Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 19
Found at i:3729943 original size:21 final size:23
Alignment explanation
Indices: 3729896--3729943 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
3729886 ACATATTTTT
* *
3729896 ATTTTATGTTTTGATAAAGCTGT
1 ATTTTATGTTTTGATAAAGATGA
*
3729919 ATTTTAT-TTTTG-TTAAGATGA
1 ATTTTATGTTTTGATAAAGATGA
3729940 ATTT
1 ATTT
3729944 AATTATGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 10 0.45
22 5 0.23
23 7 0.32
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (23 bp):
ATTTTATGTTTTGATAAAGATGA
Found at i:3732465 original size:32 final size:32
Alignment explanation
Indices: 3732421--3732516 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 32
3732411 AAGATACTAC
*
3732421 CAGTGTCGTATTCAAATAATGCACAATAGTGT
1 CAGTGTCATATTCAAATAATGCACAATAGTGT
* *
3732453 CAGTGTCATATTCAAATAATGCACAACAATGT
1 CAGTGTCATATTCAAATAATGCACAATAGTGT
* * * *
3732485 CAATGTCACATTCAGATAATGCATAATAGTGT
1 CAGTGTCATATTCAAATAATGCACAATAGTGT
3732517 GCCACGCATC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (32 bp):
CAGTGTCATATTCAAATAATGCACAATAGTGT
Found at i:3736389 original size:20 final size:20
Alignment explanation
Indices: 3736364--3736401 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3736354 TTTAAAAAGT
3736364 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
3736384 GGGGGAATCGGTTCCCCC
1 GGGGGAATCGGTACCCCC
3736402 CGAGCATACT
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:0.13, C:0.32, G:0.39, T:0.16
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:3742866 original size:22 final size:21
Alignment explanation
Indices: 3742824--3742863 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3742814 TAGTTTATTT
*
3742824 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3742845 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3742864 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3746589 original size:25 final size:25
Alignment explanation
Indices: 3746555--3746607 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
3746545 ATCCAGGAGT
3746555 TAATTTCTCAATAACGGTGGCTATC
1 TAATTTCTCAATAACGGTGGCTATC
3746580 TAATTTCTCAATAACGGTGGCTATC
1 TAATTTCTCAATAACGGTGGCTATC
3746605 TAA
1 TAA
3746608 AAGAATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (25 bp):
TAATTTCTCAATAACGGTGGCTATC
Found at i:3748089 original size:67 final size:67
Alignment explanation
Indices: 3747968--3748097 Score: 160
Period size: 67 Copynumber: 1.9 Consensus size: 67
3747958 TTCAAATCTA
* * *
3747968 AATAAATATTATTTTAATTTCAAATATTTAAAGTATATAATTATCTTAAGTATTCAAAGTTAAAA
1 AATAAATATCATTTTAAATTCAAATATTCAAAGTATATAATTATCTTAAGTATTCAAA-TTAAAA
3748033 AGT
65 AGT
*
3748036 AATAAATA-CATTTTAAATTCAAATATTCAAAG-A-GTAATTATCATACTAA-TATTCAAATTAA
1 AATAAATATCATTTTAAATTCAAATATTCAAAGTATATAATTATC-T--TAAGTATTCAAATTAA
3748097 A
63 A
3748098 TAATATATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
65 8 0.15
66 7 0.13
67 29 0.53
68 11 0.20
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (67 bp):
AATAAATATCATTTTAAATTCAAATATTCAAAGTATATAATTATCTTAAGTATTCAAATTAAAAA
GT
Found at i:3750473 original size:33 final size:34
Alignment explanation
Indices: 3750436--3750506 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
3750426 CCTTTACAAC
3750436 TCCCTAG-TTTT-TCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTAT-ACGGGATAAACTAGAACCTT
* * *
3750469 TCCCTAGCTTTTATACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTATACGGGATAAACTAGAACCTT
3750503 TCCC
1 TCCC
3750507 CTTTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 25 0.76
35 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (34 bp):
TCCCTAGCTTTTATACGGGATAAACTAGAACCTT
Found at i:3750857 original size:20 final size:20
Alignment explanation
Indices: 3750832--3750869 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3750822 CCGTTGCAGA
*
3750832 CAGGGTGTATGGATGCACAG
1 CAGGGTGCATGGATGCACAG
*
3750852 CAGGGTGCATTGATGCAC
1 CAGGGTGCATGGATGCAC
3750870 TAATTGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (20 bp):
CAGGGTGCATGGATGCACAG
Found at i:3750942 original size:20 final size:20
Alignment explanation
Indices: 3750919--3750959 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3750909 GGTGCATCGA
*
3750919 TGCACAGTACATGGATGCAC
1 TGCACAGTACATGGATACAC
* *
3750939 TGCAGAGTGCATGGATACAC
1 TGCACAGTACATGGATACAC
3750959 T
1 T
3750960 TTGACACCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (20 bp):
TGCACAGTACATGGATACAC
Found at i:3751210 original size:22 final size:21
Alignment explanation
Indices: 3751186--3751225 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3751176 ATGTTTAATA
3751186 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
3751207 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
3751226 CCAATTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:3754203 original size:20 final size:22
Alignment explanation
Indices: 3754178--3754217 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3754168 ATTCGTATAT
3754178 AGCCG-TTGGGGATG-TTTTGA
1 AGCCGTTTGGGGATGATTTTGA
3754198 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3754218 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGA
Found at i:3754378 original size:20 final size:19
Alignment explanation
Indices: 3754353--3754422 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 19
3754343 CGGTGTTTGA
3754353 GTGCATGGATGCACTACAGG
1 GTGCATGGATGCACTACA-G
*
3754373 GTGCATCGATG--C-ACA-
1 GTGCATGGATGCACTACAG
**
3754388 GTGCATGGATGCACTGGAG
1 GTGCATGGATGCACTACAG
*
3754407 AGTGCATGGATACACT
1 -GTGCATGGATGCACT
3754423 TTTCACCCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 10 0.25
17 4 0.10
18 2 0.05
20 24 0.60
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (19 bp):
GTGCATGGATGCACTACAG
Found at i:3756001 original size:10 final size:11
Alignment explanation
Indices: 3755981--3756006 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3755971 TTCTGTTACA
3755981 TTTTTATTTTT
1 TTTTTATTTTT
3755992 TTTTTATTTTT
1 TTTTTATTTTT
3756003 TTTT
1 TTTT
3756007 CGATTAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:3769479 original size:14 final size:13
Alignment explanation
Indices: 3769462--3769505 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
3769452 ATTTGAATTT
3769462 ATAAAAAAATAAAA
1 ATAAAAAAAT-AAA
3769476 ATAAAATAAATAAA
1 ATAAAA-AAATAAA
*
3769490 ATAAATAAAATGAA
1 ATAAA-AAAATAAA
3769504 AT
1 AT
3769506 GAAATGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:3769481 original size:5 final size:5
Alignment explanation
Indices: 3769467--3769516 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
3769457 AATTTATAAA
* *
3769467 AAAAT AAAAAT AAAAT -AAAT AAAAT -AAAT AAAAT GAAAT GAAAT GAAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
3769517 CAGTGAGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 8 0.21
5 22 0.56
6 9 0.23
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3769514 original size:10 final size:9
Alignment explanation
Indices: 3769474--3769510 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
3769464 AAAAAAATAA
3769474 AAATAAAAT
1 AAATAAAAT
3769483 AAATAAAAT
1 AAATAAAAT
3769492 AAATAAAAT
1 AAATAAAAT
*
3769501 GAAATGAAAT
1 -AAATAAAAT
3769511 GAAAATCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3772254 original size:35 final size:35
Alignment explanation
Indices: 3772215--3772308 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
3772205 AATGGATTAT
* * * *
3772215 GAATTTGGGGTTGGGTATATAATTGAAGTATTTTG
1 GAATTTGGGGTTGAGAATATAATTAAAGCATTTTG
** * *
3772250 GAATTTTAGGTTTAGAATGTAATTAAAGCATTTTG
1 GAATTTGGGGTTGAGAATATAATTAAAGCATTTTG
* *
3772285 GAATTTGGGGTTTAGAATGTAATT
1 GAATTTGGGGTTGAGAATATAATT
3772309 GATGACTGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.43
Consensus pattern (35 bp):
GAATTTGGGGTTGAGAATATAATTAAAGCATTTTG
Found at i:3773302 original size:16 final size:16
Alignment explanation
Indices: 3773264--3773313 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3773254 GTATTCTCTA
3773264 TTGTCTTTTTTA-TATT
1 TTGT-TTTTTTATTATT
* *
3773280 ATATTTTTATT-TTATT
1 TTGTTTTT-TTATTATT
3773296 TTGTTTTTTTATTATT
1 TTGTTTTTTTATTATT
3773312 TT
1 TT
3773314 CAATATGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (16 bp):
TTGTTTTTTTATTATT
Found at i:3774692 original size:533 final size:529
Alignment explanation
Indices: 3773683--3774715 Score: 1795
Period size: 533 Copynumber: 1.9 Consensus size: 529
3773673 ACCTGAAAGT
3773683 TATTAGTAATTTTCAAATGAATTAAAGGGCAAATAGGTCTTTGGACAAGGGAATAATTAAATAAG
1 TATTAGTAATTTTCAAATGAATTAAAGGGCAAATAGGTCTTTGGACAAGGGAATAATTAAATAAG
*
3773748 AATTTATGGGTATTATAATAACCCATGTGGAGCATGTTTGGAAACAAAGTTTCTAGACAATTCTC
66 AATTTATGGGTATTATAATAACCCATGTGGAGCATGTTTGGAAACAAAGTTTCCAGACAATTCTC
**
3773813 ATCTTCTTCCATTCTCCAACGTGAAGACCCAAGCCAAGGTAAGTTTAATTTCTTTTGGTTAATTC
131 ATCTTCTTCCATTCTCCAACGTGAAGACCCAAGCCAAGGTAAGTTTAATTTCTTTTCATTAATTC
3773878 TCAAAATTCAAGAGTGGGTTTTGATCCTTAGGTGATACTTAAGCTTAAGGAAAGCTTAAGTTGTC
196 TCAAAATTCAAGAGTGGGTTTTGATCCTTAGGTGATACTTAAGCTT----AAAGCTTAA---GTC
*
3773943 TTATAATCAAAAGATGAAGAAGTTATCAAAGATTAAAGAGAATGAGTTTCAAAGTGAAATTTTGA
254 TTATAATCAAAAGATGAAGAAGTTATCAAAGATTAAAGAAAATGAGTTTCAAAGTGAAATTTTGA
3774008 ATAAGAGGGTTTAAATGAATTTAGAGGTTGAATTTGACTTGTCATCAATCTAGTTAAGACATATG
319 ATAAGAGGGTTTAAATGAATTTAGAGGTTGAATTTGACTTGTCATCAATCTAGTTAAGACATATG
3774073 AAGTGTTAGAATTGAATTTACAACATGTTGAAATTTGAGTATGATTATTGAATTTCATAAAGAGG
384 AAGTGTTAGAATTGAATTTACAACATGTTGAAATTTGAGTATGATTATTGAATTTCATAAAGAGG
*
3774138 AGATGATATTAAGGTTAAAGATGGGATAAATCAATATTAGTGAGGGCAAATGAATATTGGGTTAA
449 AGAGGATATTAAGGTTAAAGATGGGATAAATCAATATTAGTGAGGGCAAATGAATATTGGGTTAA
3774203 AGATGGGATAAATGAA
514 AGATGGGATAAATGAA
*
3774219 TATTAGTAATTTTCAAATGAATTAAAGGGCAAATGGGTCTTTGGACAAGGGAATAATTAAATAAG
1 TATTAGTAATTTTCAAATGAATTAAAGGGCAAATAGGTCTTTGGACAAGGGAATAATTAAATAAG
3774284 AATTTATGGGTATTATAATAACCCATGTGGAGCATGTTTGGAAACAAAGTTTCCAGACAATTCTC
66 AATTTATGGGTATTATAATAACCCATGTGGAGCATGTTTGGAAACAAAGTTTCCAGAC-A-----
*
3774349 AGTTCTTCATCTTCTTCCCTTCTCCAACGTGAAGACCCAAGCCAAGGTAAGTTTAATTTCTTTTC
125 A-TTC-TCATCTTCTTCCATTCTCCAACGTGAAGACCCAAGCCAAGGTAAGTTTAATTTCTTTTC
3774414 ATTAATTCTCAAAATTCAAGAGTGGGTTTTGATCCTTAGGTGATACTTAAGCTT-AAG-TT-A-T
188 ATTAATTCTCAAAATTCAAGAGTGGGTTTTGATCCTTAGGTGATACTTAAGCTTAAAGCTTAAGT
*
3774475 CTTATAATCAAAAGATGAAGAAGTTATCAAAGATTAAAGAAAATGGGTTTCAAAGTGAAATTTTG
253 CTTATAATCAAAAGATGAAGAAGTTATCAAAGATTAAAGAAAATGAGTTTCAAAGTGAAATTTTG
**
3774540 AATAAGAGGGTTTAAATGAATTTATTGGTTGAATTTGACTTGTCATCAATCTAGTTAAGACATAT
318 AATAAGAGGGTTTAAATGAATTTAGAGGTTGAATTTGACTTGTCATCAATCTAGTTAAGACATAT
*
3774605 GAAGTGTTAGAATTGAATTTAGAACATGTTGAAATTTGAGTATGATTATTGAATTTCATAAAGAG
383 GAAGTGTTAGAATTGAATTTACAACATGTTGAAATTTGAGTATGATTATTGAATTTCATAAAGAG
*
3774670 GAGAGGATATTGAGGTTAAAGATGGGATAAATCAATATTAGTGAGG
448 GAGAGGATATTAAGGTTAAAGATGGGATAAATCAATATTAGTGAGG
3774716 CTAAGCATGT
Statistics
Matches: 477, Mismatches: 12, Indels: 19
0.94 0.02 0.04
Matches are distributed among these distances:
533 235 0.49
536 121 0.25
537 2 0.00
538 2 0.00
539 3 0.01
542 1 0.00
543 3 0.01
544 110 0.23
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (529 bp):
TATTAGTAATTTTCAAATGAATTAAAGGGCAAATAGGTCTTTGGACAAGGGAATAATTAAATAAG
AATTTATGGGTATTATAATAACCCATGTGGAGCATGTTTGGAAACAAAGTTTCCAGACAATTCTC
ATCTTCTTCCATTCTCCAACGTGAAGACCCAAGCCAAGGTAAGTTTAATTTCTTTTCATTAATTC
TCAAAATTCAAGAGTGGGTTTTGATCCTTAGGTGATACTTAAGCTTAAAGCTTAAGTCTTATAAT
CAAAAGATGAAGAAGTTATCAAAGATTAAAGAAAATGAGTTTCAAAGTGAAATTTTGAATAAGAG
GGTTTAAATGAATTTAGAGGTTGAATTTGACTTGTCATCAATCTAGTTAAGACATATGAAGTGTT
AGAATTGAATTTACAACATGTTGAAATTTGAGTATGATTATTGAATTTCATAAAGAGGAGAGGAT
ATTAAGGTTAAAGATGGGATAAATCAATATTAGTGAGGGCAAATGAATATTGGGTTAAAGATGGG
ATAAATGAA
Found at i:3775610 original size:40 final size:40
Alignment explanation
Indices: 3775563--3775642 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
3775553 AGTCGAGGGT
* *
3775563 TATACAGTTGTCCTTCGGGACTTAGTGGTCATTCGAGACA
1 TATACAGTGGTCCTTCGGGACATAGTGGTCATTCGAGACA
*
3775603 TATACAGTGGTCCTTCGGGACATAGTGGTCATTCGGGACA
1 TATACAGTGGTCCTTCGGGACATAGTGGTCATTCGAGACA
3775643 AATATTCAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (40 bp):
TATACAGTGGTCCTTCGGGACATAGTGGTCATTCGAGACA
Found at i:3775631 original size:18 final size:18
Alignment explanation
Indices: 3775576--3775642 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
3775566 ACAGTTGTCC
*
3775576 TTCGGGACTTAGTGGTCA
1 TTCGGGACATAGTGGTCA
* *
3775594 TTCGAGACATATACAGTGGTCC
1 TTCGGGAC--AT--AGTGGTCA
3775616 TTCGGGACATAGTGGTCA
1 TTCGGGACATAGTGGTCA
3775634 TTCGGGACA
1 TTCGGGACA
3775643 AATATTCAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 23 0.57
20 3 0.08
22 14 0.35
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (18 bp):
TTCGGGACATAGTGGTCA
Found at i:3779579 original size:20 final size:20
Alignment explanation
Indices: 3779556--3779593 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3779546 TTCCCCTGTG
*
3779556 GGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGATTCCCTCAA
*
3779576 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3779594 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:3779579 original size:21 final size:20
Alignment explanation
Indices: 3779533--3779593 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
3779523 CCAGAACCCT
*
3779533 AGGGGGGTATCGATTCCC-CTG
1 AGGGGGG-ATCGATTCCCTC-A
* *
3779554 TGGGGGGAATCGGTTCCCTCA
1 AGGGGGG-ATCGATTCCCTCA
3779575 AGGGGGGATCGATTCCCTC
1 AGGGGGGATCGATTCCCTC
3779594 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.33
21 21 0.64
22 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.23
Consensus pattern (20 bp):
AGGGGGGATCGATTCCCTCA
Found at i:3787424 original size:20 final size:20
Alignment explanation
Indices: 3787399--3787622 Score: 218
Period size: 20 Copynumber: 11.2 Consensus size: 20
3787389 TTTCGCGTTT
3787399 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* **
3787419 CGAATTTGAAATTCAGTGTTG
1 CGAATTTG-ACTTTTGTGTTG
* *
3787440 CGAATTTGACTATTGCGTTG
1 CGAATTTGACTTTTGTGTTG
3787460 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* * * *
3787480 CGAATTTGGCTATCGCGTTG
1 CGAATTTGACTTTTGTGTTG
3787500 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* ** * *
3787520 CG-ATTTAAAAATTCGCGTTG
1 CGAATTT-GACTTTTGTGTTG
*
3787540 CGAATTTGACTATTGCT-TTG
1 CGAATTTGACTTTTG-TGTTG
*
3787560 TGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
* * * *
3787580 CGGATTTGACTATCGCGTTG
1 CGAATTTGACTTTTGTGTTG
*
3787600 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTTTGTGTTG
3787620 CGA
1 CGA
3787623 TTTACATATT
Statistics
Matches: 158, Mismatches: 41, Indels: 10
0.76 0.20 0.05
Matches are distributed among these distances:
19 5 0.03
20 132 0.84
21 21 0.13
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTG
Found at i:3787576 original size:100 final size:100
Alignment explanation
Indices: 3787391--3787647 Score: 399
Period size: 100 Copynumber: 2.6 Consensus size: 100
3787381 ATATTGTGTT
* * *
3787391 TCGCGTTTCGAATTTGACTTTTGTGTTGCGAATTT-GAAATTCAGTGTTGCGAATTTGACTATTG
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCG-ATTTAAAAATTC-GCGTTGCGAATTTGACTATTG
*
3787455 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGGCTA
64 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
*
3787492 TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAAAAATTCGCGTTGCGAATTTGACTATTGCT
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAAAAATTCGCGTTGCGAATTTGACTATTGCG
* *
3787557 TTGTGAATTTGACTTTTGTGTTGCGGATTTGACTA
66 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
* * *
3787592 TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACATATTCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAAAAATTCGCGTTGCGAATTTG
3787648 GAAACTGGGT
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
100 110 0.76
101 35 0.24
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (100 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAAAAATTCGCGTTGCGAATTTGACTATTGCG
TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
Found at i:3787611 original size:40 final size:40
Alignment explanation
Indices: 3787391--3787647 Score: 216
Period size: 40 Copynumber: 6.4 Consensus size: 40
3787381 ATATTGTGTT
* * *
3787391 TCGCGTTTCGAATTTGACTTTTGTGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTA
* * *
3787430 TTCAGTGTTGCGAATTTGACTATTGCGTTGCGAATTTGACTT
1 -TC-GCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTA
* * * * * *
3787472 TTGTGTTGCGAATTTGGCTATCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTA
* * * ** *
3787512 TTGTGTTGCG-ATTTAAAAATTCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTT-GACTTTTGCGTTGCGAATTTGACTA
* * * * *
3787552 TTGCTTTGTGAATTTGACTTTTGTGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTA
* *
3787592 TCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACATA
1 TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGAC-TA
3787631 TTCGCGTTGCGAATTTG
1 -TCGCGTTGCGAATTTG
3787648 GAAACTGGGT
Statistics
Matches: 183, Mismatches: 28, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
38 2 0.01
39 10 0.05
40 135 0.74
41 36 0.20
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTA
Found at i:3787660 original size:40 final size:39
Alignment explanation
Indices: 3787436--3787687 Score: 118
Period size: 40 Copynumber: 6.3 Consensus size: 39
3787426 GAAATTCAGT
* * * * * *
3787436 GTTGCGAATTTGACTATTGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAACTGGGTTGCG-ATTTGACTATCGC
* * * * * *
3787476 GTTGCGAATTTGGCTA-TCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAACT-GGGTTGCG-ATTTGACTATCGC
* * * * *
3787516 GTTGCG-ATTTAAAAATTCGCGTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACAACT-GGGTTGCG-ATTTGACTATCGC
* * *** *
3787556 TTTGTGAATTTGACTTTTGTGTTGCGGATTTGACTATCGC
1 GTTGCGAATTTGACAACTGGGTTGC-GATTTGACTATCGC
** *
3787596 GTTGCGAATTTGACTTCTGTGTTGCGATTT-ACATATTCGC
1 GTTGCGAATTTGACAACTGGGTTGCGATTTGAC-TA-TCGC
* *
3787636 GTTGCGAATTTGGA-AACTGGGTTGCGAAATTGGAGT-TCGC
1 GTTGCGAATTT-GACAACTGGGTTGCG--ATTTGACTATCGC
3787676 GTTGCGAATTTG
1 GTTGCGAATTTG
3787688 TTGGTCATTT
Statistics
Matches: 179, Mismatches: 23, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
38 2 0.01
39 14 0.08
40 148 0.83
41 10 0.06
42 4 0.02
43 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.27, T:0.41
Consensus pattern (39 bp):
GTTGCGAATTTGACAACTGGGTTGCGATTTGACTATCGC
Found at i:3794367 original size:28 final size:27
Alignment explanation
Indices: 3794292--3794370 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 27
3794282 TTTATAATCG
*
3794292 TGTGAAAAATTCTAAAACAATATTATAATTA
1 TGTG-AAAATTCT--AA-AATATTACAATTA
* *
3794323 TGTAAAAAATTATAAAATATTACAATTA
1 TGT-GAAAATTCTAAAATATTACAATTA
3794351 TGTGAAAATTCTGAAAATAT
1 TGTGAAAATTCT-AAAATAT
3794371 AGTTATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
27 7 0.17
28 22 0.54
29 2 0.05
31 10 0.24
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (27 bp):
TGTGAAAATTCTAAAATATTACAATTA
Found at i:3796467 original size:25 final size:24
Alignment explanation
Indices: 3796438--3796500 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 24
3796428 TCTACAAAAA
3796438 TATTTTATTATATTA-TACATTCATT
1 TATTTTATTATATTATTACATT--TT
*
3796463 TATTTATTATTATTATTATTATATTTT
1 TA-TT-TTATTA-TATTATTACATTTT
3796490 TATTTTATTAT
1 TATTTTATTAT
3796501 TTTTGTAGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 1 0.03
25 8 0.24
26 4 0.12
27 10 0.30
28 5 0.15
29 5 0.15
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTTATTATATTATTACATTTT
Found at i:3796481 original size:16 final size:16
Alignment explanation
Indices: 3796438--3796500 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
3796428 TCTACAAAAA
3796438 TATTTTATTATATTAT
1 TATTTTATTATATTAT
*
3796454 ACATTCATTTATT-TATTAT
1 -TA-T--TTTATTATATTAT
*
3796473 TATTATTATTATATTTT
1 TATT-TTATTATATTAT
3796490 TATTTTATTAT
1 TATTTTATTAT
3796501 TTTTGTAGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
15 1 0.03
16 12 0.32
17 11 0.29
18 2 0.05
19 6 0.16
20 6 0.16
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTATTATATTAT
Found at i:3796484 original size:19 final size:19
Alignment explanation
Indices: 3796462--3796501 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3796452 ATACATTCAT
3796462 TTAT-TTATTATTATTATTA
1 TTATATTATTATT-TTATTA
*
3796481 TTATATTTTTATTTTATTA
1 TTATATTATTATTTTATTA
3796500 TT
1 TT
3796502 TTTGTAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATATTATTATTTTATTA
Found at i:3796492 original size:14 final size:14
Alignment explanation
Indices: 3796461--3796504 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3796451 TATACATTCA
3796461 TTTA-TTTATTATT
1 TTTATTTTATTATT
*
3796474 ATTATTATTA-TATT
1 TTTATT-TTATTATT
3796488 TTTATTTTATTATT
1 TTTATTTTATTATT
3796502 TTT
1 TTT
3796505 GTAGGCCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 6 0.23
14 17 0.65
15 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTTATTATT
Found at i:3796501 original size:25 final size:25
Alignment explanation
Indices: 3796438--3796501 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
3796428 TCTACAAAAA
3796438 TATTTTATTA-TATTATACATTCATT
1 TATTTTATTATTATTATACATT-ATT
*
3796463 TATTTATTATTATTATTATTATATT-TT
1 TA-TT-TTATTATTATTA-TACATTATT
3796490 TATTTTATTATT
1 TATTTTATTATT
3796502 TTTGTAGGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 10 0.29
26 4 0.12
27 10 0.29
28 5 0.15
29 5 0.15
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTATTATTATTATACATTATT
Found at i:3800857 original size:110 final size:110
Alignment explanation
Indices: 3800659--3801409 Score: 1105
Period size: 110 Copynumber: 6.9 Consensus size: 110
3800649 TTGATATGGT
* * *
3800659 AGCTCAACTTCACAGTGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
3800724 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
3800769 AGCTTAACTTCATAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
* *
3800834 CAATTTCAACTTTACAGCGAAGGATATTAGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* *
3800879 AGCTCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTGTCATTTAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
* * * *
3800944 CAATTTTAACTTCTCAGCGAAGGATATTGGACTCTAGATAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
3800989 AGCTCAACTTCACAGTGAATGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTAAAAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
* *
3801054 CAATTTCAATTTCACAGAGAAGGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* *
3801099 AGCTCAACTTCACAGCGAAGGGGGGGACTGACTATCAACAAACAACTTTTCAGTTTCATTTAGAG
1 AGCTCAACTTCACAGCGAA-GGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAG
* *
3801164 TCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACA
65 TCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
3801210 AGCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACAAATAACTTTTCAGTTTTATTTAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
*
3801275 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
** * * * * * *
3801320 AGCTCAACTTCACAATGAAGGGACGTCTGGCTGTTAATAAACAACTTTCCAG--T--TTTAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
* *
3801381 CAATTTCAACTTCACGGTGAAGGATATTG
66 CAATTTCAACTTCACAGCGAAGGATATTG
3801410 ACTTTGAAAT
Statistics
Matches: 582, Mismatches: 58, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
106 35 0.06
108 1 0.00
110 446 0.77
111 100 0.17
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (110 bp):
AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:3801274 original size:331 final size:327
Alignment explanation
Indices: 3800659--3801409 Score: 1164
Period size: 331 Copynumber: 2.3 Consensus size: 327
3800649 TTGATATGGT
3800659 AGCTCAACTTCACAGTGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAGAGT
1 AGCTCAACTTCACAGTGAA-GGGCGACTGACTGTCAACAAACAACTTTTCAG-TTTATT-AGAGT
* * *
3800724 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTTAACTTCATAGCGAAG
63 CAATTTCAACTTCACAGAGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAG
* *
3800789 GGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTTACAGCGA
128 GGGCGGCTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGA
* * *
3800854 AGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAA
193 AAGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACAA
* * * *
3800919 ACAACTTTTCAGTGTCATTTAGAGTCAATTTTAACTTCTCAGCGAAGGATATTGGACTCTAGATA
258 ACAACTTTTCAGTGTCATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACA
3800984 ACACA
323 ACACA
*
3800989 AGCTCAACTTCACAGTGAATGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTAAAAGT
1 AGCTCAACTTCACAGTGAA-GGGCGACTGACTGTCAACAAACAACTTTTCAGTTT-ATT-AGAGT
*
3801054 CAATTTCAATTTCACAGAGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAG
63 CAATTTCAACTTCACAGAGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAG
* *
3801119 GGGGGGACTGACTATCAACAAACAACTTTTCAGTTTCATTTAGAGTCAATTTCAACTTCACAGCG
128 GGGCGG-CTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCG
*
3801184 AAAGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACA
192 AAAGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACA
* * *
3801249 AATAACTTTTCAGTTTTATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
257 AACAACTTTTCAGTGTCATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
3801314 AACACA
322 AACACA
* * * * * *
3801320 AGCTCAACTTCACAATGAAGGGACGTCTGGCTGTTAATAAACAACTTTCCAG-TT-TTAGAGTCA
1 AGCTCAACTTCACAGTGAAGGG-CGACTGACTGTCAACAAACAACTTTTCAGTTTATTAGAGTCA
* *
3801383 ATTTCAACTTCACGGTGAAGGATATTG
65 ATTTCAACTTCACAGAGAAGGATATTG
3801410 ACTTTGAAAT
Statistics
Matches: 386, Mismatches: 32, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
327 30 0.08
328 2 0.01
329 3 0.01
330 129 0.33
331 222 0.58
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (327 bp):
AGCTCAACTTCACAGTGAAGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTATTAGAGTCAA
TTTCAACTTCACAGAGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGG
CGGCTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAAG
ATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGTGACTGACTGTCAACAAACA
ACTTTTCAGTGTCATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACA
CA
Found at i:3801778 original size:84 final size:84
Alignment explanation
Indices: 3801528--3802136 Score: 599
Period size: 84 Copynumber: 7.3 Consensus size: 84
3801518 AAGGGAATTA
* * * * * *
3801528 TGCCCACCAAAGGCCTTTGAGTTTGACTACGCTCAGCTCCAAGGTACATCATTTGTAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* *
3801593 TAAGTCAAGAAGGGTTATC
66 TAAGGCGAGAAGGGTTATC
* * * * ** * *
3801612 TGCCAACCGAAGACCCTCGAGTTCGATTACACTCAGCTTTTAGGGCACATCATTTACAGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAAC
* * *
3801677 TCAAGGCTAGAAGGGTTATT
65 TTAAGGCGAGAAGGGTTATC
** * * *
3801697 TG-TGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTATATCATTTGCAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
3801761 TTAAGGCGAGAAGGGTTATC
65 TTAAGGCGAGAAGGGTTATC
* *
3801781 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGTTCCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* *
3801846 TAAGTCGAGAAGGGCTATC
66 TAAGGCGAGAAGGGTTATC
* * * * * * * * **
3801865 TG----CCAAAGTCCCTCGAGTTCGATTACACTTAGCTTCGAGCGCACATCGTTTATAGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTGCAGCATAAC
* *
3801926 TCAAGGCTAGAAGGGTTATC
65 TTAAGGCGAGAAGGGTTATC
** * *
3801946 TG-TGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
*
3802010 TTAAGTCGAGAAGGGTTATC
65 TTAAGGCGAGAAGGGTTATC
* * * * * * * *
3802030 TGCCAACCAAAGACCTTTGAGTTCGACTCCACTAAGCTCAAAGACACCATCATTTGTAGCATAGC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAAC
* * *
3802095 TCAAGGCAAGAATGGTTATC
65 TTAAGGCGAGAAGGGTTATC
3802115 TG----CCAAAGACCTTCGAGTTCGA
1 TGCCAACCAAAGACCTTCGAGTTCGA
3802137 TTTCATTCAG
Statistics
Matches: 424, Mismatches: 91, Indels: 23
0.79 0.17 0.04
Matches are distributed among these distances:
80 29 0.07
81 54 0.13
84 212 0.50
85 129 0.30
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
TAAGGCGAGAAGGGTTATC
Found at i:3801975 original size:249 final size:249
Alignment explanation
Indices: 3801528--3802152 Score: 901
Period size: 249 Copynumber: 2.5 Consensus size: 249
3801518 AAGGGAATTA
* * * * *
3801528 TGCCCACCAAAGGCCTTTGAGTTTGACTACGCTCAGCTCCAAGGTACATCATTTGTAGCATAACT
1 TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCT
** *
3801593 TAAGTCAAGAAGGGTTATCTGCCAACCGAAGACCCTCGAGTTCGATTACACTCAGCTTTTAGGGC
66 TAAGTCAAGAAGGGTTATCTGCC-A---AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGCGC
* *
3801658 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACCTTTGAGTTCGA
127 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGA
* *
3801723 CTACGCTCAGCTCCAAGGTATATCATTTGCAGCATAACTTAAGGCGAGAAGGGTTATC
192 CTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGGCGAGAAGGGTTATC
* * *
3801781 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGTTCCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCT
* * * *
3801846 TAAGTCGAGAAGGGCTATCTGCCAAAGTCCCTCGAGTTCGATTACACTTAGCTTCGAGCGCACAT
66 TAAGTCAAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGCGCACAT
* *
3801911 CGTTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
131 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
*
3801976 GCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATC
196 GCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGGCGAGAAGGGTTATC
* * * * *
3802030 TGCCAACCAAAGACCTTTGAGTTCGACTCCACTAAGCTCAAAGACACCATCATTTGTAGCATAGC
1 TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGTAGCATAGC
* * * * * *
3802095 TCAAGGCAAGAATGGTTATCTGCCAAAGACCTTCGAGTTCGATTTCATTCAGC-TCGAG
65 TTAAGTCAAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAG
3802153 GGCGTATCAA
Statistics
Matches: 331, Mismatches: 40, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
249 192 0.58
250 60 0.18
252 1 0.00
253 78 0.24
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (249 bp):
TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCT
TAAGTCAAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGCGCACAT
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGGCGAGAAGGGTTATC
Found at i:3802490 original size:3 final size:3
Alignment explanation
Indices: 3802478--3802527 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
3802468 CAAAAACATT
3802478 TTA TTA -TA TTA TTTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
3802523 TTA TT
1 TTA TT
3802528 TTTGCAGGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3802926 original size:17 final size:17
Alignment explanation
Indices: 3802904--3802949 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
3802894 ACTTATTCTT
*
3802904 TTTATTTCATTTATTTA
1 TTTATTTCATTTATATA
3802921 TTTATTT-ACTTTATATA
1 TTTATTTCA-TTTATATA
3802938 TATT-TTTCATTT
1 T-TTATTTCATTT
3802950 TCTCCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 21 0.84
18 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTCATTTATATA
Found at i:3803051 original size:35 final size:35
Alignment explanation
Indices: 3802963--3803051 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
3802953 CCTAAATTTA
* *
3802963 ATATT-TTTATTTCTTTTTACATTGTTTTATATAT
1 ATATTATTTATTTATTTTTTCATTGTTTTATATAT
3802997 ATATTATTTATTTATTTTTTCATT-TTTTAT-TA-
1 ATATTATTTATTTATTTTTTCATTGTTTTATATAT
3803029 ATATTATTATATTAATATTTTTT
1 ATATTATT-TATT--TATTTTTT
3803052 ATTATTATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
32 8 0.16
33 6 0.12
34 11 0.22
35 24 0.49
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (35 bp):
ATATTATTTATTTATTTTTTCATTGTTTTATATAT
Found at i:3804004 original size:22 final size:23
Alignment explanation
Indices: 3803979--3804022 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3803969 GTTCAAATGT
* *
3803979 ACTTCTGTA-TCAGTGCTAAGGC
1 ACTTCAGTATTCAGTGCCAAGGC
3804001 ACTTCAGTATTCAGTGCCAAGG
1 ACTTCAGTATTCAGTGCCAAGG
3804023 TAATTTAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
ACTTCAGTATTCAGTGCCAAGGC
Found at i:3807038 original size:17 final size:17
Alignment explanation
Indices: 3807016--3807056 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3807006 TTGTCTTTTC
3807016 ATTTATCTACTGCTGAA
1 ATTTATCTACTGCTGAA
*
3807033 ATTTATCTATTGCTGAA
1 ATTTATCTACTGCTGAA
*
3807050 ACTTATC
1 ATTTATC
3807057 ATATACAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (17 bp):
ATTTATCTACTGCTGAA
Found at i:3807803 original size:6 final size:6
Alignment explanation
Indices: 3807792--3807820 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3807782 TTGTCATCTC
3807792 GGGAAA GGGAAA GGGAAA GGGAAA GGGAA
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAA
3807821 CGAAGGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:3808012 original size:21 final size:21
Alignment explanation
Indices: 3807996--3808049 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
3807986 GCGTTGCATT
3807996 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
3808017 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
3808038 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3808050 GGTATACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGGAAA
Found at i:3808105 original size:20 final size:21
Alignment explanation
Indices: 3808080--3808131 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3808070 TTTTCCCAAT
*
3808080 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3808100 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3808121 TCGCAATGCGA
1 TCGCAATGCGA
3808132 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3808145 original size:20 final size:20
Alignment explanation
Indices: 3808120--3808220 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
3808110 AATTGGGAAA
3808120 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3808140 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
3808160 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
3808181 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
3808201 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
3808221 TTCTCAACGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3808164 original size:61 final size:61
Alignment explanation
Indices: 3808117--3808233 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
3808107 GCGAATTGGG
* * * * *
3808117 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
3808178 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCTCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
3808234 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3808221 original size:20 final size:20
Alignment explanation
Indices: 3808182--3808234 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3808172 TAATACAAAA
* *
3808182 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
3808202 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
3808222 TCTCAACGCGATT
1 TCGCAACGCGATT
3808235 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:3808832 original size:19 final size:19
Alignment explanation
Indices: 3808805--3808988 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
3808795 AAAAATCGCA
* *
3808805 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
3808824 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3808843 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
3808862 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
3808882 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
3808898 T---GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
3808914 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
3808928 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
3808947 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
3808967 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3808987 TC
1 TC
3808989 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 16, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
13 10 0.07
14 10 0.07
16 4 0.03
17 2 0.01
19 59 0.44
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3808882 original size:39 final size:38
Alignment explanation
Indices: 3808805--3808894 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 38
3808795 AAAAATCGCA
*
3808805 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
3808843 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
3808882 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3808895 GTCTGTCGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 22 0.44
39 28 0.56
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:3808913 original size:32 final size:33
Alignment explanation
Indices: 3808877--3808963 Score: 140
Period size: 32 Copynumber: 2.6 Consensus size: 33
3808867 GTTGCGATTT
*
3808877 TCATTTCGCGTTGCGATTGTCT-GTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
3808909 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
3808942 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
3808964 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 21 0.41
33 15 0.29
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:3808965 original size:20 final size:20
Alignment explanation
Indices: 3808931--3808988 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
3808921 GCGATTCTCT
**
3808931 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
3808951 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
3808971 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
3808989 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:3811047 original size:42 final size:42
Alignment explanation
Indices: 3810987--3811109 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
3810977 GCCCGACTCG
* * *
3810987 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
3811029 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
3811071 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
3811110 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:3811067 original size:21 final size:21
Alignment explanation
Indices: 3811043--3811109 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3811033 TCATTCCTCG
3811043 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3811064 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3811085 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3811106 AGAG
1 AGAG
3811110 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3812483 original size:14 final size:14
Alignment explanation
Indices: 3812464--3812499 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3812454 ATTGTTTAAT
3812464 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3812478 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3812492 TGATTTGT
1 TGATTTGT
3812500 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3812650 original size:19 final size:19
Alignment explanation
Indices: 3812626--3812684 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
3812616 GAAATTAGCG
3812626 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3812645 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3812659 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3812678 TTGCGAT
1 TTGCGAT
3812685 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3812650 original size:33 final size:34
Alignment explanation
Indices: 3812607--3812683 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
3812597 AAAAGTACTA
*
3812607 TCGCAATGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
* **
3812640 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
3812673 TCGCATTGCGA
1 TCGCATTGCGA
3812684 TAGTAATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
Found at i:3814990 original size:12 final size:12
Alignment explanation
Indices: 3814973--3814997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3814963 TCTTCGGGGA
3814973 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3814985 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3814997 C
1 C
3814998 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3815222 original size:23 final size:24
Alignment explanation
Indices: 3815172--3815224 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3815162 CTGAAACATC
* *
3815172 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
3815196 ATCAAAGTCCGGGTATT-ACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
3815219 ATCAAA
1 ATCAAA
3815225 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:3816340 original size:14 final size:14
Alignment explanation
Indices: 3816321--3816374 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
3816311 GAAAATCGCA
3816321 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
3816335 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
3816352 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
3816368 TTGCGAT
1 TTGCGAT
3816375 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:3816340 original size:33 final size:33
Alignment explanation
Indices: 3816303--3816373 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
3816293 AAAATCGCAA
3816303 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
3816336 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
3816369 TGCGA
1 TGCGA
3816374 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:3816374 original size:33 final size:33
Alignment explanation
Indices: 3816316--3816393 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
3816306 GAAATGAAAA
***
3816316 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
3816349 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
3816382 TCGCGTTGCGAT
1 TCGCATTGCGAT
3816394 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:3816500 original size:14 final size:14
Alignment explanation
Indices: 3816481--3816517 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3816471 CATCAATTAA
3816481 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3816495 ACAAATCATCTTTT
1 ACAAATCAACATTT
3816509 ACAAATCAA
1 ACAAATCAA
3816518 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3818405 original size:20 final size:19
Alignment explanation
Indices: 3818370--3818436 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
3818360 GAAACTTAAA
3818370 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3818389 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3818409 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3818428 ATCGCAACG
1 ATCGCAACG
3818437 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3818503 original size:14 final size:14
Alignment explanation
Indices: 3818484--3818541 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3818474 TTTCATTTCG
3818484 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3818498 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3818514 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3818530 CGTTGCGATTTT
1 CGTTGCGATTTT
3818542 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3818548 original size:33 final size:33
Alignment explanation
Indices: 3818467--3818557 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3818457 ACAAATCGCA
*
3818467 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3818500 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3818532 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
3818558 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:3818576 original size:20 final size:19
Alignment explanation
Indices: 3818542--3818596 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3818532 TTGCGATTTT
*
3818542 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3818561 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3818581 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3818597 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3819102 original size:18 final size:18
Alignment explanation
Indices: 3819076--3819120 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3819066 GTCGATCAGA
*
3819076 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
3819094 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
3819112 TGATGGCTC
1 TGATGGCTC
3819121 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:3820484 original size:20 final size:20
Alignment explanation
Indices: 3820442--3820515 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
3820432 AATAGTTTCT
**
3820442 GAAAATGAAAATCGCAATAC
1 GAAAATGAAAATCGCAACGC
3820462 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
* **
3820482 G-AATTCGACTATCGCAACGC
1 GAAAAT-GAAAATCGCAACGC
*
3820502 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
3820516 GTTGCGATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.20
20 32 0.73
21 3 0.07
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.15
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:3820775 original size:22 final size:22
Alignment explanation
Indices: 3820748--3820791 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3820738 GATGGAGATA
3820748 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3820770 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3820792 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3821004 original size:20 final size:20
Alignment explanation
Indices: 3820979--3821051 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
3820969 GATTATGTAT
3820979 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
3820999 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3821019 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
3821039 TATCTCGTTGCGA
1 TATCGCGTTGCGA
3821052 TTTTTTATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3821096 original size:21 final size:21
Alignment explanation
Indices: 3821072--3821142 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
3821062 TCGCATTGCA
3821072 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
3821093 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
3821113 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
3821134 TTGCGATTT
1 TTGCGATTT
3821143 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:3821111 original size:20 final size:20
Alignment explanation
Indices: 3821086--3821159 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
3821076 GATTTTCCCA
*
3821086 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
3821106 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
3821127 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
3821147 ATTCGCATTGCGA
1 ATTCGCATTGCGA
3821160 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:3821126 original size:41 final size:41
Alignment explanation
Indices: 3821069--3821159 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
3821059 TTATCGCATT
3821069 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
1 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
3821110 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
1 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
3821151 GCATTGCGA
1 GCATTGCGA
3821160 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.40
Consensus pattern (41 bp):
GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
Found at i:3827802 original size:24 final size:23
Alignment explanation
Indices: 3827759--3827803 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
3827749 TTTAATTATT
*
3827759 TATTATTAGAATTTTTAGTTTAC
1 TATTATTAGAATTTTAAGTTTAC
3827782 TATTAATTAGGAA-TTTAAGTTT
1 TATT-ATTA-GAATTTTAAGTTT
3827804 TAAATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.53
Consensus pattern (23 bp):
TATTATTAGAATTTTAAGTTTAC
Found at i:3831073 original size:21 final size:21
Alignment explanation
Indices: 3831047--3831191 Score: 164
Period size: 21 Copynumber: 6.8 Consensus size: 21
3831037 CCATATAGAA
3831047 ATGTCCCGAAGGACCACATAT
1 ATGTCCCGAAGGACCACATAT
* *
3831068 ATGTCCCGAATGACCACATAGA
1 ATGTCCCGAAGGACCACATA-T
*
3831090 ATTGTCCCTAAGGACCACATAT
1 A-TGTCCCGAAGGACCACATAT
* * *
3831112 ATGTTCCAAAGGACCAAATAT
1 ATGTCCCGAAGGACCACATAT
*
3831133 ATGTCCCGAAGGACCGCATAT
1 ATGTCCCGAAGGACCACATAT
* * * * *
3831154 ATATTCCAAAAGATCACATAT
1 ATGTCCCGAAGGACCACATAT
3831175 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
3831192 GTAGAACCCT
Statistics
Matches: 99, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
21 80 0.81
22 2 0.02
23 17 0.17
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAT
Found at i:3831083 original size:44 final size:43
Alignment explanation
Indices: 3831025--3831191 Score: 151
Period size: 42 Copynumber: 3.9 Consensus size: 43
3831015 CATATAAAAT
* *
3831025 TGTCCTAAAAGACCATATAGAAATGTCCCGAAGGACCACATATA
1 TGTCCCAAAGGACCA-ATAGAAATGTCCCGAAGGACCACATATA
* * * *
3831069 TGTCCCGAATGACCACATAGAATTGTCCCTAAGGACCACATATA
1 TGTCCCAAAGGACCA-ATAGAAATGTCCCGAAGGACCACATATA
* * * *
3831113 TGTTCCAAAGGACCAA-ATATATGTCCCGAAGGACCGCATATA
1 TGTCCCAAAGGACCAATAGAAATGTCCCGAAGGACCACATATA
* * * * *
3831155 TATTCCAAAAGATCACAT--ATATGTCCCGAAGGACCAC
1 TGTCCCAAAGGACCA-ATAGAAATGTCCCGAAGGACCAC
3831192 GTAGAACCCT
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 51 0.50
43 2 0.02
44 50 0.49
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (43 bp):
TGTCCCAAAGGACCAATAGAAATGTCCCGAAGGACCACATATA
Found at i:3831153 original size:42 final size:42
Alignment explanation
Indices: 3831047--3831191 Score: 182
Period size: 42 Copynumber: 3.4 Consensus size: 42
3831037 CCATATAGAA
* * * *
3831047 ATGTCCCGAAGGACCACATATATGTCCCGAATGACCACATAGA
1 ATGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATA-T
* * *
3831090 ATTGTCCCTAAGGACCACATATATGTTCCAAAGGACCAAATAT
1 A-TGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATAT
* * *
3831133 ATGTCCCGAAGGACCGCATATATATTCCAAAAGATCACATAT
1 ATGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATAT
3831175 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
3831192 GTAGAACCCT
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 51 0.58
43 2 0.02
44 35 0.40
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (42 bp):
ATGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATAT
Found at i:3835827 original size:24 final size:24
Alignment explanation
Indices: 3835800--3835858 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
3835790 CACATATATC
*
3835800 ATCATTATCATCATCAATATTCTT
1 ATCATTATCATCATCAACATTCTT
3835824 ATCATTATCATCATCAACATTCTT
1 ATCATTATCATCATCAACATTCTT
3835848 ATCATTATCAT
1 ATCATTATCAT
3835859 ATTTTATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (24 bp):
ATCATTATCATCATCAACATTCTT
Found at i:3836106 original size:25 final size:24
Alignment explanation
Indices: 3836078--3836131 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
3836068 CACTGAGTGC
3836078 CATATAAAATTATCCCGAAGGACCA
1 CATATAAAA-TATCCCGAAGGACCA
* * * *
3836103 CATA-GAAATGTCCTGAATGACCA
1 CATATAAAATATCCCGAAGGACCA
3836126 CATATA
1 CATATA
3836132 TCCCGAATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
23 16 0.70
24 3 0.13
25 4 0.17
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (24 bp):
CATATAAAATATCCCGAAGGACCA
Found at i:3836150 original size:42 final size:42
Alignment explanation
Indices: 3836088--3836174 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
3836078 CATATAAAAT
* *
3836088 TATCCCGAAGGACCACATAGAAATGT-CCTGAATGACCACATA
1 TATCCCGAAGGACCAAATAGAAATGTCCCT-AAAGACCACATA
* *
3836130 TATCCCGAATGACCAAATAGAATTGTCCCTAAAGACCACATA
1 TATCCCGAAGGACCAAATAGAAATGTCCCTAAAGACCACATA
3836172 TAT
1 TAT
3836175 GTTCCAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (42 bp):
TATCCCGAAGGACCAAATAGAAATGTCCCTAAAGACCACATA
Found at i:3836166 original size:23 final size:21
Alignment explanation
Indices: 3836140--3836192 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
3836130 TATCCCGAAT
*
3836140 GACCAAATAGAATTGTCCCTAAA
1 GACCAAATA-AA-TGTCCCAAAA
* * *
3836163 GACCACATATATGTTCCAAAA
1 GACCAAATAAATGTCCCAAAA
3836184 GACCAAATA
1 GACCAAATA
3836193 TATCCCGAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 16 0.64
22 1 0.04
23 8 0.32
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.21
Consensus pattern (21 bp):
GACCAAATAAATGTCCCAAAA
Found at i:3836185 original size:21 final size:21
Alignment explanation
Indices: 3836160--3836233 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
3836150 AATTGTCCCT
3836160 AAAGACCACATATATGTTCCA
1 AAAGACCACATATATGTTCCA
* * *
3836181 AAAGACCA-A-ATATATCCCG
1 AAAGACCACATATATGTTCCA
* *
3836200 AAGGACCGCATATATGTTCCA
1 AAAGACCACATATATGTTCCA
* *
3836221 AATGATCACATAT
1 AAAGACCACATAT
3836234 GTGTCCTGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 25 0.62
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAGACCACATATATGTTCCA
Found at i:3844661 original size:18 final size:18
Alignment explanation
Indices: 3844629--3844663 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3844619 AATTAGGAAT
**
3844629 TTAAGAGTTTTTATTTTC
1 TTAAGAGTTAGTATTTTC
3844647 TTAAGAGTTAGTATTTT
1 TTAAGAGTTAGTATTTT
3844664 ATTTCATTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (18 bp):
TTAAGAGTTAGTATTTTC
Found at i:3851498 original size:20 final size:20
Alignment explanation
Indices: 3851473--3851516 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3851463 TTCTAATAAC
3851473 AACTACGAAAGTAAATGACT
1 AACTACGAAAGTAAATGACT
*
3851493 AACTACGAAAGTAAATGATT
1 AACTACGAAAGTAAATGACT
3851513 AACT
1 AACT
3851517 GTGGTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (20 bp):
AACTACGAAAGTAAATGACT
Found at i:3853413 original size:6 final size:6
Alignment explanation
Indices: 3853394--3853423 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3853384 TTCGCAATAT
*
3853394 ACCCGA ACCTGA ACCCGA ACCCGA ACCCGA
1 ACCCGA ACCCGA ACCCGA ACCCGA ACCCGA
3853424 TGAAGTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.47, G:0.17, T:0.03
Consensus pattern (6 bp):
ACCCGA
Found at i:3854063 original size:21 final size:21
Alignment explanation
Indices: 3854039--3854081 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3854029 TTACATTCCT
*
3854039 AGCCCACAGGGGTACATACTC
1 AGCCCACAAGGGTACATACTC
*
3854060 AGCCCACAAGGTTACATACTC
1 AGCCCACAAGGGTACATACTC
3854081 A
1 A
3854082 ACCTGTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.16
Consensus pattern (21 bp):
AGCCCACAAGGGTACATACTC
Found at i:3855178 original size:65 final size:64
Alignment explanation
Indices: 3855073--3855224 Score: 182
Period size: 65 Copynumber: 2.4 Consensus size: 64
3855063 AATTAAATTG
* * *
3855073 AACATCGAATGCATTTGATGCATCGATGCATATACGATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATATTT-TG-
3855137 A
64 A
* * * *
3855138 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCGATGCACTCAGGATATTTTGA
* *
3855202 AACATCGAAAGCACTTGATGCAT
1 AACATCGAATGCATTTGATGCAT
3855225 TGATAAGAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 22 0.29
65 50 0.66
66 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:3859104 original size:15 final size:15
Alignment explanation
Indices: 3859084--3859118 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3859074 ATCAAAGGAA
3859084 GAAACGAAAAATGAG
1 GAAACGAAAAATGAG
3859099 GAAACGAAAAATGAG
1 GAAACGAAAAATGAG
3859114 GAAAC
1 GAAAC
3859119 TCATGATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.26, T:0.06
Consensus pattern (15 bp):
GAAACGAAAAATGAG
Found at i:3864373 original size:30 final size:29
Alignment explanation
Indices: 3864313--3864400 Score: 104
Period size: 30 Copynumber: 3.0 Consensus size: 29
3864303 AATGGATTTA
* *
3864313 TTTAATGACCAAATTATAAATTTGGTAAAG
1 TTTAGTGACCAAAATATAAATTTGG-AAAG
*
3864343 TTTAGTGATCAAAATATAAACTTTGGAAAG
1 TTTAGTGACCAAAATATAAA-TTTGGAAAG
* * *
3864373 TTTAGGGACCAAAATGTAATTTTGGAAA
1 TTTAGTGACCAAAATATAAATTTGGAAA
3864401 AATTACAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 8 0.16
30 37 0.74
31 5 0.10
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (29 bp):
TTTAGTGACCAAAATATAAATTTGGAAAG
Found at i:3866125 original size:40 final size:40
Alignment explanation
Indices: 3866070--3866231 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
3866060 GCAGGTTTTA
*
3866070 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3866110 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
3866150 TAATACACTTTGGTGTATATGGTGGGCACGGCCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3866190 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
3866230 TA
1 TA
3866232 GCACTACGGT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:3866952 original size:22 final size:22
Alignment explanation
Indices: 3866909--3866963 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3866899 CGCATCGGTA
* *
3866909 CACTGTTCACGGGTTTTGTTCAT
1 CACTGTTCA-TGGTATTGTTCAT
3866932 CACTGTTCATGGTATTGTTCAT
1 CACTGTTCATGGTATTGTTCAT
*
3866954 CACTATTCAT
1 CACTGTTCAT
3866964 AAAAAAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (22 bp):
CACTGTTCATGGTATTGTTCAT
Found at i:3868461 original size:13 final size:13
Alignment explanation
Indices: 3868443--3868470 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3868433 TGATATAAGC
3868443 AATGGTTGCGATT
1 AATGGTTGCGATT
3868456 AATGGTTGCGATT
1 AATGGTTGCGATT
3868469 AA
1 AA
3868471 GATGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (13 bp):
AATGGTTGCGATT
Found at i:3868787 original size:2 final size:2
Alignment explanation
Indices: 3868780--3868805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3868770 GGTGTTGTAA
3868780 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
3868806 GCGATTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3869296 original size:2 final size:2
Alignment explanation
Indices: 3869289--3869322 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3869279 TAAGAGCTAA
3869289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3869323 AAAAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3869340 original size:13 final size:13
Alignment explanation
Indices: 3869324--3869382 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
3869314 TATAATATAA
3869324 AAAAAAGAAACAG
1 AAAAAAGAAACAG
3869337 AAAAAAG--A-AG
1 AAAAAAGAAACAG
3869347 -AAAAAGAAAACAG
1 AAAAAAG-AAACAG
*
3869360 AAAACAGAAAACAG
1 AAAAAAG-AAACAG
3869374 -AAAAAGAAA
1 AAAAAAGAAA
3869383 AAAAATGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
11 1 0.03
12 4 0.10
13 14 0.36
14 12 0.31
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAACAG
Found at i:3869353 original size:6 final size:6
Alignment explanation
Indices: 3869325--3869436 Score: 81
Period size: 6 Copynumber: 18.8 Consensus size: 6
3869315 ATAATATAAA
* *
3869325 AAAAAG AAACAG -AAAA- AAGAAG AAAAAG AAAACAG AAAACAG AAAACAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AAAA-AG AAAA-AG
* * * *
3869374 AAAAAG -AAAA- AAAATG AAAGAAT AAAAAG AAAAAG AAAACG AATAA-
1 AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
**
3869420 AAATTG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAA
3869437 AAATGAGAGG
Statistics
Matches: 83, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
5 15 0.18
6 44 0.53
7 24 0.29
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:3869357 original size:23 final size:22
Alignment explanation
Indices: 3869325--3869437 Score: 86
Period size: 23 Copynumber: 4.8 Consensus size: 22
3869315 ATAATATAAA
*
3869325 AAAAAGAAACAGAAAAAAGAAG
1 AAAAAGAAAAAGAAAAAAGAAG
*
3869347 AAAAAGAAAACAGAAAACAGAAAACAG
1 AAAAAGAAAA-AG-AAA-A-AAGA-AG
*
3869374 AAAAAGAAAAA-AAATGAAAGAAT
1 AAAAAGAAAAAGAAA--AAAGAAG
* *
3869397 AAAAAGAAAAAG-AAAACGAAT
1 AAAAAGAAAAAGAAAAAAGAAG
3869418 AAAAATTGAAAAAGAAAAAA
1 AAAAA--GAAAAAGAAAAAA
3869438 AATGAGAGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
21 11 0.15
22 9 0.12
23 23 0.31
24 13 0.18
25 2 0.03
26 4 0.05
27 12 0.16
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.04
Consensus pattern (22 bp):
AAAAAGAAAAAGAAAAAAGAAG
Found at i:3869361 original size:7 final size:7
Alignment explanation
Indices: 3869345--3869383 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
3869335 AGAAAAAAGA
3869345 AGAAAA-
1 AGAAAAC
3869351 AGAAAAC
1 AGAAAAC
3869358 AGAAAAC
1 AGAAAAC
3869365 AGAAAAC
1 AGAAAAC
3869372 AGAAAA-
1 AGAAAAC
3869378 AGAAAA
1 AGAAAA
3869384 AAAATGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.38
7 20 0.62
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (7 bp):
AGAAAAC
Found at i:3869383 original size:13 final size:13
Alignment explanation
Indices: 3869325--3869383 Score: 72
Period size: 14 Copynumber: 4.8 Consensus size: 13
3869315 ATAATATAAA
3869325 AAAAAG-AAACAG
1 AAAAAGAAAACAG
*
3869337 -AAAA-AAGA-AG
1 AAAAAGAAAACAG
3869347 AAAAAGAAAACAG
1 AAAAAGAAAACAG
3869360 AAAACAGAAAACAG
1 AAAA-AGAAAACAG
3869374 AAAAAGAAAA
1 AAAAAGAAAA
3869384 AAAATGAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 2 0.05
11 10 0.25
12 3 0.08
13 12 0.30
14 13 0.32
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAACAG
Found at i:3869384 original size:7 final size:7
Alignment explanation
Indices: 3869324--3869412 Score: 60
Period size: 7 Copynumber: 12.6 Consensus size: 7
3869314 TATAATATAA
3869324 AAAAAAG
1 AAAAAAG
*
3869331 -AAACAG
1 AAAAAAG
3869337 AAAAAAG
1 AAAAAAG
3869344 AAGAAAAAG
1 -A-AAAAAG
*
3869353 AAAACAG
1 AAAAAAG
*
3869360 AAAACAG
1 AAAAAAG
*
3869367 AAAACAG
1 AAAAAAG
3869374 -AAAAAG
1 AAAAAAG
3869380 AAAAAA-
1 AAAAAAG
*
3869386 AATGAAAG
1 AA-AAAAG
3869394 AATAAAA-
1 AA-AAAAG
3869401 AGAAAAAG
1 A-AAAAAG
3869409 AAAA
1 AAAA
3869413 CGAATAAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
6 12 0.18
7 40 0.59
8 10 0.15
9 6 0.09
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:3869429 original size:29 final size:30
Alignment explanation
Indices: 3869366--3869436 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
3869356 ACAGAAAACA
3869366 GAAAACAGAAAAAGAAAAAAAATGAAAGAAT
1 GAAAA-AGAAAAAGAAAAAAAATGAAAGAAT
**
3869397 -AAAAAGAAAAAGAAAACGAAT-AAA-AATT
1 GAAAAAGAAAAAGAAAAAAAATGAAAGAA-T
3869425 GAAAAAGAAAAA
1 GAAAAAGAAAAA
3869437 AAATGAGAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 26 0.72
30 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (30 bp):
GAAAAAGAAAAAGAAAAAAAATGAAAGAAT
Found at i:3871181 original size:30 final size:29
Alignment explanation
Indices: 3871113--3871195 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
3871103 ATTTATTTAA
* *
3871113 TGACCAAATTATAAATTTGGTAAAGTTTGG
1 TGACCAAAATATAAATTTGG-AAAGTTAGG
*
3871143 TGATCAAAATATAAACTTTGGAAAGTTCAGG
1 TGACCAAAATATAAA-TTTGGAAAGTT-AGG
* *
3871174 -GACCAAAATGTAATTTTGGAAA
1 TGACCAAAATATAAATTTGGAAA
3871196 AATTACAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 8 0.18
30 30 0.67
31 7 0.16
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.31
Consensus pattern (29 bp):
TGACCAAAATATAAATTTGGAAAGTTAGG
Found at i:3873211 original size:40 final size:40
Alignment explanation
Indices: 3873156--3873317 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
3873146 TGCAAGTTTA
3873156 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3873196 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATTTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3873236 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
3873276 TAATACACTTCGGTGTATATGGTGGACACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
3873316 TA
1 TA
3873318 GCACTACGGT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 116 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:3873515 original size:45 final size:45
Alignment explanation
Indices: 3873425--3873531 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
3873415 AGCATGCAAG
* *
3873425 TAAGCTTACGAGCTTATGGAATATTGGCAAGTATATGGGTAAAAA
1 TAAGCTTACGAGCTTATGGAATAATGACAAGTATATGGGTAAAAA
* * *
3873470 TAAGCTTACGAGCTTATGGGACA-AATGATAAGTATTTTGGT-AAAA
1 TAAGCTTACGAGCTTAT-GGA-ATAATGACAAGTATATGGGTAAAAA
3873515 TAAGCTTACGAGCTTAT
1 TAAGCTTACGAGCTTAT
3873532 TGTTAATAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 38 0.69
46 16 0.29
47 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (45 bp):
TAAGCTTACGAGCTTATGGAATAATGACAAGTATATGGGTAAAAA
Found at i:3873897 original size:18 final size:18
Alignment explanation
Indices: 3873874--3873912 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3873864 TTATGATTTT
3873874 TGTAGCACGTCGATGGAC
1 TGTAGCACGTCGATGGAC
* * *
3873892 TGTAGCCCGTTGATGTAC
1 TGTAGCACGTCGATGGAC
3873910 TGT
1 TGT
3873913 TGCAGTGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.31
Consensus pattern (18 bp):
TGTAGCACGTCGATGGAC
Found at i:3874276 original size:39 final size:39
Alignment explanation
Indices: 3874233--3874324 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 39
3874223 GGTGTTAAAC
*
3874233 TAACATTCTAAATTCCTAATTTCTTAAATTTTTTCACCA-
1 TAACATTCTAAATTCCTAATTTCTTAAATTATTTCA-CAT
* *
3874272 TAACATTCTAAATTCTTAATTTGTTAAATTATTTCACAT
1 TAACATTCTAAATTCCTAATTTCTTAAATTATTTCACAT
*
3874311 TAACATTATAAATT
1 TAACATTCTAAATT
3874325 ATTTTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.04
39 46 0.96
ACGTcount: A:0.37, C:0.15, G:0.01, T:0.47
Consensus pattern (39 bp):
TAACATTCTAAATTCCTAATTTCTTAAATTATTTCACAT
Found at i:3874647 original size:30 final size:30
Alignment explanation
Indices: 3874590--3874649 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3874580 ACACGGACTG
***
3874590 AAATTTTGATACCCGAAAATTTTGGGTACC
1 AAATTTTGATACCCGAAAATCACGGGTACC
3874620 AAATTTTGGATACCCGAAAA-CACGGGTACC
1 AAATTTT-GATACCCGAAAATCACGGGTACC
3874650 TGGTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (30 bp):
AAATTTTGATACCCGAAAATCACGGGTACC
Found at i:3879320 original size:16 final size:15
Alignment explanation
Indices: 3879282--3879326 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
3879272 GCCCTAAATT
3879282 GAAAAAAATGAAAAAA
1 GAAAAAAA-GAAAAAA
3879298 GAGAAAAAAGAACAAAA
1 GA-AAAAAAGAA-AAAA
*
3879315 GAAAAAGAGAAA
1 GAAAAAAAGAAA
3879327 GAACAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
17 12 0.46
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (15 bp):
GAAAAAAAGAAAAAA
Found at i:3880201 original size:146 final size:146
Alignment explanation
Indices: 3879937--3880230 Score: 561
Period size: 146 Copynumber: 2.0 Consensus size: 146
3879927 TCAAGATTCC
*
3879937 AGACATATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
1 AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
* *
3880002 AGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
66 AGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
3880067 TTCAACTTCACATCGA
131 TTCAACTTCACATCGA
3880083 AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
1 AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
3880148 AGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
66 AGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
3880213 TTCAACTTCACATCGA
131 TTCAACTTCACATCGA
3880229 AG
1 AG
3880231 GATGTTGGAC
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
146 145 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (146 bp):
AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
AGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
TTCAACTTCACATCGA
Found at i:3880432 original size:95 final size:98
Alignment explanation
Indices: 3880256--3880710 Score: 496
Period size: 106 Copynumber: 4.5 Consensus size: 98
3880246 ACAACCAAGA
3880256 ACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCACTTTCAACTTCAC
1 ACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAG---C--TCAAC-T--C
*
3880321 AGCGAAGGATATTGGACTTAG-GACAACACAAGTTCAACTTC
58 AGCGAAGGATATTGGAC-TAGAGACGACACAAGTTCAACTTC
*
3880362 ACAACGAAGGGACGACTGGTTGTCAACAAACAATCTCCCAATTTCAGAGC-CAA-T-AGCGAAGG
1 ACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCTCAACTCAGCGAAGG
3880424 ATATTGGACTAGAGACGACACAAGTTCAACTTC
66 ATATTGGACTAGAGACGACACAAGTTCAACTTC
* * * *
3880457 ACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCTAATTTTAGGGTCAATTTCAACTTCAC
1 ACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAG-C----TCAAC-T--C
* * * *
3880522 ATCGAAGGATATTGAACTCGAGAC--CACAAGTTTAACTTC
58 AGCGAAGGATATTGGACTAGAGACGACACAAGTTCAACTTC
* * *
3880561 ACAACAAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTCATAGCAAATTTCAACTTCAC
1 ACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC-----TCAAC-T--C
*
3880626 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTC
58 AGCGAAGGATATTGGACTAGAGACGACACAAGTTCAACTTC
3880667 ACAACGAAGGGACG---GGTTGTCAACAAACAATTTCCCAATTTCAG
1 ACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAG
3880711 GGTCAATTTT
Statistics
Matches: 310, Mismatches: 24, Indels: 33
0.84 0.07 0.09
Matches are distributed among these distances:
94 3 0.01
95 80 0.26
96 1 0.00
98 1 0.00
100 3 0.01
101 3 0.01
103 31 0.10
104 92 0.30
106 96 0.31
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (98 bp):
ACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCTCAACTCAGCGAAGG
ATATTGGACTAGAGACGACACAAGTTCAACTTC
Found at i:3880673 original size:305 final size:295
Alignment explanation
Indices: 3880122--3880833 Score: 874
Period size: 298 Copynumber: 2.3 Consensus size: 295
3880112 CTGCACAGTA
3880122 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACA
* * *
3880187 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGTTGGACTCGGGACAACC
66 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGAGACAACC
* *
3880252 AAGAACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCACTTTCAACT
131 AAGAACAACAAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACT
*
3880317 TCACAGCGAAGGATATTGGACTTAGGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGT
196 TCACAGCGAAGGATATTGGACTGAGGACAACACAAGTTCAACTTCACAACGAAGGGACG---GGT
3880382 TGTCAACAAACAATCTCCCAATTTCAGAGCCAATAGCG
258 TGTCAACAAACAATCTCCCAATTTCAGAGCCAATAGCG
* *
3880420 AAGGATATTGGACT-AGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
1 AAGGATATTGGACTCA-AGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAAC
* * * * *
3880484 AAACAATTTCCTAATTTTAGGGTCAATTTCAACTTCACATCGAAGGATATTGAACTCGAGACCA-
65 AAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGAGACAAC
* *
3880548 CAAGTTTAACTTCACAACAAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTCATAG-CA
130 CAAG----A----ACAACAAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTC-
*
3880612 AATTTCAACTTCACAGCGAAGGATATTGGACTCGA-GACGACACAAGTTCAACTTCACAACGAAG
186 AATTTCAACTTCACAGCGAAGGATATTGGACT-GAGGACAACACAAGTTCAACTTCACAACGAAG
* * * *
3880676 GGACGGGTTGTCAACAAACAATTTCCCAATTTCAGGGTCAATTTTAACTTCATATCG
250 GGACGGGTTGTCAACAAACAATCTCCCAATTTCAGAG-C--------C--AATAGCG
* * * * * * * *
3880733 AAGGATATTAGACTCAAGATAGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGGCTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACA
*** * *
3880798 AACAATTTTTGAGTTCCAGAGCCAATTTCAACTTCA
66 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
3880834 TGGTGGAGGA
Statistics
Matches: 355, Mismatches: 36, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
297 5 0.01
298 116 0.33
301 1 0.00
302 30 0.08
303 1 0.00
304 1 0.00
305 110 0.31
306 1 0.00
311 1 0.00
313 88 0.25
314 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (295 bp):
AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACA
AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGAGACAACC
AAGAACAACAAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACT
TCACAGCGAAGGATATTGGACTGAGGACAACACAAGTTCAACTTCACAACGAAGGGACGGGTTGT
CAACAAACAATCTCCCAATTTCAGAGCCAATAGCG
Found at i:3880725 original size:103 final size:105
Alignment explanation
Indices: 3880416--3880805 Score: 513
Period size: 104 Copynumber: 3.7 Consensus size: 105
3880406 CAGAGCCAAT
*
3880416 AGCGAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGG-TGGTTGTC
* *
3880481 AACAAACAATTTCCTAATTTTAGGGTCAATTTCAACTTCAC
65 AACAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCAC
* * * * *
3880522 ATCGAAGGATATTGAACTCGAGAC--CACAAGTTTAACTTCACAACAAAGGGACGACTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACG-GTGGTTGTC
* **
3880585 AACAAATAATTTCCCAATTTCATAG-CAAATTTCAACTTCAC
65 AACAAACAATTTCCCAATTTCAGGGTC-AATTTCAACTTCAC
3880626 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGAC-G-GGTTGTCA
1 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGTGGTTGTCA
* *
3880689 ACAAACAATTTCCCAATTTCAGGGTCAATTTTAACTTCAT
66 ACAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCAC
* * * * * * *
3880729 ATCGAAGGATATTAGACTCAAGA-TAGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGGCTGT
1 AGCGAAGGATATTGGACTCGAGACGA-CACAAGTTCAACTTCACAACGAAGGGACGG-TGGTTGT
3880793 CAACAAACAATTT
64 CAACAAACAATTT
3880806 TTGAGTTCCA
Statistics
Matches: 247, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
102 1 0.00
103 88 0.36
104 93 0.38
106 65 0.26
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (105 bp):
AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGTGGTTGTCA
ACAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCAC
Found at i:3881383 original size:35 final size:35
Alignment explanation
Indices: 3881337--3881408 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
3881327 ACCAAAAAGA
3881337 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
*
3881372 AGAGTTGGATTAGGACTCGAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
3881407 AG
1 AG
3881409 GGTTTTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:3882252 original size:41 final size:39
Alignment explanation
Indices: 3882207--3882283 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
3882197 AGGGCCCATT
* *
3882207 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
*
3882248 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
3882284 GGTGAAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 22 0.67
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:3882350 original size:38 final size:40
Alignment explanation
Indices: 3882299--3882378 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
3882289 AGTGAGAGGG
*
3882299 TAACTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAACTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
3882337 TAACTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAACTT-TTCTATTTTATAAATACTTTGATGTATATATATA
3882377 TA
1 TA
3882379 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (40 bp):
TAACTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:3882374 original size:2 final size:2
Alignment explanation
Indices: 3882367--3882391 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3882357 TACTTTGATG
3882367 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 T
3882392 TTTCCTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3882464 original size:9 final size:9
Alignment explanation
Indices: 3882452--3882519 Score: 61
Period size: 9 Copynumber: 7.9 Consensus size: 9
3882442 CCTTATCTTA
3882452 TTTATTTAT
1 TTTATTTAT
3882461 TTTATTTAT
1 TTTATTTAT
3882470 TTTATTT-T
1 TTTATTTAT
*
3882478 TTTCTTT-T
1 TTTATTTAT
*
3882486 TAT-TTTAT
1 TTTATTTAT
* *
3882494 TCTCTTTAT
1 TTTATTTAT
* *
3882503 CTTATTTGT
1 TTTATTTAT
3882512 TTTATTTA
1 TTTATTTA
3882520 CCTTGTTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
7 3 0.06
8 13 0.27
9 32 0.67
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:3882475 original size:14 final size:14
Alignment explanation
Indices: 3882444--3882518 Score: 66
Period size: 14 Copynumber: 5.4 Consensus size: 14
3882434 ATTTTTTTCC
*
3882444 TTATCTTATTTA-T
1 TTATTTTATTTATT
3882457 TTATTTTATTTATT
1 TTATTTTATTTATT
*
3882471 TTATTTT-TTTCTTT
1 TTATTTTATTT-ATT
*
3882485 TTATTTTATTCT-CT
1 TTATTTTATT-TATT
* *
3882499 TTATCTTATTTGTT
1 TTATTTTATTTATT
3882513 TTATTT
1 TTATTT
3882519 ACCTTGTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
13 15 0.29
14 33 0.65
15 2 0.04
16 1 0.02
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:3883940 original size:90 final size:90
Alignment explanation
Indices: 3883769--3883940 Score: 220
Period size: 90 Copynumber: 1.9 Consensus size: 90
3883759 CGCAAACATA
* * * * * * *
3883769 AACACATAAGTTGATGTAGGAATCATGATGCAGCTGAGGGGCTACATCTCGGAGCTCACACGCCC
1 AACACACAAGTTAAAGTAGGAATCATGATGCAACTAAGGGGCTACATCTCGAAGCTCACACACCC
*
3883834 CTCTAGCCTACTTGTACTACTATAC
66 CTCTAGCCTACCTGTACTACTATAC
* * * *
3883859 AACACACAAGTTAAAGTAGGCATCATGGTGTAACTAAGGGGCTACATCTCGAAGCTCATACACCC
1 AACACACAAGTTAAAGTAGGAATCATGATGCAACTAAGGGGCTACATCTCGAAGCTCACACACCC
3883924 CTCTATG-CTACCTGTAC
66 CTCTA-GCCTACCTGTAC
3883941 CCATGTCTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
90 68 0.99
91 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (90 bp):
AACACACAAGTTAAAGTAGGAATCATGATGCAACTAAGGGGCTACATCTCGAAGCTCACACACCC
CTCTAGCCTACCTGTACTACTATAC
Done.