Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 15
Found at i:2463288 original size:22 final size:22
Alignment explanation
Indices: 2463214--2463280 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
2463204 TTATGGACAA
2463214 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2463236 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2463258 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2463280 A
1 A
2463281 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:2468955 original size:3 final size:3
Alignment explanation
Indices: 2468947--2468974 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2468937 AGAAACCCTG
2468947 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
2468975 AAAAGGGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:2469607 original size:31 final size:31
Alignment explanation
Indices: 2469572--2469667 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
2469562 ATTTTGATCG
* *
2469572 AATTTAATGATTAAATTGATATTTTATTTAA
1 AATTTAATGATTAAAATAATATTTTATTTAA
*
2469603 AATTTAAAGATTAAAATAATA-TTTATTTTAA
1 AATTTAATGATTAAAATAATATTTTA-TTTAA
* * * *
2469634 AATTCAAT-ATCAAACTAATATTTTATCTAA
1 AATTTAATGATTAAAATAATATTTTATTTAA
2469664 AATT
1 AATT
2469668 AAGAATCATA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 22 0.40
31 33 0.60
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (31 bp):
AATTTAATGATTAAAATAATATTTTATTTAA
Found at i:2469665 original size:30 final size:30
Alignment explanation
Indices: 2469590--2469669 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
2469580 GATTAAATTG
*
2469590 ATATTTTATTTAAAATTTAAAGATTAAAATA
1 ATATTTTATTTAAAA-TTAAAGATCAAAATA
* * *
2469621 ATA-TTTATTTTAAAATTCAATATCAAACTA
1 ATATTTTA-TTTAAAATTAAAGATCAAAATA
*
2469651 ATATTTTATCTAAAATTAA
1 ATATTTTATTTAAAATTAA
2469670 GAATCATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 27 0.66
31 14 0.34
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (30 bp):
ATATTTTATTTAAAATTAAAGATCAAAATA
Found at i:2478226 original size:31 final size:31
Alignment explanation
Indices: 2478190--2478262 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
2478180 ACATGTTATG
2478190 TGTCAC-TCACTTAAAATAATGATATGACATA
1 TGTCACATCA-TTAAAATAATGATATGACATA
* * * *
2478221 TGTCACATCATTAAAGTCATTATATGATATA
1 TGTCACATCATTAAAATAATGATATGACATA
* *
2478252 TGCCATATCAT
1 TGTCACATCAT
2478263 CCTAAAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (31 bp):
TGTCACATCATTAAAATAATGATATGACATA
Found at i:2478289 original size:21 final size:21
Alignment explanation
Indices: 2478265--2478305 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2478255 CATATCATCC
* *
2478265 TAAAGTAATGACATAGCATGA
1 TAAAATAATGACATAACATGA
*
2478286 TAAAATAATTACATAACATG
1 TAAAATAATGACATAACATG
2478306 TGTCACATCT
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:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (21 bp):
TAAAATAATGACATAACATGA
Found at i:2479153 original size:20 final size:19
Alignment explanation
Indices: 2479108--2479156 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2479098 CGCAAAACAA
*
2479108 AAGTCAAATTCGCAACGCG
1 AAGTCAAATTCGCAACACG
* *
2479127 ATGGTCAAATTCGTAACACGG
1 A-AGTCAAATTCGCAACAC-G
2479148 AAGTCAAAT
1 AAGTCAAAT
2479157 GTTTTTATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
AAGTCAAATTCGCAACACG
Found at i:2479309 original size:22 final size:22
Alignment explanation
Indices: 2479284--2479334 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2479274 CTACGGCGAC
2479284 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
2479306 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
2479328 ATCCGTC
1 ATCCGTC
2479335 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:2479696 original size:20 final size:20
Alignment explanation
Indices: 2479622--2479685 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
2479612 CAACGCGGAC
2479622 GCGATTTTCAATTTT-GCGTT
1 GCGATTTTC-ATTTTCGCGTT
*
2479642 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
2479662 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
2479682 GCGA
1 GCGA
2479686 ATTTAAGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.12
20 36 0.88
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:2481414 original size:21 final size:21
Alignment explanation
Indices: 2481390--2481435 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2481380 GTTAGGGGAA
* *
2481390 TTACATGATGAGGTCAGTGCT
1 TTACATCATGAGGTCAGTACT
* *
2481411 TTACGTCATGAGGTCGGTACT
1 TTACATCATGAGGTCAGTACT
2481432 TTAC
1 TTAC
2481436 GTGAAGATAT
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:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (21 bp):
TTACATCATGAGGTCAGTACT
Found at i:2481436 original size:21 final size:21
Alignment explanation
Indices: 2481397--2481437 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2481387 GAATTACATG
*
2481397 ATGAGGTCAGTGCTTTACGTC
1 ATGAGGTCAGTACTTTACGTC
*
2481418 ATGAGGTCGGTACTTTACGT
1 ATGAGGTCAGTACTTTACGT
2481438 GAAGATATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (21 bp):
ATGAGGTCAGTACTTTACGTC
Found at i:2481663 original size:4 final size:4
Alignment explanation
Indices: 2481654--2481695 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
2481644 TTTTTCGACA
* * *
2481654 TTAT TTAT TTAT TTAT TTAT TGAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2481696 TTAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:2481931 original size:21 final size:21
Alignment explanation
Indices: 2481862--2481933 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
2481852 GACGTCTCCT
2481862 ATCGTTCAAGAGGCCCCTCTC
1 ATCGTTCAAGAGGCCCCTCTC
* * *
2481883 ATC-ATCGAAGAAGCCCCTCCC
1 ATCGTTC-AAGAGGCCCCTCTC
*
2481904 A-CAGTTCAAGAGGCCCCTGTC
1 ATC-GTTCAAGAGGCCCCTCTC
2481925 ATCGTTCAA
1 ATCGTTCAA
2481934 CTGGTCTCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
20 3 0.08
21 34 0.85
22 3 0.08
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCTC
Found at i:2482902 original size:14 final size:14
Alignment explanation
Indices: 2482883--2482922 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2482873 TTTTGATTAA
2482883 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
2482897 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
2482911 TTGATTTGTAAA
1 TTGATTTGTAAA
2482923 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2482933 original size:61 final size:62
Alignment explanation
Indices: 2482833--2482972 Score: 176
Period size: 66 Copynumber: 2.2 Consensus size: 62
2482823 TTTTATATTG
* *
2482833 AAAGTTGATTTATTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
** * *
2482893 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
2482958 A
62 A
2482959 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
2482973 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 16 0.24
61 17 0.25
64 4 0.06
66 31 0.46
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:2483327 original size:39 final size:39
Alignment explanation
Indices: 2483272--2483354 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
2483262 TCAAGTTGTA
*
2483272 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* * *
2483311 GATTTGGATTTTCTTTTGTTTGGCACCATATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
2483350 GATTT
1 GATTT
2483355 TGATGAGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.17, C:0.13, G:0.22, T:0.48
Consensus pattern (39 bp):
GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:2483658 original size:18 final size:18
Alignment explanation
Indices: 2483635--2483671 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2483625 CAAAATTTAT
2483635 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2483653 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2483671 A
1 A
2483672 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2484092 original size:25 final size:25
Alignment explanation
Indices: 2484058--2484107 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2484048 ATTATTTTTC
* *
2484058 CAAATAATGTACTCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2484083 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2484108 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2484198 original size:20 final size:20
Alignment explanation
Indices: 2484173--2484239 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
2484163 TGTTGAAGGT
2484173 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
* * * *
2484193 AAATTCACTATGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
2484213 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
2484233 AAATTCG
1 AAATTCG
2484240 ATTTGCGATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:2484247 original size:20 final size:20
Alignment explanation
Indices: 2484184--2484247 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2484174 AATTCGCAAC
2484184 GCGAAAGTCAAATTC-ACTAT
1 GCGAAAGTCAAATTCGA-TAT
* *
2484204 GCGATAGTCAAATTCGCA-AC
1 GCGAAAGTCAAATTCG-ATAT
*
2484224 GCGAAAGTCAAATTCGATTT
1 GCGAAAGTCAAATTCGATAT
2484244 GCGA
1 GCGA
2484248 TTTCGCGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
22 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGATAT
Found at i:2484275 original size:20 final size:20
Alignment explanation
Indices: 2484250--2484313 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
2484240 ATTTGCGATT
2484250 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
2484270 TCGCGTTGTGAATTT-ATCTT
1 TCGCGTTGCGAATTTGA-CTA
2484290 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
2484310 TCGC
1 TCGC
2484314 AACGCTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:2484351 original size:20 final size:20
Alignment explanation
Indices: 2484322--2484366 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2484312 GCAACGCTTA
*
2484322 TTTCGTGTTGCAAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
*
2484342 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
2484362 TTTCG
1 TTTCG
2484367 TATTGATCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTGAC
Found at i:2484680 original size:18 final size:18
Alignment explanation
Indices: 2484657--2484692 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2484647 AAGCCGGTTG
*
2484657 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2484675 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2484693 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2489129 original size:24 final size:24
Alignment explanation
Indices: 2489095--2489148 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2489085 CCATCACATC
2489095 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2489119 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2489143 ATCAAA
1 ATCAAA
2489149 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2490076 original size:20 final size:20
Alignment explanation
Indices: 2490040--2490189 Score: 114
Period size: 19 Copynumber: 7.6 Consensus size: 20
2490030 ACTAAAACCT
*
2490040 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
2490059 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
**
2490078 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
*
2490098 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
*** *
2490118 AACGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
**
2490139 AATGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
*
2490159 GTTGCGAATTTGAGA-TCGC
1 GTTGCGAATTTGAAATTCGC
2490178 GTTGCGAATTTG
1 GTTGCGAATTTG
2490190 TTGGTCATTT
Statistics
Matches: 105, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
18 1 0.01
19 44 0.42
20 44 0.42
21 14 0.13
22 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:2491397 original size:12 final size:12
Alignment explanation
Indices: 2491370--2491447 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 12
2491360 TTTAATGAAA
*
2491370 ATATTTTTATAGT
1 ATATTTTT-TAAT
2491383 ATATTTTTTAAT
1 ATATTTTTTAAT
*
2491395 ATATTTTCTAA-
1 ATATTTTTTAAT
* * *
2491406 AAATGTATT-AT
1 ATATTTTTTAAT
* *
2491417 CTATTTTGTAAT
1 ATATTTTTTAAT
*
2491429 ATGTTTTTTAAT
1 ATATTTTTTAAT
2491441 ATTATTT
1 A-TATTT
2491448 GACGTTACTT
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
10 1 0.02
11 9 0.19
12 25 0.53
13 12 0.26
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (12 bp):
ATATTTTTTAAT
Found at i:2491473 original size:16 final size:17
Alignment explanation
Indices: 2491442--2491474 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2491432 TTTTTTAATA
2491442 TTATTTGACGTTACTTTT
1 TTATTTGAC-TTACTTTT
2491460 TTATTTGA-TTACTTT
1 TTATTTGACTTACTTT
2491475 GTTAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (17 bp):
TTATTTGACTTACTTTT
Found at i:2492078 original size:20 final size:20
Alignment explanation
Indices: 2492055--2492092 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2492045 AACATTACTC
2492055 GTAAAAT-TATAGTATATAAA
1 GTAAAATATATA-TATATAAA
*
2492075 GTAATATATATATATATA
1 GTAAAATATATATATATA
2492093 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (20 bp):
GTAAAATATATATATATAAA
Found at i:2492083 original size:2 final size:2
Alignment explanation
Indices: 2492078--2492105 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2492068 ATATAAAGTA
2492078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2492106 TATTAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2492500 original size:121 final size:127
Alignment explanation
Indices: 2492267--2492508 Score: 329
Period size: 121 Copynumber: 2.0 Consensus size: 127
2492257 CACAAAAGAA
* *
2492267 AAAAAGAAAAAGAGAAATAAAAAGAATAATGGTTTCTAATTTCTAATAATTGGATGATGTGAGAG
1 AAAAAGAAAAAGAGAAATAAAAAGAATAATGGTTTATAATTTCTAATAATTGGATGATGTCAGAG
* * *
2492332 AAAAAAAGATTGAATTGAATTAAAGAGGCAAGTACGCATCTTTTGACCATATATATAAAAGG
66 AAAAAAAGAGTGAATGGAATTAAAGAGGCAAGAACGCATCTTTTGACCATATATATAAAAGG
* *
2492394 AAAAA-AAAAAGAGAAATAAAAAGAATAATATGTTTATAATTTTTAATAATTGGATGATG-CA-A
1 AAAAAGAAAAAGAGAAATAAAAAGAATAAT-GGTTTATAATTTCTAATAATTGGATGATGTCAGA
* *
2492456 -AAAAAAA-AGTG-A-GGAATT-GAGAAGGCAAGAAGGCATCTTTTGACCATATATAT
65 GAAAAAAAGAGTGAATGGAATTAAAG-AGGCAAGAACGCATCTTTTGACCATATATAT
2492509 GCATATATTG
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
120 2 0.02
121 34 0.33
122 1 0.01
123 3 0.03
124 7 0.07
125 1 0.01
126 25 0.24
127 31 0.30
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (127 bp):
AAAAAGAAAAAGAGAAATAAAAAGAATAATGGTTTATAATTTCTAATAATTGGATGATGTCAGAG
AAAAAAAGAGTGAATGGAATTAAAGAGGCAAGAACGCATCTTTTGACCATATATATAAAAGG
Found at i:2492898 original size:2 final size:2
Alignment explanation
Indices: 2492891--2492926 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2492881 ATCCTAACCC
2492891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2492927 GTGTTAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2495148 original size:19 final size:20
Alignment explanation
Indices: 2495126--2495168 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2495116 TAAAATTAAT
*
2495126 ATAAAGATA-TTTTAAAAAA
1 ATAAACATATTTTTAAAAAA
*
2495145 ATAAACATATTTTTAAAAGA
1 ATAAACATATTTTTAAAAAA
2495165 ATAA
1 ATAA
2495169 TATAAAGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAAACATATTTTTAAAAAA
Found at i:2498357 original size:32 final size:31
Alignment explanation
Indices: 2498324--2498400 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
2498314 ATTGTAAAAT
*
2498324 TTTGATAAATTTAATTACCATTTCATAACAA
1 TTTGATAAATTTAATTACAATTTCATAACAA
* * *
2498355 TTTGATAAAATTTAAATATAATTTTATAAC-A
1 TTTGAT-AAATTTAATTACAATTTCATAACAA
*
2498386 GTTGATAAATTTAAT
1 TTTGATAAATTTAAT
2498401 GAATACTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 8 0.21
31 12 0.31
32 19 0.49
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTGATAAATTTAATTACAATTTCATAACAA
Found at i:2501833 original size:2 final size:2
Alignment explanation
Indices: 2501826--2501853 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2501816 TTTTCAAACC
2501826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2501854 GATCTAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2505700 original size:11 final size:10
Alignment explanation
Indices: 2505678--2505742 Score: 67
Period size: 11 Copynumber: 6.1 Consensus size: 10
2505668 AAATTATGTA
2505678 TATATATGTTT
1 TATATAT-TTT
2505689 TATATCATTTT
1 TATAT-ATTTT
*
2505700 TATATATATAT
1 TATATAT-TTT
* *
2505711 TATTTATTAT
1 TATATATTTT
2505721 TATTATATTTT
1 TA-TATATTTT
2505732 TATATATTTT
1 TATATATTTT
2505742 T
1 T
2505743 TATTTATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
10 16 0.34
11 29 0.62
12 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TATATATTTT
Found at i:2505716 original size:15 final size:14
Alignment explanation
Indices: 2505676--2505738 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 14
2505666 TTAAATTATG
*
2505676 TATATATATGTTT-
1 TATATATATTTTTA
*
2505689 TATAT-CATTTTTA
1 TATATATATTTTTA
2505702 TATATATATTATTTA
1 TATATATATT-TTTA
2505717 TTATTATTATATTTTTA
1 -TA-TA-TATATTTTTA
2505734 TATAT
1 TATAT
2505739 TTTTTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 5 0.12
13 10 0.24
14 4 0.10
15 6 0.15
16 4 0.10
17 6 0.15
18 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TATATATATTTTTA
Found at i:2505743 original size:11 final size:11
Alignment explanation
Indices: 2505678--2505751 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
2505668 AAATTATGTA
*
2505678 TATATATGTTT
1 TATATATTTTT
2505689 TATATCA-TTTT
1 TATAT-ATTTTT
* *
2505700 TATATATATAT
1 TATATATTTTT
* *
2505711 TATTTA-TTAT
1 TATATATTTTT
2505721 TAT-TATATTTT
1 TATATAT-TTTT
2505732 TATATATTTTT
1 TATATATTTTT
*
2505743 TATTTATTT
1 TATATATTT
2505752 ATTTTCAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
9 2 0.04
10 7 0.14
11 38 0.75
12 4 0.08
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (11 bp):
TATATATTTTT
Found at i:2505748 original size:15 final size:15
Alignment explanation
Indices: 2505687--2505756 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 15
2505677 ATATATATGT
2505687 TTTATATCA-TTTTTA
1 TTTATAT-ATTTTTTA
* *
2505702 TATATATATTATTTA
1 TTTATATATTTTTTA
*
2505717 -TTAT-TATTATATT-
1 TTTATATATT-TTTTA
2505730 TTTATATATTTTTTA
1 TTTATATATTTTTTA
*
2505745 TTTATTTATTTT
1 TTTATATATTTT
2505757 CAATTATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
13 4 0.09
14 13 0.30
15 26 0.60
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATATATTTTTTA
Found at i:2505763 original size:43 final size:47
Alignment explanation
Indices: 2505663--2505764 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 47
2505653 TTAATATTAC
2505663 ATTTTAAATTATGTATATATATGTTTTATATCATTTTTATATATATATT
1 ATTTT-AATTAT-TATATATATGTTTTATATCATTTTTATATATATATT
*
2505712 A-TTT-ATTATTAT-TATAT-TTTTATAT-ATTTTT-TATTTAT-TT
1 ATTTTAATTATTATATATATGTTTTATATCATTTTTATATATATATT
2505752 ATTTTCAATTATT
1 ATTTT-AATTATT
2505765 TTGTTTTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
40 3 0.06
41 9 0.18
42 6 0.12
43 14 0.29
44 5 0.10
45 3 0.06
46 5 0.10
48 3 0.06
49 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (47 bp):
ATTTTAATTATTATATATATGTTTTATATCATTTTTATATATATATT
Found at i:2505787 original size:25 final size:24
Alignment explanation
Indices: 2505697--2505791 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 24
2505687 TTTATATCAT
* *
2505697 TTTTATATATATATTATTTATTATTA
1 TTTTAT-TAT-TATTATTTTTTTTTA
* *
2505723 TTATATTTTTATATATTTTTTATTTA
1 TTTTATTATTAT-TATTTTTT-TTTA
2505749 -TTTATT-TTCAATTATTTTGTTTTTA
1 TTTTATTATT--ATTATTTT-TTTTTA
2505774 TTTTATTATTATTATTTT
1 TTTTATTATTATTATTTT
2505792 ACTTTTTTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
24 5 0.09
25 32 0.56
26 18 0.32
27 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (24 bp):
TTTTATTATTATTATTTTTTTTTA
Found at i:2505920 original size:5 final size:5
Alignment explanation
Indices: 2505910--2505951 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
2505900 CTTAGTCTCA
* *
2505910 TTTAT TTTAT TTTAT TTTGT TTTAT TTT-T ATTTGT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TT
2505952 ATCTCTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 1 0.03
5 30 0.94
6 1 0.03
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:2505934 original size:15 final size:15
Alignment explanation
Indices: 2505909--2505951 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2505899 TCTTAGTCTC
*
2505909 ATTTATTTTA-TTTT
1 ATTTGTTTTATTTTT
2505923 ATTTTGTTTTATTTTT
1 A-TTTGTTTTATTTTT
2505939 ATTTGTTTTATTT
1 ATTTGTTTTATTT
2505952 ATCTCTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 20 0.77
16 5 0.19
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (15 bp):
ATTTGTTTTATTTTT
Found at i:2506959 original size:2 final size:2
Alignment explanation
Indices: 2506952--2506978 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2506942 TCTATCTATC
2506952 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 T
2506979 GCGCGGGTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2509719 original size:19 final size:19
Alignment explanation
Indices: 2509660--2509719 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2509650 AATAATTAAG
*
2509660 TAAATAAATGAATAAAATAA
1 TAAAT-AATAAATAAAATAA
* * *
2509680 TAAATACTAAATAACACAA
1 TAAATAATAAATAAAATAA
* *
2509699 TAAATAATATATAATATAA
1 TAAATAATAAATAAAATAA
2509718 TA
1 TA
2509720 TGTACTATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 27 0.84
20 5 0.16
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAATAATAAATAAAATAA
Found at i:2509784 original size:29 final size:26
Alignment explanation
Indices: 2509725--2509784 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
2509715 TAATATGTAC
2509725 TATATATTTATTTAAAAACTATAAAA
1 TATATATTTATTTAAAAACTATAAAA
* * *
2509751 CATATATTATATTTTCAAAAATTATATAA
1 TATATATT-TA-TTT-AAAAACTATAAAA
2509780 TATAT
1 TATAT
2509785 TTTCAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.26
27 2 0.07
28 3 0.11
29 15 0.56
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (26 bp):
TATATATTTATTTAAAAACTATAAAA
Found at i:2509809 original size:23 final size:22
Alignment explanation
Indices: 2509752--2509815 Score: 96
Period size: 22 Copynumber: 2.9 Consensus size: 22
2509742 ACTATAAAAC
2509752 ATATAT-TATATTTTCAAAAATT
1 ATATATATATATTTTC-AAAATT
2509774 ATATA-ATATATTTTCAAAATT
1 ATATATATATATTTTCAAAATT
2509795 ATATTATATATATTTTCAAAA
1 ATA-TATATATATTTTCAAAA
2509816 ACCGTTTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.23
22 16 0.41
23 14 0.36
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATATATATATTTTCAAAATT
Found at i:2509872 original size:38 final size:38
Alignment explanation
Indices: 2509820--2510024 Score: 263
Period size: 39 Copynumber: 5.4 Consensus size: 38
2509810 TCAAAAACCG
* *
2509820 TTTTGAAAAACTATATATTATACGTTTTCAAAAATTATC
1 TTTT-AAAAACTATATATTATATGTTTTCAAAAAATATC
*
2509859 TTTTAAAAACTATATATTATATGTTTTC-AAAATTAT-
1 TTTTAAAAACTATATATTATATGTTTTCAAAAAATATC
* * * *
2509895 TTTTGAAAACTATATATTATATGTTTTAAAAAAAAAACC
1 TTTTAAAAACTATATATTATATGTTTT-CAAAAAATATC
*
2509934 ATTTTAAAAACTATATATTATATGTTTTCAAAAACCTATC
1 -TTTTAAAAACTATATATTATATGTTTTCAAAAA-ATATC
*
2509974 TTTTAAAAACTATATATTATATGTTTTAAAAAAATAT-
1 TTTTAAAAACTATATATTATATGTTTTCAAAAAATATC
*
2510011 TTTCAAAAACTATA
1 TTTTAAAAACTATA
2510025 CTATATACTT
Statistics
Matches: 147, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
36 26 0.18
37 21 0.14
38 31 0.21
39 41 0.28
40 28 0.19
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (38 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAAAATATC
Found at i:2509955 original size:76 final size:78
Alignment explanation
Indices: 2509820--2510007 Score: 267
Period size: 79 Copynumber: 2.4 Consensus size: 78
2509810 TCAAAAACCG
* * ** *
2509820 TTTTGAAAAACTATATATTATACGTTTT-CAAAAATTATCTTTTAAAAACTATATATTATATGTT
1 TTTTG-AAAACTATATATTATATGTTTTAAAAAAAAAACCTTTTAAAAACTATATATTATATGTT
*
2509884 TTC-AAAA-TTAT-
65 TTCAAAAACCTATC
2509895 TTTTGAAAACTATATATTATATGTTTTAAAAAAAAAACCATTTTAAAAACTATATATTATATGTT
1 TTTTGAAAACTATATATTATATGTTTTAAAAAAAAAACC-TTTTAAAAACTATATATTATATGTT
2509960 TTCAAAAACCTATC
65 TTCAAAAACCTATC
*
2509974 TTTTAAAAACTATATATTATATGTTTTAAAAAAA
1 TTTTGAAAACTATATATTATATGTTTTAAAAAAA
2510008 TATTTTCAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
74 21 0.21
75 12 0.12
76 28 0.28
77 4 0.04
78 3 0.03
79 33 0.33
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (78 bp):
TTTTGAAAACTATATATTATATGTTTTAAAAAAAAAACCTTTTAAAAACTATATATTATATGTTT
TCAAAAACCTATC
Found at i:2509995 original size:115 final size:116
Alignment explanation
Indices: 2509812--2510024 Score: 340
Period size: 115 Copynumber: 1.8 Consensus size: 116
2509802 ATATATTTTC
* *
2509812 AAAAACCGTTTTGAAAAACTATATATTATACGTTTTCAAAAATTATCTTTTAAAAACTATATATT
1 AAAAACCATTTTGAAAAACTATATATTATACGTTTTCAAAAACTATCTTTTAAAAACTATATATT
* * **
2509877 ATATGTTTT-CAAAATTATTTTTGAAAACTATATATTATATGTTTTAAAAA
66 ATATGTTTTAAAAAAATATTTTCAAAAACTATATATTATATGTTTTAAAAA
*
2509927 AAAAACCATTTT-AAAAACTATATATTATATGTTTTCAAAAACCTATCTTTTAAAAACTATATAT
1 AAAAACCATTTTGAAAAACTATATATTATACGTTTTCAAAAA-CTATCTTTTAAAAACTATATAT
2509991 TATATGTTTTAAAAAAATATTTTCAAAAACTATA
65 TATATGTTTTAAAAAAATATTTTCAAAAACTATA
2510025 CTATATACTT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
114 28 0.31
115 42 0.47
116 19 0.21
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (116 bp):
AAAAACCATTTTGAAAAACTATATATTATACGTTTTCAAAAACTATCTTTTAAAAACTATATATT
ATATGTTTTAAAAAAATATTTTCAAAAACTATATATTATATGTTTTAAAAA
Found at i:2510019 original size:76 final size:75
Alignment explanation
Indices: 2509781--2510024 Score: 284
Period size: 76 Copynumber: 3.2 Consensus size: 75
2509771 ATTATATAAT
* * * * *
2509781 ATATTTTC-AAAATTATAT-TATATATATTTTCAAAAACC-GTTTTGAAAAACTATATATTATAC
1 ATATTTTCAAAAACTATATAT-TATATGTTTTCAAAAACCTATTTTTAAAAACTATATATTATAT
*
2509843 GTTTTCAAAAA
65 GTTTTAAAAAA
* * * *
2509854 TTATCTTTTAAAAACTATATATTATATGTTTTC-AAAA-TTATTTTTGAAAACTATATATTATAT
1 ATAT-TTTCAAAAACTATATATTATATGTTTTCAAAAACCTATTTTTAAAAACTATATATTATAT
2509917 GTTTTAAAAAAAAA
65 GTTTT---AAAAAA
*
2509931 ACCATTTT-AAAAACTATATATTATATGTTTTCAAAAACCTATCTTTTAAAAACTATATATTATA
1 A-TATTTTCAAAAACTATATATTATATGTTTTCAAAAACCTAT-TTTTAAAAACTATATATTATA
2509995 TGTTTTAAAAAA
64 TGTTTTAAAAAA
2510007 ATATTTTCAAAAACTATA
1 ATATTTTCAAAAACTATA
2510025 CTATATACTT
Statistics
Matches: 144, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
73 3 0.02
74 32 0.22
75 24 0.17
76 42 0.29
77 12 0.08
78 5 0.03
79 26 0.18
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (75 bp):
ATATTTTCAAAAACTATATATTATATGTTTTCAAAAACCTATTTTTAAAAACTATATATTATATG
TTTTAAAAAA
Found at i:2510036 original size:21 final size:22
Alignment explanation
Indices: 2510012--2510053 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2510002 AAAAAATATT
2510012 TTCAAAAACTAT-ACTATATAC
1 TTCAAAAACTATCACTATATAC
* *
2510033 TTCATAAACTATCATTATATA
1 TTCAAAAACTATCACTATATA
2510054 TTATCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (22 bp):
TTCAAAAACTATCACTATATAC
Found at i:2511820 original size:2 final size:2
Alignment explanation
Indices: 2511809--2511839 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2511799 ATATGAGCAT
2511809 TA TA -A 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
2511840 ATAAAGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2535424 original size:3 final size:3
Alignment explanation
Indices: 2535418--2535445 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2535408 AATCATCATC
2535418 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2535446 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2536646 original size:2 final size:2
Alignment explanation
Indices: 2536639--2536675 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2536629 ATCATCGACA
2536639 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
2536676 ACAACACATA
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:2545728 original size:44 final size:44
Alignment explanation
Indices: 2545680--2545797 Score: 137
Period size: 44 Copynumber: 2.7 Consensus size: 44
2545670 GTAATCCGTA
*
2545680 GGAATTGGAATCAAATTTCATATTCTGTTTAATTGGCAGTAAAT
1 GGAATTGGAATCAAATTTCATATTCTGTTTAATTGGCAGAAAAT
** * * * ** *
2545724 GGAATTAAAATCCAATTCCATATTATGTTTGGTTGGTAGAAAAT
1 GGAATTGGAATCAAATTTCATATTCTGTTTAATTGGCAGAAAAT
* *
2545768 AGAATTGGATTCAAATTTCATATTCTGTTT
1 GGAATTGGAATCAAATTTCATATTCTGTTT
2545798 TGTTCGCAGA
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (44 bp):
GGAATTGGAATCAAATTTCATATTCTGTTTAATTGGCAGAAAAT
Found at i:2553489 original size:22 final size:22
Alignment explanation
Indices: 2553464--2553514 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2553454 CACCACAGCT
*
2553464 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
2553486 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2553508 CGTAGAA
1 CGTAGAA
2553515 TTTTGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:2553515 original size:22 final size:22
Alignment explanation
Indices: 2553472--2553516 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2553462 CTCGTATAAA
2553472 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2553494 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2553516 T
1 T
2553517 TTGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2553777 original size:30 final size:31
Alignment explanation
Indices: 2553736--2553795 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2553726 TAGACATAGT
*
2553736 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2553766 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2553796 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2553844 original size:28 final size:28
Alignment explanation
Indices: 2553809--2553879 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
2553799 TTTTCTGCAT
*
2553809 ATTCATGTCATGTAATACATATAATATA
1 ATTCATGTCATGTAATACATATAATACA
*
2553837 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
2553865 ATTTCATGTCATGTA
1 A-TTCATGTCATGTA
2553880 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 27 0.68
29 13 0.32
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:2553852 original size:14 final size:14
Alignment explanation
Indices: 2553809--2553852 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2553799 TTTTCTGCAT
2553809 ATTCATGTCATGTA
1 ATTCATGTCATGTA
* * * *
2553823 ATACATATAATATA
1 ATTCATGTCATGTA
2553837 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2553851 AT
1 AT
2553853 ACATTTAATA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (14 bp):
ATTCATGTCATGTA
Found at i:2554340 original size:21 final size:21
Alignment explanation
Indices: 2554310--2554352 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2554300 ATCATATTCG
* *
2554310 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2554331 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2554352 T
1 T
2554353 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2554352 original size:67 final size:66
Alignment explanation
Indices: 2554183--2554353 Score: 184
Period size: 65 Copynumber: 2.6 Consensus size: 66
2554173 TTTTCTCATG
* * * * * *
2554183 GGGGAATCGGTTCCCCCCCT-GGGGTATCGGTTCCCCTATAGCCTTCTGGAATTTCTTATACGAT
1 GGGGTATCGGTT--CCCCCTGGGGGTACCGATTCCCCTATAGCATTCTGGAATATCATATACGAT
*
2554247 GAG
64 GAA
* * *
2554250 GGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTTGA
1 GGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTATAGCATTCTGGAATATCATATACGATGA
2554314 A
66 A
* *
2554315 GGGGTATCGGTTCCCCTTGAATGGGTACCGATTCCCCTA
1 GGGGTATCGGTTCCCCCTG--GGGGTACCGATTCCCCTA
2554354 ACCCAGAAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
65 34 0.39
66 27 0.31
67 27 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTATAGCATTCTGGAATATCATATACGATGA
A
Found at i:2560406 original size:22 final size:22
Alignment explanation
Indices: 2560389--2560455 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
2560379 CTCGTATAAA
2560389 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2560411 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2560433 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2560455 T
1 T
2560456 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2560716 original size:30 final size:31
Alignment explanation
Indices: 2560675--2560734 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2560665 TAGACATAGT
*
2560675 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2560705 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2560735 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2560783 original size:28 final size:28
Alignment explanation
Indices: 2560748--2560818 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
2560738 TTTTCTGCAT
*
2560748 ATTCATGTCATGTAATACATATAATATA
1 ATTCATGTCATGTAATACATATAATACA
*
2560776 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
2560804 ATTTCATGTCATGTA
1 A-TTCATGTCATGTA
2560819 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 27 0.68
29 13 0.32
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:2560791 original size:14 final size:14
Alignment explanation
Indices: 2560748--2560791 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2560738 TTTTCTGCAT
2560748 ATTCATGTCATGTA
1 ATTCATGTCATGTA
* * * *
2560762 ATACATATAATATA
1 ATTCATGTCATGTA
2560776 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2560790 AT
1 AT
2560792 ACATTTAATA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (14 bp):
ATTCATGTCATGTA
Found at i:2561267 original size:67 final size:67
Alignment explanation
Indices: 2561122--2561272 Score: 187
Period size: 68 Copynumber: 2.2 Consensus size: 67
2561112 TTTTCTCATG
* * * * * *
2561122 GGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTATAGCCTTCTGGAATTTCTTATACGAT
1 GGGGTATCGGTT-CCCCCCCTGGGGTACCGATTCCCCTATAGCATTCTGGAATATCATATACGAT
*
2561187 GAG
65 GAA
* * *
2561190 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCTATAGCATTCTGGAATATCATATACGAT
2561254 GAA
65 GAA
2561257 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
2561273 TTGAATGGGT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
67 34 0.47
68 38 0.53
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTATAGCATTCTGGAATATCATATACGATG
AA
Found at i:2561282 original size:21 final size:21
Alignment explanation
Indices: 2561252--2561294 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2561242 ATCATATTCG
* *
2561252 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2561273 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2561294 T
1 T
2561295 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2562880 original size:10 final size:10
Alignment explanation
Indices: 2562855--2562914 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 10
2562845 TACATATATA
2562855 TATATGTATG
1 TATATGTATG
2562865 --TATGTATG
1 TATATGTATG
*
2562873 TATATGTATA
1 TATATGTATG
* **
2562883 TATATATAAA
1 TATATGTATG
2562893 TATATGTATG
1 TATATGTATG
*
2562903 TATGTGTATG
1 TATATGTATG
2562913 TA
1 TA
2562915 ATCTTTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
8 8 0.20
10 33 0.80
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (10 bp):
TATATGTATG
Found at i:2562883 original size:30 final size:30
Alignment explanation
Indices: 2562849--2562911 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2562839 AACATATACA
** *
2562849 TATATATATATGTATGTATGTATGTATATG
1 TATATATATATAAATATATGTATGTATATG
*
2562879 TATATATATATAAATATATGTATGTATGTG
1 TATATATATATAAATATATGTATGTATATG
2562909 TAT
1 TAT
2562912 GTAATCTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (30 bp):
TATATATATATAAATATATGTATGTATATG
Found at i:2562899 original size:34 final size:34
Alignment explanation
Indices: 2562848--2562914 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
2562838 GAACATATAC
* *
2562848 ATATATATATATGTATGTATGTATGTATATGTAT
1 ATATATATAAATATATGTATGTATGTATATGTAT
*
2562882 ATATATATAAATATATGTATGTATGTGTATGTA
1 ATATATATAAATATATGTATGTATGTATATGTA
2562915 ATCTTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (34 bp):
ATATATATAAATATATGTATGTATGTATATGTAT
Found at i:2574748 original size:20 final size:20
Alignment explanation
Indices: 2574723--2574762 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2574713 TAAGTGACAC
2574723 GTGTCAAGTTTATATTTAAT
1 GTGTCAAGTTTATATTTAAT
2574743 GTGTCAAGTTTATATTTAAT
1 GTGTCAAGTTTATATTTAAT
2574763 CTTAATACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
GTGTCAAGTTTATATTTAAT
Found at i:2576761 original size:2 final size:2
Alignment explanation
Indices: 2576749--2576793 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2576739 TTTTGAGATT
*
2576749 TA TA AA 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
2576791 TA T
1 TA T
2576794 TAGCTATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2576811 original size:10 final size:9
Alignment explanation
Indices: 2576749--2576814 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 9
2576739 TTTTGAGATT
2576749 TATA-AATA
1 TATATAATA
2576757 TATATATATA
1 TATATA-ATA
2576767 TATATATATA
1 TATATA-ATA
2576777 TATATATATA
1 TATATA-ATA
*
2576787 TATATATTA
1 TATATAATA
**
2576796 GCTATAATA
1 TATATAATA
2576805 TGATATAATA
1 T-ATATAATA
2576815 CCATAATACC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
8 4 0.08
9 9 0.18
10 36 0.73
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (9 bp):
TATATAATA
Found at i:2589579 original size:2 final size:2
Alignment explanation
Indices: 2589572--2589601 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2589562 ACTAGGAATA
2589572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2589602 TCATACACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2590987 original size:48 final size:48
Alignment explanation
Indices: 2590913--2591009 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
2590903 TCGGAAGATC
2590913 GGCACAACGATTCGAGCTTTTATTTCTGATTCTTCATCTTCTCCAGTT
1 GGCACAACGATTCGAGCTTTTATTTCTGATTCTTCATCTTCTCCAGTT
* *
2590961 GGCACAACGATTCGAGCTTTTCTTTCTGGTTCTTCATCTTCTCCAGTT
1 GGCACAACGATTCGAGCTTTTATTTCTGATTCTTCATCTTCTCCAGTT
2591009 G
1 G
2591010 TTTCTTCAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.41
Consensus pattern (48 bp):
GGCACAACGATTCGAGCTTTTATTTCTGATTCTTCATCTTCTCCAGTT
Found at i:2595175 original size:22 final size:22
Alignment explanation
Indices: 2595133--2595175 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2595123 TTTATTTTAA
*
2595133 TTTATTACAAATTTTTAATTAT
1 TTTATTACAAATTTGTAATTAT
*
2595155 TTTATTA-AATATTTGTGATTA
1 TTTATTACAA-ATTTGTAATTA
2595176 AATTCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTATTACAAATTTGTAATTAT
Found at i:2595459 original size:16 final size:16
Alignment explanation
Indices: 2595438--2595471 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2595428 TTTTTTTTAC
2595438 TTTTATTATTG-TTTTT
1 TTTTATT-TTGATTTTT
2595454 TTTTATTTTGATTTTT
1 TTTTATTTTGATTTTT
2595470 TT
1 TT
2595472 CTTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTATTTTGATTTTT
Found at i:2595462 original size:21 final size:23
Alignment explanation
Indices: 2595424--2595478 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2595414 TTTGAAGTTA
2595424 ATTG-TTTTTTTTACTTTT-ATT
1 ATTGTTTTTTTTTACTTTTGATT
2595445 ATTGTTTTTTTTTA-TTTTGATT
1 ATTGTTTTTTTTTACTTTTGATT
*
2595467 -TT-TTTCTTTTTA
1 ATTGTTTTTTTTTA
2595479 AAACTCCGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 10 0.32
22 12 0.39
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.78
Consensus pattern (23 bp):
ATTGTTTTTTTTTACTTTTGATT
Found at i:2595468 original size:15 final size:16
Alignment explanation
Indices: 2595438--2595471 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2595428 TTTTTTTTAC
*
2595438 TTTTATTATTGTTTTT
1 TTTTATTATTGATTTT
2595454 TTTTATT-TTGATTTT
1 TTTTATTATTGATTTT
2595469 TTT
1 TTT
2595472 CTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTATTATTGATTTT
Found at i:2603970 original size:31 final size:31
Alignment explanation
Indices: 2603912--2603970 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2603902 TAAAAATGAT
** *
2603912 TAAAAAATGATTTAATAAATCATAATTTTGA
1 TAAAAAATGATGAAATAAATCAAAATTTTGA
2603943 TAAAAAATGATGAAATAGAAT-AAAATTT
1 TAAAAAATGATGAAATA-AATCAAAATTT
2603971 ATTTGTCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (31 bp):
TAAAAAATGATGAAATAAATCAAAATTTTGA
Found at i:2604055 original size:3 final size:3
Alignment explanation
Indices: 2604047--2604078 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2604037 TTAACGACCC
2604047 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2604079 AGATATGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2604321 original size:19 final size:20
Alignment explanation
Indices: 2604299--2604337 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2604289 AACATATTTT
2604299 CAATA-AAAAAATATAAAGA
1 CAATATAAAAAATATAAAGA
**
2604318 CAATATCTAAAATATAAAGA
1 CAATATAAAAAATATAAAGA
2604338 AATTTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.21
Consensus pattern (20 bp):
CAATATAAAAAATATAAAGA
Found at i:2613138 original size:22 final size:22
Alignment explanation
Indices: 2613110--2613167 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
2613100 TAAATATCGG
2613110 TTCTCGCATCTCTCCTCACATC
1 TTCTCGCATCTCTCCTCACATC
2613132 TTCTCGCATCTCTCCTCACATC
1 TTCTCGCATCTCTCCTCACATC
*
2613154 TCCTCGCATCTCTC
1 TTCTCGCATCTCTC
2613168 ATCTCTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.12, C:0.47, G:0.05, T:0.36
Consensus pattern (22 bp):
TTCTCGCATCTCTCCTCACATC
Found at i:2613155 original size:12 final size:12
Alignment explanation
Indices: 2613116--2613167 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 12
2613106 TCGGTTCTCG
2613116 CATCTCTCCTCA
1 CATCTCTCCTCA
*
2613128 CATCT-T-CTCG
1 CATCTCTCCTCA
2613138 CATCTCTCCTCA
1 CATCTCTCCTCA
*
2613150 CA--TCTCCTCG
1 CATCTCTCCTCA
2613160 CATCTCTC
1 CATCTCTC
2613168 ATCTCTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 17 0.52
11 2 0.06
12 14 0.42
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (12 bp):
CATCTCTCCTCA
Found at i:2614591 original size:111 final size:111
Alignment explanation
Indices: 2614331--2614664 Score: 562
Period size: 111 Copynumber: 3.0 Consensus size: 111
2614321 ATTACAAAAA
* *
2614331 TTAATTC-TTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTAATAATAATTTAAATT
1 TTAATTCTTTA-TATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
*
2614395 AAATTAAAACGTTAAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
65 AAATTAAAACGTT-AAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
2614443 TTAATTCTTAATTTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTTATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
2614508 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
2614554 TTAATTCTTTATATAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTTATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
2614619 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
2614665 ATGATTTCCA
Statistics
Matches: 211, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
111 138 0.65
112 71 0.34
113 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTTATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:2621003 original size:2 final size:2
Alignment explanation
Indices: 2620996--2621022 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2620986 TTTAAAAATA
2620996 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
2621023 AATTGTAACA
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:2621781 original size:23 final size:24
Alignment explanation
Indices: 2621741--2621790 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
2621731 CCACTAGGGG
2621741 CTATGAAATTTGTCCCGAAGGACCA
1 CTATGAAA-TTGTCCCGAAGGACCA
*
2621766 CTATGAAA-TGTCCCGAAGGATCA
1 CTATGAAATTGTCCCGAAGGACCA
2621789 CT
1 CT
2621791 GTGTCCCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.67
25 8 0.33
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (24 bp):
CTATGAAATTGTCCCGAAGGACCA
Found at i:2621948 original size:18 final size:19
Alignment explanation
Indices: 2621914--2621950 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2621904 CATATGATTC
2621914 ACTTTCACTTGTCATATAT
1 ACTTTCACTTGTCATATAT
*
2621933 ACTTTCTCTT-TCATATAT
1 ACTTTCACTTGTCATATAT
2621951 CTCATGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.24, C:0.22, G:0.03, T:0.51
Consensus pattern (19 bp):
ACTTTCACTTGTCATATAT
Found at i:2626679 original size:22 final size:22
Alignment explanation
Indices: 2626654--2626736 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
2626644 CCATTTTAAT
2626654 TTAAATAATTTAATAATAAATA
1 TTAAATAATTTAATAATAAATA
* *
2626676 TTAATATAATTTAGTAA-CAAT-
1 TTAA-ATAATTTAATAATAAATA
*
2626697 TT-AATAATTTAGTAAT-AATGA
1 TTAAATAATTTAATAATAAAT-A
** *
2626718 TTTCATAATTTAATGATAA
1 TTAAATAATTTAATAATAA
2626737 TTTATTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
19 15 0.30
20 1 0.02
21 4 0.08
22 18 0.36
23 12 0.24
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (22 bp):
TTAAATAATTTAATAATAAATA
Found at i:2626712 original size:11 final size:11
Alignment explanation
Indices: 2626657--2626780 Score: 56
Period size: 11 Copynumber: 12.0 Consensus size: 11
2626647 TTTTAATTTA
2626657 AATAATTTAAT
1 AATAATTTAAT
2626668 AATAAATATTAAT
1 AAT-AAT-TTAAT
*
2626681 -ATAATTTAGT
1 AATAATTTAAT
*
2626691 AACAA-TT--T
1 AATAATTTAAT
*
2626699 AATAATTTAGT
1 AATAATTTAAT
2626710 AATAATGATT--T
1 AATAAT--TTAAT
*
2626721 CATAATTTAAT
1 AATAATTTAAT
*
2626732 GATAATTT-AT
1 AATAATTTAAT
2626742 --T-ATTT--T
1 AATAATTTAAT
*
2626748 AATAAATTAAT
1 AATAATTTAAT
*
2626759 ATTAATTTAAT
1 AATAATTTAAT
*
2626770 GATAATTTAAT
1 AATAATTTAAT
2626781 CATTTAATTA
Statistics
Matches: 88, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 7 0.08
9 7 0.08
10 8 0.09
11 49 0.56
12 5 0.06
13 7 0.08
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.47
Consensus pattern (11 bp):
AATAATTTAAT
Found at i:2626739 original size:19 final size:19
Alignment explanation
Indices: 2626723--2626788 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
2626713 AATGATTTCA
2626723 TAATTTAATGATAATTTAT
1 TAATTTAATGATAATTTAT
*
2626742 TATTTTAAT-A-AATTAATAT
1 TAATTTAATGATAATT--TAT
*
2626761 TAATTTAATGATAATTTAA
1 TAATTTAATGATAATTTAT
*
2626780 TCATTTAAT
1 TAATTTAAT
2626789 TAAAATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.10
18 1 0.03
19 29 0.74
20 1 0.03
21 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (19 bp):
TAATTTAATGATAATTTAT
Found at i:2626787 original size:38 final size:40
Alignment explanation
Indices: 2626723--2626802 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 40
2626713 AATGATTTCA
*
2626723 TAATTTAATGATAATTTATTATTTTAA-T-AAATTAATAT
1 TAATTTAATGATAATTTATCATTTTAATTAAAATTAATAT
*
2626761 TAATTTAATGATAATTTAATCA-TTTAATTAAAATTATTAT
1 TAATTTAATGATAATTT-ATCATTTTAATTAAAATTAATAT
2626801 TA
1 TA
2626803 TTATTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 22 0.59
39 4 0.11
40 11 0.30
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (40 bp):
TAATTTAATGATAATTTATCATTTTAATTAAAATTAATAT
Found at i:2628571 original size:21 final size:22
Alignment explanation
Indices: 2628545--2628587 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2628535 TATATTATTT
2628545 TTTTAAAAATAT-TATTTTAAA
1 TTTTAAAAATATATATTTTAAA
* *
2628566 TTTTAAATATATATCTTTTAAA
1 TTTTAAAAATATATATTTTAAA
2628588 AAGTATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATATATATTTTAAA
Found at i:2630610 original size:14 final size:15
Alignment explanation
Indices: 2630582--2630611 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2630572 ATTTTAACCG
2630582 ATTTTTTAAAGTTTA
1 ATTTTTTAAAGTTTA
2630597 ATTTTTTAAA-TTTA
1 ATTTTTTAAAGTTTA
2630611 A
1 A
2630612 AGTCGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTTTAAAGTTTA
Found at i:2634191 original size:19 final size:19
Alignment explanation
Indices: 2634153--2634192 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2634143 TATTTTTTAT
*
2634153 TATTTTTAATAAAACCAAC
1 TATTTTTAATAAAACAAAC
2634172 TATTTTTATATAAAA-AAAC
1 TATTTTTA-ATAAAACAAAC
2634191 TA
1 TA
2634193 AAATATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (19 bp):
TATTTTTAATAAAACAAAC
Found at i:2644387 original size:29 final size:29
Alignment explanation
Indices: 2644344--2644402 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2644334 GTGTTTATTT
*
2644344 TCAAGTTTTTTACCAATCCAAGTGCTTCG
1 TCAAGTTTTTCACCAATCCAAGTGCTTCG
*
2644373 TCAAGTTTTTCACCAATCCAAGTTCTTCG
1 TCAAGTTTTTCACCAATCCAAGTGCTTCG
2644402 T
1 T
2644403 AACCACGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (29 bp):
TCAAGTTTTTCACCAATCCAAGTGCTTCG
Found at i:2648553 original size:6 final size:6
Alignment explanation
Indices: 2648542--2648586 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
2648532 TCTCGTCTCG
2648542 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2648587 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2648689 original size:20 final size:20
Alignment explanation
Indices: 2648664--2648707 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2648654 TTTTTAACTA
*
2648664 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
2648684 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
2648704 TTCT
1 TTCT
2648708 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:2648777 original size:43 final size:42
Alignment explanation
Indices: 2648721--2648853 Score: 173
Period size: 43 Copynumber: 3.2 Consensus size: 42
2648711 TCGCGTTGCA
*
2648721 TTGCGATCCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGAT-CTCTCAATCGCATTGCGATTTTCTTCTAAATCGCG
* * *
2648764 TTGCGACTCTCTCAATCGCATTGCGA--TT-ATATAAATCGCA
1 TTGCGA-TCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCG
*
2648804 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGA-TCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCG
2648847 TTGCGAT
1 TTGCGAT
2648854 TTTCTTTTGA
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
40 33 0.43
41 2 0.03
42 3 0.04
43 38 0.49
44 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (42 bp):
TTGCGATCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCG
Found at i:2648831 original size:20 final size:20
Alignment explanation
Indices: 2648718--2648831 Score: 113
Period size: 20 Copynumber: 5.5 Consensus size: 20
2648708 AAATCGCGTT
* * *
2648718 GCATTGCGATCCTCTCAGTC
1 GCATTGCGATTCTATCAATC
2648738 GCATTGCGATTTTCT-TCTAAATC
1 GCATTGCGA--TTCTATC--AATC
* * *
2648761 GCGTTGCGACTCTCTCAATC
1 GCATTGCGATTCTATCAATC
* *
2648781 GCATTGCGATTATATAAATC
1 GCATTGCGATTCTATCAATC
2648801 GCATTGCGATTCTATCAATC
1 GCATTGCGATTCTATCAATC
2648821 GCATTGCGATT
1 GCATTGCGATT
2648832 TTCTTCTAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
20 57 0.73
21 5 0.06
22 5 0.06
23 11 0.14
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (20 bp):
GCATTGCGATTCTATCAATC
Found at i:2648868 original size:20 final size:20
Alignment explanation
Indices: 2648845--2648896 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2648835 TTCTAAATCG
*
2648845 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
2648865 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
2648885 CGTTGCGATTTT
1 CGTTGCGATTTT
2648897 GATATCGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:2648871 original size:83 final size:85
Alignment explanation
Indices: 2648674--2648874 Score: 223
Period size: 83 Copynumber: 2.4 Consensus size: 85
2648664 TTCTTTTGAC
* * * *
2648674 CGTTGCGATTTTCTTTTTAA-CGTTGCGATTTTCTAAATCGCGTTGCATTGCGATCCTCTCAGTC
1 CGTTGCGATTTTC-TTTTAACCGTTGCGATTATATAAATC-C--TGCATTGCGATCCTATCAATC
2648738 GCATTGCGATTTTCTTCTAAATCG
62 GCATTGCGATTTTCTTCTAAATCG
* * * * *
2648762 CGTTGCGA--CTCTCTCAATCGCATTGCGATTATATAAAT-C-GCATTGCGATTCTATCAATCGC
1 CGTTGCGATTTTCTTTTAA-C-CGTTGCGATTATATAAATCCTGCATTGCGATCCTATCAATCGC
2648823 ATTGCGATTTTCTTCTAAATCG
64 ATTGCGATTTTCTTCTAAATCG
*
2648845 CGTTGCGATTTTCTTTTGACCGTTGCGATT
1 CGTTGCGATTTTCTTTTAACCGTTGCGATT
2648875 TTCTTTTTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
83 58 0.62
84 1 0.01
85 9 0.10
86 3 0.03
88 23 0.24
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (85 bp):
CGTTGCGATTTTCTTTTAACCGTTGCGATTATATAAATCCTGCATTGCGATCCTATCAATCGCAT
TGCGATTTTCTTCTAAATCG
Found at i:2653104 original size:112 final size:112
Alignment explanation
Indices: 2652897--2653139 Score: 387
Period size: 112 Copynumber: 2.2 Consensus size: 112
2652887 CTTATGAATA
*
2652897 TGTCGTTAGGGTGCAGGATGAACTGATCTCAGAGAAAATAAAGAGTCGGAGCAACATAGAGTCCT
1 TGTCGATAGGGTGCAGGATGAACTGATCTCAGAGAAAATAAAGAGTCGGAGCAACATAGAGTCCT
*
2652962 AGAACCGTAAAGTTCTTGAACTGTTATAGAGTTTAGCATCAACTATG
66 AGAACCGTAAAGTTCTTGAACTGCTATAGAGTTTAGCATCAACTATG
* * * * *
2653009 TTTCGATAGGGTGCGGGATGCACTGATCTCAGAGAAAATAAAGAGTCGGGGCAATATAGAGTCCT
1 TGTCGATAGGGTGCAGGATGAACTGATCTCAGAGAAAATAAAGAGTCGGAGCAACATAGAGTCCT
* * * *
2653074 AGAACTGTGAAGTTCTTGAACTGCTCTAGAGTTTAGCATCGACTATG
66 AGAACCGTAAAGTTCTTGAACTGCTATAGAGTTTAGCATCAACTATG
2653121 TGTCGATAGGGTGCAGGAT
1 TGTCGATAGGGTGCAGGAT
2653140 ACATTGATAA
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 118 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (112 bp):
TGTCGATAGGGTGCAGGATGAACTGATCTCAGAGAAAATAAAGAGTCGGAGCAACATAGAGTCCT
AGAACCGTAAAGTTCTTGAACTGCTATAGAGTTTAGCATCAACTATG
Found at i:2653775 original size:20 final size:20
Alignment explanation
Indices: 2653750--2653924 Score: 181
Period size: 20 Copynumber: 8.7 Consensus size: 20
2653740 TTTTCCTAAT
*
2653750 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2653770 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2653791 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
2653811 TCACAACGCGAATTTA-GAAAA
1 TCGCAATGCGAA--TACGTAAA
*
2653832 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
2653852 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2653872 TCGCAATGGGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2653892 TTGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2653912 TCGTAACGCGAAT
1 TCGCAATGCGAAT
2653925 CTGACTATCG
Statistics
Matches: 125, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.02
20 93 0.74
21 28 0.22
22 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2653795 original size:41 final size:41
Alignment explanation
Indices: 2653750--2653904 Score: 197
Period size: 41 Copynumber: 3.8 Consensus size: 41
2653740 TTTTCCTAAT
* *
2653750 TCGCAATGTGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTAGAAAA
* *
2653791 TCGCAATGCGATTACGTAAATCACAACGCGAATTTAGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTAGAAAA
* * *
2653832 TCGCAATGCGATTACGTAAATCGCAATGCGAA--TACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTA-GAAAA
* * *
2653872 TCGCAATGGGAATACGTAAATTGCAATGCGAAT
1 TCGCAATGCGAATACGTAAATCGCAACGCGAAT
2653905 ATGTAAATCG
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 2 0.02
40 33 0.32
41 67 0.66
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATTTAGAAAA
Found at i:2653911 original size:40 final size:41
Alignment explanation
Indices: 2653750--2653924 Score: 192
Period size: 41 Copynumber: 4.3 Consensus size: 41
2653740 TTTTCCTAAT
* * *
2653750 TCGCAATGTGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATATAGAAAA
* * *
2653791 TCGCAATGCGATTACGTAAATCACAACGCGAATTTAGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATATAGAAAA
* * * *
2653832 TCGCAATGCGATTACGTAAATCGCAATGCGAATA-CGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATATAGAAAA
* * * *
2653872 TCGCAATGGGAATACGTAAATTGCAATGCGAATAT-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATATAGAAAA
* *
2653912 TCGTAACGCGAAT
1 TCGCAATGCGAAT
2653925 CTGACTATCG
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
40 50 0.42
41 68 0.58
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATATAGAAAA
Found at i:2654139 original size:22 final size:22
Alignment explanation
Indices: 2654114--2654183 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
2654104 CTAAAGCGAC
*
2654114 ATCAATCCCCATCTCCGACGAA
1 ATCAGTCCCCATCTCCGACGAA
*
2654136 ATCAGTCCCCATCTCCGACGAT
1 ATCAGTCCCCATCTCCGACGAA
*
2654158 ATCAGTCTCCATCTCCGACGAA
1 ATCAGTCCCCATCTCCGACGAA
2654180 ATCA
1 ATCA
2654184 TTCACGGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.29, C:0.39, G:0.11, T:0.21
Consensus pattern (22 bp):
ATCAGTCCCCATCTCCGACGAA
Found at i:2654556 original size:33 final size:34
Alignment explanation
Indices: 2654508--2654581 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
2654498 ACTATCGCAA
**
2654508 TGCGATTCTGTCGTTGCGATTTTCA-TTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCATTTTCGCGT
*
2654541 TGCGATTCT-TGCGTTGCGATAGTCATTTTCGTGT
1 TGCGATTCTGT-CGTTGCGATAGTCATTTTCGCGT
2654575 TGCGATT
1 TGCGATT
2654582 TTCATTTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.58
34 14 0.39
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.45
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCATTTTCGCGT
Found at i:2654578 original size:20 final size:20
Alignment explanation
Indices: 2654553--2654600 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2654543 CGATTCTTGC
2654553 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
2654573 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
*
2654593 GTTACGAT
1 GTTGCGAT
2654601 TTAAAGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.48
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2654601 original size:20 final size:20
Alignment explanation
Indices: 2654563--2654602 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2654553 GTTGCGATAG
*
2654563 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTACGATTT
2654583 TCATTTTCGTGTTACGATTT
1 TCATTTTCGTGTTACGATTT
2654603 AAAGTTTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.55
Consensus pattern (20 bp):
TCATTTTCGTGTTACGATTT
Found at i:2654610 original size:20 final size:20
Alignment explanation
Indices: 2654567--2654610 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2654557 CGATAGTCAT
* ** *
2654567 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTAAAG
2654587 TTTCGTGTTACGATTTAAAG
1 TTTCGTGTTACGATTTAAAG
2654607 TTTC
1 TTTC
2654611 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTACGATTTAAAG
Found at i:2656516 original size:20 final size:20
Alignment explanation
Indices: 2656491--2656542 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2656481 AGAATAGTTT
*
2656491 ACTATCACAATGCGAAAATG
1 ACTATCACAACGCGAAAATG
*
2656511 ACTATCGCAACGCGAAAATG
1 ACTATCACAACGCGAAAATG
*
2656531 ACTATCGCAACG
1 ACTATCACAACG
2656543 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
ACTATCACAACGCGAAAATG
Found at i:2656560 original size:34 final size:34
Alignment explanation
Indices: 2656514--2656628 Score: 126
Period size: 34 Copynumber: 3.4 Consensus size: 34
2656504 GAAAATGACT
*
2656514 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGAAAATGACTATCGCAACGAAAGA
* ** * *
2656548 ATCGCAATGCG-AAATGAAAATCACAAC-AACAAA
1 ATCGCAACGCGAAAATGACTATCGCAACGAA-AGA
* *
2656581 ATCGCAACGCGTAAATGACTATCGCAAGGAAAGA
1 ATCGCAACGCGAAAATGACTATCGCAACGAAAGA
*
2656615 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
2656629 TGAAAATCGC
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
32 1 0.02
33 25 0.39
34 36 0.56
35 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACGAAAGA
Found at i:2656638 original size:33 final size:33
Alignment explanation
Indices: 2656514--2656639 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 33
2656504 GAAAATGACT
** *
2656514 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGAAAATGAAAATCGCAA-GAAAGA
* * * *
2656548 ATCGCAATGCG-AAATGAAAATCACAACAACAAA
1 ATCGCAACGCGAAAATGAAAATCGCAAGAA-AGA
* **
2656581 ATCGCAACGCGTAAATGACTATCGCAAGGAAAGA
1 ATCGCAACGCGAAAATGAAAATCGCAA-GAAAGA
*
2656615 ATCGCAATGCG-AAATGAAAATCGCA
1 ATCGCAACGCGAAAATGAAAATCGCA
2656640 TTGCGATTCT
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
32 1 0.01
33 36 0.49
34 34 0.47
35 2 0.03
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAAATGAAAATCGCAAGAAAGA
Found at i:2656708 original size:20 final size:20
Alignment explanation
Indices: 2656657--2656720 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
2656647 TCTCTCGTTT
**
2656657 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
2656677 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
* *
2656697 CGATAGTTATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
2656717 CGAT
1 CGAT
2656721 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:2657295 original size:21 final size:21
Alignment explanation
Indices: 2657204--2657302 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 21
2657194 GACTCACTTG
2657204 TCATCGTTCAAGAGG-CA-TCC
1 TCATCGTTCAAGAGGCCACT-C
* * *
2657224 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCACTC
** * *
2657246 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCACTC
* * *
2657267 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCACTC
*
2657288 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
2657303 TCCCTCCCAA
Statistics
Matches: 58, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 54 0.93
22 2 0.03
23 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCACTC
Found at i:2657301 original size:42 final size:42
Alignment explanation
Indices: 2657229--2657311 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2657219 CATCCCCTAT
*
2657229 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
2657271 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
2657312 ACATTCTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:2658914 original size:34 final size:33
Alignment explanation
Indices: 2658826--2658921 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
2658816 AAAACAGACT
* ** *
2658826 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
2658860 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2658893 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
2658922 TGAAACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2658980 original size:34 final size:34
Alignment explanation
Indices: 2658936--2659031 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
2658926 ACTAAATTCG
*
2658936 CGTTGTGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
2658970 CGTTGCGATTTTCA-TTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
2659003 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2659032 AGTCAAATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Done.