATAAATTA
1 TTTTATGATACTATGTGTTTTAATTATAAATTA
** *
72525 TTTTATGATTTTATGTGTTTTAATTATAAATTG
1 TTTTATGATACTATGTGTTTTAATTATAAATTA
**
72558 TTTTATG-TTTTATGTGTTTTAA
1 TTTTATGATACTATGTGTTTTAA
72580 CAGAAATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 8 0.16
32 16 0.33
33 25 0.51
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (33 bp):
TTTTATGATACTATGTGTTTTAATTATAAATTA
Found at i:72574 original size:32 final size:33
Alignment explanation
Indices: 72505--72579 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
72495 TTTATGAACT
*
72505 TGTGTTTTACTTATAAATTATTTTATGATTTTA
1 TGTGTTTTAATTATAAATTATTTTATGATTTTA
*
72538 TGTGTTTTAATTATAAATTGTTTTATG-TTTTA
1 TGTGTTTTAATTATAAATTATTTTATGATTTTA
72570 TGTGTTTTAA
1 TGTGTTTTAA
72580 CAGAAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.38
33 25 0.62
ACGTcount: A:0.25, C:0.01, G:0.12, T:0.61
Consensus pattern (33 bp):
TGTGTTTTAATTATAAATTATTTTATGATTTTA
Found at i:73226 original size:19 final size:18
Alignment explanation
Indices: 73187--73227 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
73177 TGTATTTTTC
*
73187 ATTTTAATAAAAATATTA
1 ATTTTAATAAAAATATAA
*
73205 ATTTTAATTAAAATAATAA
1 ATTTTAATAAAAAT-ATAA
73224 ATTT
1 ATTT
73228 ATGATATGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTAATAAAAATATAA
Found at i:74792 original size:109 final size:107
Alignment explanation
Indices: 74665--74919 Score: 273
Period size: 108 Copynumber: 2.3 Consensus size: 107
74655 TACATATGAT
* *
74665 CAAAATGCAAAAACACGCTTAAA-TAAGAGGGATTAAACAGAGAA-TATTCCAATAAATATATAA
1 CAAAATGCAAAAACACGC-TAAACT-AG-GGGACTAAACAGA-AATTAATCCAATAAATATATAA
* ** * *
74728 CATACAAGAAAAGGGGTAAATAACAATTTTGGTCCTCGTAGGTGAC
62 CACACAAGAAAAAAGGTAAATAACAATTTTGGTCCTCGCAGGTAAC
* * *
74774 CAAAATGCAAAAATACGCTAAACCTAGGGGACTAAACATAAATTAATCCAATCAATATATAACAC
1 CAAAATGCAAAAACACGCTAAA-CTAGGGGACTAAACAGAAATTAATCCAATAAATATATAACAC
** * * *
74839 GTATGAAAAAAGGTAAATACCAATTTTGGTCCTTGCAGGTAAC
65 ACAAGAAAAAAGGTAAATAACAATTTTGGTCCTCGCAGGTAAC
*
74882 CAAAATACAAAAACGA-GCTAAACCTAGGGGACTTAAAC
1 CAAAATGCAAAAAC-ACGCTAAA-CTAGGGGAC-TAAAC
74920 TTTATCACCC
Statistics
Matches: 124, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
107 2 0.02
108 96 0.77
109 25 0.20
110 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (107 bp):
CAAAATGCAAAAACACGCTAAACTAGGGGACTAAACAGAAATTAATCCAATAAATATATAACACA
CAAGAAAAAAGGTAAATAACAATTTTGGTCCTCGCAGGTAAC
Found at i:75805 original size:12 final size:12
Alignment explanation
Indices: 75788--75823 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
75778 AGAAAGAAAG
75788 AAGTATAAATAT
1 AAGTATAAATAT
75800 AAGTATAAATAT
1 AAGTATAAATAT
*
75812 AA-AATAAATAT
1 AAGTATAAATAT
75823 A
1 A
75824 TAAAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (12 bp):
AAGTATAAATAT
Found at i:75806 original size:6 final size:6
Alignment explanation
Indices: 75791--75823 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
75781 AAGAAAGAAG
*
75791 TATAAA TATAAG TATAAA TATAAA -ATAAA TATA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATA
75824 TAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (6 bp):
TATAAA
Found at i:76941 original size:69 final size:69
Alignment explanation
Indices: 76826--77519 Score: 739
Period size: 69 Copynumber: 9.9 Consensus size: 69
76816 CTTCAAAGAG
** * * * * * * * *
76826 TTCATGGCCTTTTGAGATAGGTAGTGGTATTGAGGACGGTTCGGGTCGAAATCTTTGAGAAAAAC
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
*
76891 ATTC
66 GTTC
* *
76895 TTCATGGCCTCTTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCTTTGAGAAAAGC
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
76960 GTTC
66 GTTC
* * *** *
76964 TTCATAGCCTCCTGAGATAGATAATGGTACTGGGGACAGTTGATATCAAAATCGTTGAGAAAAGC
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
*
77029 ATTC
66 GTTC
* * * * *
77033 TTCATTGCCTCTTGAGATAGATAATGCTACTGGGGATGGTTGGGGTCAAAATCCTTGAGAAAAGT
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
*
77098 GTTT
66 GTTC
* * * * ** *
77102 TTCATGGCCTCCTGAGATGGATAATGGTATTGGGCACGATTGGGGTCAAAATCCCAGAGAAAAGA
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
*
77167 GTTA
66 GTTC
* * * *
77171 TTCATGG--T-CTCA-TTAGATAATGGTACTGGGGACGGTTGAGATCAAAATCATTGGTCAAAAT
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTC-AAA--A----T------
77232 CCTTGAGAAAAGCGTTC
53 CCTTGAGAAAAGCGTTC
* * * *
77249 TTCATGGTCTCCTTAGATAGATAATGGTACTGGGCACGATTGGGGTCAAAATCCTTGAGAAAAGC
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
77314 GTTC
66 GTTC
* * *
77318 TTCGTGGCCTCCTTAGATAGATAATGGTACTGGGGACGGTTGGGGTTAAAATCCTTGAGAAAAGC
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
77383 GTTC
66 GTTC
* * * *
77387 TTCGTGGCCTCCTGAGATAGATAATGATACTGGGGACGTTTGGGGTCAAAGTCCTTGAGAAAAGC
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
*
77452 ATTC
66 GTTC
* * * ** *
77456 TTCATTGCCTCCTGAGATAGATAATGGTACTAGAGACTATTCGGGTCAAAATCCTTGAGAAAAG
1 TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAG
77520 ATTTATCGGC
Statistics
Matches: 529, Mismatches: 79, Indels: 34
0.82 0.12 0.05
Matches are distributed among these distances:
65 24 0.05
66 6 0.01
67 1 0.00
68 1 0.00
69 441 0.83
72 1 0.00
75 1 0.00
78 20 0.04
79 1 0.00
80 1 0.00
81 6 0.01
82 26 0.05
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (69 bp):
TTCATGGCCTCCTGAGATAGATAATGGTACTGGGGACGGTTGGGGTCAAAATCCTTGAGAAAAGC
GTTC
Found at i:77300 original size:285 final size:285
Alignment explanation
Indices: 76938--77450 Score: 760
Period size: 285 Copynumber: 1.8 Consensus size: 285
76928 GGACGGTTGG
* *
76938 GGTCAAAATCTTTGAGAAAAGCGTTCTTCATAGCCTCCTGAGATAGATAATGGTACTGGGGACAG
1 GGTCAAAATCCTTGAGAAAAGCGTTCTTCATAGCCTCCTGAGATAGATAATGGTACTGGGCACAG
* * *
77003 TTGATATCAAAATCGTTGAGAAAAGCATTCTTCATTGCCT-CTTGAGATAGATAATGCTACTGGG
66 TTGAGATCAAAATCCTTGAGAAAAGCATTCTTCATGGCCTCCTT-AGATAGATAATGCTACTGGG
* * * * * *
77067 GATGGTTGGGGTCAAAATCCTTGAGAAAAGTGTTTTTCATGGCCTCCTGAGATGGATAATGGTAT
130 GACGGTTGGGGTCAAAATCCTTGAGAAAAGCGTTCTTCATGGCCTCCTGAGATAGATAATGATAC
77132 TGGGCACGATTGGGGTCAAAATCCCAGAGAAAAGAGTTATTCATGGTCTCATTAGATAATGGTAC
195 TGGGCACGATTGGGGTCAAAATCCCAGAGAAAAGAGTTATTCATGGTCTCATTAGATAATGGTAC
77197 TGGGGACGGTTGAGATCAAAATCATT
260 TGGGGACGGTTGAGATCAAAATCATT
* * *
77223 GGTCAAAATCCTTGAGAAAAGCGTTCTTCATGGTCTCCTTAGATAGATAATGGTACTGGGCAC-G
1 GGTCAAAATCCTTGAGAAAAGCGTTCTTCATAGCCTCCTGAGATAGATAATGGTACTGGGCACAG
* * * * *
77287 ATTGGGGTCAAAATCCTTGAGAAAAGCGTTCTTCGTGGCCTCCTTAGATAGATAATGGTACTGGG
66 -TTGAGATCAAAATCCTTGAGAAAAGCATTCTTCATGGCCTCCTTAGATAGATAATGCTACTGGG
* *
77352 GACGGTTGGGGTTAAAATCCTTGAGAAAAGCGTTCTTCGTGGCCTCCTGAGATAGATAATGATAC
130 GACGGTTGGGGTCAAAATCCTTGAGAAAAGCGTTCTTCATGGCCTCCTGAGATAGATAATGATAC
* * * **
77417 TGGGGACGTTTGGGGTCAAAGTCCTTGAGAAAAG
195 TGGGCACGATTGGGGTCAAAATCCCAGAGAAAAG
77451 CATTCTTCAT
Statistics
Matches: 200, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
284 1 0.00
285 196 0.98
286 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (285 bp):
GGTCAAAATCCTTGAGAAAAGCGTTCTTCATAGCCTCCTGAGATAGATAATGGTACTGGGCACAG
TTGAGATCAAAATCCTTGAGAAAAGCATTCTTCATGGCCTCCTTAGATAGATAATGCTACTGGGG
ACGGTTGGGGTCAAAATCCTTGAGAAAAGCGTTCTTCATGGCCTCCTGAGATAGATAATGATACT
GGGCACGATTGGGGTCAAAATCCCAGAGAAAAGAGTTATTCATGGTCTCATTAGATAATGGTACT
GGGGACGGTTGAGATCAAAATCATT
Found at i:78353 original size:32 final size:32
Alignment explanation
Indices: 78317--78385 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
78307 TAATTTTTTT
**
78317 AATCAACTAAACTTAATCTGCTAATATTAAAA
1 AATCAACTAAACTTAATAAGCTAATATTAAAA
* *
78349 AATCAGCTAAATTTAATAAGCTAATATTAAAA
1 AATCAACTAAACTTAATAAGCTAATATTAAAA
78381 AATCA
1 AATCA
78386 CATATACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (32 bp):
AATCAACTAAACTTAATAAGCTAATATTAAAA
Found at i:78357 original size:18 final size:18
Alignment explanation
Indices: 78331--78385 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
78321 AACTAAACTT
*
78331 AATCTGCTAATATTAAAA
1 AATCAGCTAATATTAAAA
*
78349 AATCAGCTAA-ATT---T
1 AATCAGCTAATATTAAAA
*
78363 AATAAGCTAATATTAAAA
1 AATCAGCTAATATTAAAA
78381 AATCA
1 AATCA
78386 CATATACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
14 9 0.32
15 3 0.11
17 3 0.11
18 13 0.46
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (18 bp):
AATCAGCTAATATTAAAA
Found at i:78450 original size:2 final size:2
Alignment explanation
Indices: 78445--78469 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78435 GGGGGAAATG
78445 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 A
78470 AACGTGGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78696 original size:27 final size:27
Alignment explanation
Indices: 78664--78716 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
78654 TAACAAGACA
78664 AAGATTTTGTTGTGGAAATTTACAAGT
1 AAGATTTTGTTGTGGAAATTTACAAGT
78691 AAGATTTTGTTGTGGAAATTTACAAG
1 AAGATTTTGTTGTGGAAATTTACAAG
78717 GACTATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.40
Consensus pattern (27 bp):
AAGATTTTGTTGTGGAAATTTACAAGT
Found at i:84308 original size:4 final size:4
Alignment explanation
Indices: 84301--84327 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
84291 ACATGCATGT
84301 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
84328 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:85034 original size:15 final size:15
Alignment explanation
Indices: 84999--85039 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
84989 AATATTAATT
84999 CATTTAAATAATTTG
1 CATTTAAATAATTTG
** *
85014 TGTTTATATAATTTG
1 CATTTAAATAATTTG
85029 CATTTAAATAA
1 CATTTAAATAA
85040 GTTTATTTAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (15 bp):
CATTTAAATAATTTG
Found at i:85859 original size:60 final size:60
Alignment explanation
Indices: 85761--85899 Score: 203
Period size: 60 Copynumber: 2.3 Consensus size: 60
85751 ATTTAAGAGT
*
85761 AAAG-TACACAAATAGTCCCTCGACTATATGGTGATGCTTTGTTGAG-CCCCTCGACTATTA
1 AAAGTTACA-AAATAGTCACTCGACTATATGGTGATGCTTTGTTGAGTCCCC-CGACTATTA
* *
85821 AAAGTTACAAAATAGTCATTCGACTATA-GGATGTTGCTTTGTTGAGTCCCCCGACTATTA
1 AAAGTTACAAAATAGTCACTCGACTATATGG-TGATGCTTTGTTGAGTCCCCCGACTATTA
85881 AAAGTTACAAAATAGTCAC
1 AAAGTTACAAAATAGTCAC
85900 CCAACTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
59 2 0.03
60 62 0.86
61 8 0.11
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (60 bp):
AAAGTTACAAAATAGTCACTCGACTATATGGTGATGCTTTGTTGAGTCCCCCGACTATTA
Found at i:86190 original size:60 final size:60
Alignment explanation
Indices: 86113--86225 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
86103 AATAGTCCAG
* * * *
86113 TGATTATTTTGTAACTTTTAATAGTCGATGAACTTAACAAAGCAACACCCTATTGTCGAA
1 TGATCATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAACAACACCCTATTGTCGAA
* * *
86173 TGATCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAACATCACCCTAT
1 TGATCATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAACAACACCCTAT
86226 AGTCAGAGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (60 bp):
TGATCATTTTGTAACTTTTAATAGTCGAGGAACTCAACAAAACAACACCCTATTGTCGAA
Found at i:87376 original size:14 final size:14
Alignment explanation
Indices: 87359--87396 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
87349 TTTGACCGGT
*
87359 CTGACCCGACCCGA
1 CTGACCCGACCAGA
87373 CTGACCCGACCAGA
1 CTGACCCGACCAGA
*
87387 CCGACCCGAC
1 CTGACCCGAC
87397 TGTTGGCCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.24, C:0.50, G:0.21, T:0.05
Consensus pattern (14 bp):
CTGACCCGACCAGA
Found at i:93891 original size:14 final size:14
Alignment explanation
Indices: 93872--93906 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
93862 TTAAACCGGT
93872 CTGACCCGACCCGA
1 CTGACCCGACCCGA
93886 CTGACCCGACCCGA
1 CTGACCCGACCCGA
*
93900 CCGACCC
1 CTGACCC
93907 AACTGTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.54, G:0.20, T:0.06
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:93922 original size:17 final size:17
Alignment explanation
Indices: 93900--93934 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
93890 CCCGACCCGA
*
93900 CCGACCCAACTGTTGAC
1 CCGACCCAACCGTTGAC
*
93917 CCGACCCGACCGTTGAC
1 CCGACCCAACCGTTGAC
93934 C
1 C
93935 GTTGACCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.46, G:0.20, T:0.14
Consensus pattern (17 bp):
CCGACCCAACCGTTGAC
Found at i:93936 original size:7 final size:7
Alignment explanation
Indices: 93924--93954 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
93914 GACCCGACCC
93924 GACCGTT
1 GACCGTT
93931 GACCGTT
1 GACCGTT
93938 GACCGTT
1 GACCGTT
93945 GACCGTT
1 GACCGTT
93952 GAC
1 GAC
93955 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:104677 original size:6 final size:6
Alignment explanation
Indices: 104666--104779 Score: 90
Period size: 6 Copynumber: 18.8 Consensus size: 6
104656 CATATTATAG
* *
104666 GAAAAA GAAAAA G--AAA -AAAAA GAAAAA GAAAAA GAAGAA GAAGAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
* * * * * *
104711 GAAGAA GAATAA GAATAA GAATAAGAA GAAGAA GAAGAA GAAGAA GAAAAA
1 GAAAAA GAAAAA GAAAAA G-A-AA-AA GAAAAA GAAAAA GAAAAA GAAAAA
*
104762 GAAAATA GAAAAA TAAAA
1 GAAAA-A GAAAAA GAAAA
104780 TAAAAAATAC
Statistics
Matches: 95, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
4 3 0.03
5 3 0.03
6 76 0.80
7 8 0.08
8 2 0.02
9 3 0.03
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:104685 original size:15 final size:15
Alignment explanation
Indices: 104670--104774 Score: 104
Period size: 15 Copynumber: 6.9 Consensus size: 15
104660 TTATAGGAAA
*
104670 AAGAAAAAGAAAAAA
1 AAGAAAAAGAAAAAG
104685 AAGAAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
* *
104700 AAGAAGAAGAAGAAG
1 AAGAAAAAGAAAAAG
* *
104715 AAGAATAAGAATAAG
1 AAGAAAAAGAAAAAG
* * *
104730 AATAAGAAGAAGAAG
1 AAGAAAAAGAAAAAG
*
104745 AAGAAGAAGAAGAAA-
1 AAGAAAAAGAA-AAAG
104760 AAGAAAATAGAAAAA
1 AAGAAAA-AGAAAAA
104775 TAAAATAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
15 71 0.92
16 6 0.08
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (15 bp):
AAGAAAAAGAAAAAG
Found at i:104687 original size:9 final size:9
Alignment explanation
Indices: 104670--104764 Score: 82
Period size: 9 Copynumber: 10.2 Consensus size: 9
104660 TTATAGGAAA
104670 AAGAAAAAG
1 AAGAAAAAG
*
104679 AAAAAAAAG
1 AAGAAAAAG
104688 AAAAAGAAAAAG
1 ---AAGAAAAAG
*
104700 AAGAAGAAG
1 AAGAAAAAG
*
104709 AAGAAGAAG
1 AAGAAAAAG
* * *
104718 AATAAGAAT
1 AAGAAAAAG
*
104727 AAGAATAAG
1 AAGAAAAAG
*
104736 AAGAAGAAG
1 AAGAAAAAG
*
104745 AAGAAGAAG
1 AAGAAAAAG
104754 AAGAAAAAG
1 AAGAAAAAG
104763 AA
1 AA
104765 AATAGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
9 65 0.89
12 8 0.11
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:104780 original size:13 final size:12
Alignment explanation
Indices: 104757--104802 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 12
104747 GAAGAAGAAG
*
104757 AAAAAGAAAATA
1 AAAAATAAAATA
104769 GAAAAATAAAATA
1 -AAAAATAAAATA
104782 AAAAATACAAATA
1 AAAAATA-AAATA
104795 AAAAATAA
1 AAAAATAA
104803 TAATGAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:104788 original size:20 final size:20
Alignment explanation
Indices: 104763--104802 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
104753 GAAGAAAAAG
*
104763 AAAATAGAAA-AATAAAATAA
1 AAAATACAAATAA-AAAATAA
104783 AAAATACAAATAAAAAATAA
1 AAAATACAAATAAAAAATAA
104803 TAATGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (20 bp):
AAAATACAAATAAAAAATAA
Found at i:108169 original size:40 final size:40
Alignment explanation
Indices: 108124--108204 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
108114 TACAGTGTAC
* *
108124 TAGGTGGGTAAAT-ATCGACCTCAGCACTACGGTGCATTAT
1 TAGGTGAG-AAATGATCGACCTCAGCACTACGGTGCAATAT
** * *
108164 TAGGTGAGCCATGCTCGACCTCAGCACTTCGGTGCAATAT
1 TAGGTGAGAAATGATCGACCTCAGCACTACGGTGCAATAT
108204 T
1 T
108205 TGACTCTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (40 bp):
TAGGTGAGAAATGATCGACCTCAGCACTACGGTGCAATAT
Found at i:108352 original size:24 final size:24
Alignment explanation
Indices: 108324--108441 Score: 63
Period size: 24 Copynumber: 5.2 Consensus size: 24
108314 GTAAGTATAT
108324 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
* * ** *
108348 TGGTACAAAT--GGTAATTA--TTT
1 TGGTA-AAATAAGCTTACGAGCTTA
*
108369 TGGTAAAATAAGCTTACAAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
* * ** *
108393 TGGTACAAAT--GGTAATTA--TTT
1 TGGTA-AAATAAGCTTACGAGCTTA
108414 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
108438 TGGT
1 TGGT
108442 TAATAAATGG
Statistics
Matches: 64, Mismatches: 20, Indels: 20
0.62 0.19 0.19
Matches are distributed among these distances:
20 8 0.12
21 14 0.22
22 8 0.12
23 8 0.12
24 18 0.28
25 8 0.12
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (24 bp):
TGGTAAAATAAGCTTACGAGCTTA
Found at i:108374 original size:45 final size:45
Alignment explanation
Indices: 108285--108441 Score: 264
Period size: 45 Copynumber: 3.5 Consensus size: 45
108275 GTAAGCATAC
* *
108285 AAATAAGCTTACGAGCTTATGG-A-ATAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTACA-AATGGTAATTATTTTGGTA
108329 AAATAAGCTTACGAGCTTATGGTACAAATGGTAATTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGTACAAATGGTAATTATTTTGGTA
*
108374 AAATAAGCTTACAAGCTTATGGTACAAATGGTAATTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGTACAAATGGTAATTATTTTGGTA
108419 AAATAAGCTTACGAGCTTATGGT
1 AAATAAGCTTACGAGCTTATGGT
108442 TAATAAATGG
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
44 22 0.21
45 84 0.79
46 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGTACAAATGGTAATTATTTTGGTA
Found at i:108923 original size:7 final size:7
Alignment explanation
Indices: 108911--108941 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
108901 ACCGATACCC
108911 TCACTAT
1 TCACTAT
108918 TCACTAT
1 TCACTAT
108925 TCACTAT
1 TCACTAT
108932 TCACTAT
1 TCACTAT
108939 TCA
1 TCA
108942 TAAAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (7 bp):
TCACTAT
Found at i:111859 original size:42 final size:42
Alignment explanation
Indices: 111812--111965 Score: 184
Period size: 42 Copynumber: 3.7 Consensus size: 42
111802 TAGTAAGTGC
* *
111812 CATCAGTAAGTCTTTCGAGCATGATGATTGAGTCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTGAATCATTCGGGT
* *
111854 CATCAGTAAGCCTTTCGAGCATGATGATTAAATCATTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTGAATCATTCGGGT
** * * *
111896 CATTTGTAAGTCTTTCGAGCGTGATGA-TGAAATAATTCAGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTG-AATCATTCGGGT
** *
111938 CATTTGTAAGTCTTTCGAGCAAGATGAT
1 CATCAGTAAGTCTTTCGAGCATGATGAT
111966 AAGTCCTCCA
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
41 1 0.01
42 96 0.99
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTGAATCATTCGGGT
Found at i:115258 original size:19 final size:19
Alignment explanation
Indices: 115234--115283 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
115224 CATAAAATCC
115234 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
*
115253 GAGTGCATCGGTGCATGGA
1 GAGTGCATCGATGCATGGA
115272 -A-TGCATTCGATG
1 GAGTGCA-TCGATG
115284 TTCAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (19 bp):
GAGTGCATCGATGCATGGA
Found at i:115261 original size:65 final size:65
Alignment explanation
Indices: 115127--115285 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 65
115117 GCACTAAGAA
* * * ***
115127 TGCATCGATGCATGAAGTGCATTCGATG--TTTGAAAAATAGCCTAGTGCATCGATGCATGGCTT
1 TGCATCGATGCATGAAATGCATTCGATGTTTTTCAAAAATA-CCGAGTGCATCGATGCATGGAGA
115190 G
65 G
* *
115191 TGCATCGTTGCATCAAATGCATTCGATGTTTTTCATAAAAT-CCGAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTTCA-AAAATACCGAGTGCATCGATGCATGGAGA
115255 G
65 G
* *
115256 TGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGAAATGCATTCGATGTT
115286 CAATTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 25 0.31
65 47 0.58
66 4 0.05
67 5 0.06
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTTCAAAAATACCGAGTGCATCGATGCATGGAGAG
Found at i:115321 original size:20 final size:20
Alignment explanation
Indices: 115296--115333 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
115286 CAATTTATTC
115296 ATTGATGCATCGATGCATTG
1 ATTGATGCATCGATGCATTG
*
115316 ATTGATGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
115334 GCGTCTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
ATTGATGCATCGATGCATTG
Found at i:115697 original size:28 final size:28
Alignment explanation
Indices: 115657--115712 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
115647 TTTGAAATAA
115657 AAAAAATTACTCCCCCTTACTATGACAC
1 AAAAAATTACTCCCCCTTACTATGACAC
115685 AAAAAATTACTCCCCCTTACTATGACAC
1 AAAAAATTACTCCCCCTTACTATGACAC
115713 GCATCTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.32, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAAAATTACTCCCCCTTACTATGACAC
Found at i:118043 original size:45 final size:44
Alignment explanation
Indices: 117950--118044 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 44
117940 GGACTTATGC
* * * *
117950 ATCGATGCATATTCAAGGCATGCATCGGTGCATCATGCTCATGC
1 ATCGATACATATTCAAGGCATGCATCGATGCATCATGCTAATGA
*
117994 ATCGATACATATTCAAAGGGATGCATCGATGCA-C-TGCTTAAGTGA
1 ATCGATACATATTC-AAGGCATGCATCGATGCATCATGC-TAA-TGA
118039 ATCGAT
1 ATCGAT
118045 GCATGAAGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
43 3 0.07
44 16 0.37
45 24 0.56
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCGATACATATTCAAGGCATGCATCGATGCATCATGCTAATGA
Found at i:123972 original size:19 final size:18
Alignment explanation
Indices: 123948--123996 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
123938 CATAAAATCC
123948 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGC-TGGA
*
123967 GAGTGCATCGGTGCTGGA
1 GAGTGCATCGATGCTGGA
123985 -A-TGCATTCGATG
1 GAGTGCA-TCGATG
123997 TTCAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
18 4 0.15
19 13 0.48
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.24
Consensus pattern (18 bp):
GAGTGCATCGATGCTGGA
Found at i:124045 original size:20 final size:20
Alignment explanation
Indices: 124009--124047 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
123999 CAATTTATTC
*
124009 ATTGATGCATCGATGCATGG
1 ATTGATGCATAGATGCATGG
124029 ATTGATGCATTAG-TGCATG
1 ATTGATGCA-TAGATGCATG
124048 CATCTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
ATTGATGCATAGATGCATGG
Found at i:125703 original size:60 final size:59
Alignment explanation
Indices: 125592--125703 Score: 134
Period size: 60 Copynumber: 1.9 Consensus size: 59
125582 ATAGTCGGGT
* * **
125592 GACCATTTTGTAACTTTAAATAGTCAGGAACTCAATAAAGCAGTGCACTATAAATGAGG
1 GACCATTTTGTAACTTTAAATAGTCAGAAACTCAACAAAGCAACGCACTATAAATGAGG
* * * * *
125651 GACCATTTTTTATCTTTTAATAGTTGAGAAACTCAACAAAGCAACGCTCTATA
1 GACCATTTTGTAACTTTAAATAG-TCAGAAACTCAACAAAGCAACGCACTATA
125704 GTCGGGAAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 20 0.47
60 23 0.53
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (59 bp):
GACCATTTTGTAACTTTAAATAGTCAGAAACTCAACAAAGCAACGCACTATAAATGAGG
Found at i:142146 original size:21 final size:21
Alignment explanation
Indices: 142117--142157 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
142107 TGCTTGAAGA
142117 AAAAAAAAAGAAGAAAAAAAT
1 AAAAAAAAAGAAGAAAAAAAT
* * *
142138 AAAATAAAATAATAAAAAAA
1 AAAAAAAAAGAAGAAAAAAA
142158 GTTCAAGATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAAAAAAAGAAGAAAAAAAT
Found at i:143436 original size:20 final size:20
Alignment explanation
Indices: 143373--143437 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
143363 TCAATTGAAA
143373 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
143393 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
143412 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
143432 TGTTCA
1 AGTTCA
143438 ACCTTTTGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:144509 original size:30 final size:30
Alignment explanation
Indices: 144430--144512 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
144420 CCCGAAGGAC
* *
144430 CTATCCAGAGGTTACAAAG-ACCCCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
*
144459 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* * *
144489 CTATCCATAGGTCCCGAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
144513 AGGTAAACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 17 0.37
30 29 0.63
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:145787 original size:20 final size:22
Alignment explanation
Indices: 145762--145819 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
145752 TTCCCCTTGA
145762 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
145782 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
145805 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
145820 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:153232 original size:3 final size:3
Alignment explanation
Indices: 153224--153248 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
153214 CCGTTAACCC
153224 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
153249 AAGAGCTTAA
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:169600 original size:20 final size:20
Alignment explanation
Indices: 169564--169601 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
169554 CGAAGCAGTT
*
169564 GTTACACACTTCCGAATCTA
1 GTTACACACTTCAGAATCTA
169584 GTTACACCACTT-AGAATC
1 GTTACA-CACTTCAGAATC
169602 GAACCCCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (20 bp):
GTTACACACTTCAGAATCTA
Found at i:173856 original size:26 final size:26
Alignment explanation
Indices: 173827--173876 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
173817 GCTGAGTTGC
*
173827 TTACAACATTAGAATCTTACTAGGAT
1 TTACAACATTAGAATCCTACTAGGAT
*
173853 TTACAACATTAGAGTCCTACTAGG
1 TTACAACATTAGAATCCTACTAGG
173877 TGTTTACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (26 bp):
TTACAACATTAGAATCCTACTAGGAT
Found at i:175046 original size:12 final size:12
Alignment explanation
Indices: 175029--175075 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
175019 GATACGATAT
175029 TGAGAGAGAGTA
1 TGAGAGAGAGTA
*
175041 TGAGAGAGAGTG
1 TGAGAGAGAGTA
*
175053 TTAGAGAGAG-A
1 TGAGAGAGAGTA
175064 GTGAGAGAGAGT
1 -TGAGAGAGAGT
175076 CGTAAAGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.17
Consensus pattern (12 bp):
TGAGAGAGAGTA
Found at i:185973 original size:7 final size:7
Alignment explanation
Indices: 185958--185992 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
185948 GTTCTTTCGC
185958 GGCGGGG
1 GGCGGGG
185965 GG-GGGG
1 GGCGGGG
185971 GG-GGGG
1 GGCGGGG
185977 GGCGGGG
1 GGCGGGG
185984 GGCGGGG
1 GGCGGGG
185991 GG
1 GG
185993 AACACTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.00, C:0.09, G:0.91, T:0.00
Consensus pattern (7 bp):
GGCGGGG
Found at i:186476 original size:24 final size:24
Alignment explanation
Indices: 186449--186527 Score: 149
Period size: 24 Copynumber: 3.3 Consensus size: 24
186439 CTTAAAGATC
186449 ATAAATTTAATTGTTATAAATGAA
1 ATAAATTTAATTGTTATAAATGAA
186473 ATAAATTTAATTGTTATAAATGAA
1 ATAAATTTAATTGTTATAAATGAA
*
186497 GTAAATTTAATTGTTATAAATGAA
1 ATAAATTTAATTGTTATAAATGAA
186521 ATAAATT
1 ATAAATT
186528 ATGTTAGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (24 bp):
ATAAATTTAATTGTTATAAATGAA
Found at i:197157 original size:21 final size:20
Alignment explanation
Indices: 197071--197228 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
197061 AAATGACCAA
**
197071 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
197090 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
197110 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
197130 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
197151 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* ** *
197172 CAAATTCGCATTGCGGTTTT
1 CAAAATCGCAACGCGATTTT
* *
197192 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
197213 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
197229 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:197219 original size:20 final size:20
Alignment explanation
Indices: 197195--197444 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
197185 CGGTTTTCCA
** *
197195 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
197215 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
197235 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
197255 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
197275 AAATCGCAACGC-ATATGGGT
1 AAATCGCAACGCGA-ATCCGT
* *
197295 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
197315 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
197335 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
197355 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
197375 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
197395 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
197415 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
197435 AAATCACAAC
1 AAATCGCAAC
197445 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:198166 original size:24 final size:24
Alignment explanation
Indices: 198127--198173 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
198117 AAATTTGGTC
198127 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
198151 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
198174 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:198364 original size:12 final size:12
Alignment explanation
Indices: 198347--198371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
198337 ATATAATCCT
198347 GAAGAAGAAAAA
1 GAAGAAGAAAAA
198359 GAAGAAGAAAAA
1 GAAGAAGAAAAA
198371 G
1 G
198372 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:199710 original size:19 final size:19
Alignment explanation
Indices: 199670--199767 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
199660 GATTCTCTCG
199670 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
199690 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
199709 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
199723 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
199742 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
199761 TTGCGAT
1 TTGCGAT
199768 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:199764 original size:52 final size:53
Alignment explanation
Indices: 199651--199767 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
199641 GAAATGAAAA
199651 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
199704 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
199756 TCGCATTGCGAT
1 TCGCATTGCGAT
199768 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:199863 original size:14 final size:14
Alignment explanation
Indices: 199844--199898 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
199834 CGGAAATGAA
199844 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
199858 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
199877 AATCGCAACGAGAG
1 AATCGCAACGAGAG
199891 AATCGCAA
1 AATCGCAA
199899 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:199878 original size:33 final size:33
Alignment explanation
Indices: 199826--199916 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
199816 CCATTACATT
199826 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
199860 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
199893 TCGCAATGCGAAATG-AAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
199917 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
32 9 0.16
33 39 0.68
34 9 0.16
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:199916 original size:51 final size:52
Alignment explanation
Indices: 199858--199973 Score: 198
Period size: 51 Copynumber: 2.2 Consensus size: 52
199848 GCAACGAGAG
*
199858 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAA-TGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
*
199909 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
*
199961 AATCGCATTGCGA
1 AATCGCAATGCGA
199974 TTCTCCCATT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
51 47 0.77
52 14 0.23
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
Found at i:200022 original size:19 final size:19
Alignment explanation
Indices: 199980--200079 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
199970 GCGATTCTCC
199980 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
200000 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
200019 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
200035 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
200052 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
200071 CATTGCGAT
1 CATTGCGAT
200080 AGTCAATTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:200076 original size:52 final size:53
Alignment explanation
Indices: 199963--200079 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
199953 GAAATTAAAA
199963 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
200016 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
200068 TCGCATTGCGAT
1 TCGCATTGCGAT
200080 AGTCAATTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:200204 original size:14 final size:14
Alignment explanation
Indices: 200185--200221 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
200175 CATCAATTAC
200185 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
200199 ACAAATCATCTTTT
1 ACAAATCAACTTTT
200213 ACAAATCAA
1 ACAAATCAA
200222 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:202218 original size:14 final size:14
Alignment explanation
Indices: 202199--202255 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
202189 GCGAAATGAA
*
202199 AATCGCAACGACAG
1 AATCGCAACGAAAG
202213 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
202230 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
202246 AATCGCAACG
1 AATCGCAACG
202256 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:202226 original size:33 final size:33
Alignment explanation
Indices: 202180--202272 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
202170 GCGAAACCAA
*
202180 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
202213 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
202246 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
202273 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:202237 original size:19 final size:19
Alignment explanation
Indices: 202143--202277 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
202133 TAGTTTACTT
* *
202143 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
202163 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
202182 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
202201 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
202215 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
202234 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
202248 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
202267 TCGCAATGCGA
1 TCGCAACGCGA
202278 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:202295 original size:19 final size:18
Alignment explanation
Indices: 202273--202382 Score: 83
Period size: 19 Copynumber: 6.3 Consensus size: 18
202263 AAAATCGCAA
202273 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
202292 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
202306 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
202325 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
202339 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
202358 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
202378 TGCGA
1 TGCGA
202383 AAGTAAACTA
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 22 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 31 0.43
20 12 0.17
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:202315 original size:33 final size:33
Alignment explanation
Indices: 202273--202364 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
202263 AAAATCGCAA
202273 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
202306 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
202339 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
202365 TTAAGTTTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:202585 original size:93 final size:93
Alignment explanation
Indices: 202426--202899 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
202416 TTGAATGGAT
202426 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
202491 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
202519 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
202584 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
202612 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
202677 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
202705 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
202770 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
202798 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
202863 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
202891 AAATTTACT
1 AAATTTACT
202900 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:204626 original size:14 final size:14
Alignment explanation
Indices: 204607--204696 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
204597 TTGAAATGAA
204607 AATCGCAACGAGAG
1 AATCGCAACGAGAG
204621 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
204638 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
204654 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
204673 AATCGCAACGAGAG
1 AATCGCAACGAGAG
204687 AATCGCAACG
1 AATCGCAACG
204697 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:204644 original size:33 final size:33
Alignment explanation
Indices: 204599--204713 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
204589 TCTTTTGGTT
204599 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
204632 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
204665 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
204698 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
204714 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:204645 original size:19 final size:18
Alignment explanation
Indices: 204606--204718 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
204596 GTTGAAATGA
204606 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
204621 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
204638 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
204654 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
204671 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
204687 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
204704 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
204719 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:204749 original size:14 final size:14
Alignment explanation
Indices: 204730--204785 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
204720 TTTGGTTTCG
204730 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
204744 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
204762 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
204776 CGTTGCGATT
1 CGTTGCGATT
204786 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 20 0.56
15 3 0.08
17 3 0.08
18 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:204764 original size:32 final size:33
Alignment explanation
Indices: 204725--204793 Score: 131
Period size: 32 Copynumber: 2.1 Consensus size: 33
204715 GCGATTTTGG
204725 TTTCGCGTTGCGATTCTCTCGTTGCGATT-TCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
204757 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
204790 TTTC
1 TTTC
204794 TCTCGTTGCG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 29 0.81
33 7 0.19
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
Found at i:204796 original size:21 final size:20
Alignment explanation
Indices: 204769--204844 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
204759 TCGCGTTGCG
204769 ATTCTCTCGTTGCGATTGTC
1 ATTCTCTCGTTGCGATTGTC
**
204789 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTGTC
*
204810 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTGTC
*
204830 ATTATCTCGTTGCGA
1 ATTCTCTCGTTGCGA
204845 CTCTTCTGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 31 0.63
21 18 0.37
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTGTC
Found at i:204814 original size:41 final size:40
Alignment explanation
Indices: 204769--204845 Score: 127
Period size: 41 Copynumber: 1.9 Consensus size: 40
204759 TCGCGTTGCG
*
204769 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCA-TTATCTCGTTGCGACAGTC
*
204810 ATTCTCTCGTTGCGATTTTCATTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTATCTCGTTGCGAC
204846 TCTTCTGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 14 0.41
41 20 0.59
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.43
Consensus pattern (40 bp):
ATTCTCTCGTTGCGATTGTCATTATCTCGTTGCGACAGTC
Found at i:204971 original size:33 final size:33
Alignment explanation
Indices: 204924--204994 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
204914 AATACTAACT
* *
204924 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
204957 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
204990 TGAAA
1 TGAAA
204995 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:205228 original size:22 final size:22
Alignment explanation
Indices: 205176--205230 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
205166 TGGTTGTGAG
**
205176 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
205198 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
205220 GGATTTCTTCG
1 GGATTTCTTCG
205231 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:205396 original size:39 final size:40
Alignment explanation
Indices: 205353--205434 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
205343 TACGCGTAGC
*
205353 GATTATAATGGCGTTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
205392 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
205432 GAT
1 GAT
205435 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:205403 original size:20 final size:20
Alignment explanation
Indices: 205376--205568 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
205366 TTTTAAATAT
205376 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
205397 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
205416 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
205436 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
205456 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
205476 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
205496 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
205516 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
205536 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
205556 CGCGTTGCGATTT
1 CGCGTTGCGATTT
205569 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:205562 original size:60 final size:60
Alignment explanation
Indices: 205375--205690 Score: 200
Period size: 60 Copynumber: 5.2 Consensus size: 60
205365 GTTTTAAATA
* * * **
205375 TCGCGTTGCGATTTACGGATTATCG--TTGCGATTTACAG-ATTCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGA-TA-CGCATTGCGATTTA-TGTATTCGCGTTGCGATTTTCATAT
* * *** * * **
205435 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * *
205495 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * * * *
205555 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TGTACTATCGCATTGCGATTTTCAATAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-ATAT
* * ** * *
205618 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTAT-T
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCATAT
205677 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
205691 TGTTGGTCAT
Statistics
Matches: 210, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
58 2 0.01
59 18 0.09
60 115 0.55
61 27 0.13
62 25 0.12
63 21 0.10
64 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
Found at i:205585 original size:21 final size:21
Alignment explanation
Indices: 205555--205637 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
205545 ATTTTCATAT
*
205555 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
205576 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
205597 TCGCATTGCGATTTT-CAATAA
1 TCGCATTGCGATTTTGGAA-AA
*
205618 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
205638 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:205628 original size:42 final size:43
Alignment explanation
Indices: 205535--205633 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
205525 ATTTATGTGT
* *
205535 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
205576 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAATAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
205618 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
205634 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:213041 original size:16 final size:17
Alignment explanation
Indices: 213010--213042 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
213000 GCTGATTCGA
*
213010 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
213027 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
213043 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Found at i:216420 original size:18 final size:19
Alignment explanation
Indices: 216378--216417 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
216368 TTTGGTTCAC
* *
216378 GGAACGTAAGATTATCAGTG
1 GGAATGTAAGATTACCAG-G
216398 GGAATGTAAGATTACCAGG
1 GGAATGTAAGATTACCAGG
216417 G
1 G
216418 AATATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.35, C:0.10, G:0.33, T:0.23
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Done.