Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 11 of 352
Found at i:3365547 original size:127 final size:127
Alignment explanation
Indices: 3365316--3365560 Score: 409
Period size: 127 Copynumber: 1.9 Consensus size: 127
3365306 TATCTTTCAA
* ** * **
3365316 CCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTC
1 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC
*
3365381 ATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
66 ATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCAGGTTGCCATG
3365443 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC
1 CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC
* *
3365508 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTTTTACACATTCCATATCAG
66 ATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCAG
3365561 AGAGCACACT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
127 109 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (127 bp):
CCATGGTCTTACACATTTCACATCAGGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC
ATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCAGGTTGCCATG
Found at i:3369729 original size:38 final size:38
Alignment explanation
Indices: 3369677--3369762 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
3369667 CAAATGAGGT
* *
3369677 ACTGGGTACC-ACTTTACTTCG-GCTAGGCCGATAAGAC
1 ACTGGGTGCCAACTTTACTTCGAACTA-GCCGATAAGAC
* * *
3369714 ACTGGGTGCCAACTTTACTTCGAACTATCCGATGAGTC
1 ACTGGGTGCCAACTTTACTTCGAACTAGCCGATAAGAC
3369752 ACTGGGTGCCA
1 ACTGGGTGCCA
3369763 TTCTAGTGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 9 0.21
38 30 0.71
39 3 0.07
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (38 bp):
ACTGGGTGCCAACTTTACTTCGAACTAGCCGATAAGAC
Found at i:3371498 original size:21 final size:21
Alignment explanation
Indices: 3371463--3371512 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3371453 TATATAACTT
* *
3371463 TATAATTAAT-ATTTTAATTAT
1 TATAATTATTGATTTT-ATTAA
3371484 TA-AATTATTGATTTTATTAA
1 TATAATTATTGATTTTATTAA
3371504 TATAATTAT
1 TATAATTAT
3371513 ACTTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TATAATTATTGATTTTATTAA
Found at i:3381417 original size:32 final size:32
Alignment explanation
Indices: 3381326--3381418 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
3381316 CAATCAAAAT
3381326 TGAACCCCACATATATGCGAACCATTATGTATG
1 TGAACCCCACATATATGCGAACCA-TATGTATG
* *
3381359 TGAATCCC-CATATATGCGAGCCATATGTATG
1 TGAACCCCACATATATGCGAACCATATGTATG
* * *
3381390 TGAACCCCACATATTTGCAAACTATATGT
1 TGAACCCCACATATATGCGAACCATATGT
3381419 GAACCCCCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 15 0.29
32 30 0.58
33 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (32 bp):
TGAACCCCACATATATGCGAACCATATGTATG
Found at i:3384220 original size:24 final size:22
Alignment explanation
Indices: 3384193--3384242 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
3384183 ATAAATTAAT
*
3384193 TAAATCTAAAATATGTAGAAAATA
1 TAAATATAAAATATG-A-AAAATA
* *
3384217 TAAATATATAATGTGAAAAATA
1 TAAATATAAAATATGAAAAATA
3384239 TAAA
1 TAAA
3384243 AAAATCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 1 0.04
24 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (22 bp):
TAAATATAAAATATGAAAAATA
Found at i:3385968 original size:14 final size:13
Alignment explanation
Indices: 3385934--3385972 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
3385924 GTACTAAGAA
3385934 AAAATATATATAT
1 AAAATATATATAT
* *
3385947 ACAATATAGTATTT
1 AAAATATA-TATAT
3385961 AAAATATATATA
1 AAAATATATATA
3385973 CATAAGATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (13 bp):
AAAATATATATAT
Found at i:3385985 original size:27 final size:27
Alignment explanation
Indices: 3385934--3385985 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3385924 GTACTAAGAA
* *
3385934 AAAATATATATATACAATATAGTATTT
1 AAAATATATATACACAAGATAGTATTT
* *
3385961 AAAATATATATACATAAGATGGTAT
1 AAAATATATATACACAAGATAGTAT
3385986 AGAAATATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (27 bp):
AAAATATATATACACAAGATAGTATTT
Found at i:3386237 original size:16 final size:16
Alignment explanation
Indices: 3386208--3386278 Score: 52
Period size: 19 Copynumber: 4.1 Consensus size: 16
3386198 TAATATTAAA
* *
3386208 ATATATACATGATAAT
1 ATATATAAAAGATAAT
3386224 ATATATAAAAGATATATGT
1 ATATATAAAAGATA-A--T
*
3386243 ATATATAAATATATAAT
1 ATATATAAA-AGATAAT
*
3386260 ATAATATTAAAATATAAT
1 AT-ATA-TAAAAGATAAT
3386278 A
1 A
3386279 AGACAACATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 12 0.26
17 4 0.09
18 11 0.24
19 15 0.33
20 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (16 bp):
ATATATAAAAGATAAT
Found at i:3386266 original size:18 final size:17
Alignment explanation
Indices: 3386219--3386278 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
3386209 TATATACATG
*
3386219 ATAATAT-ATATAAAAG
1 ATAATATAATATAAAAT
*
3386235 ATATATGTATATATAAATAT
1 ATA-ATATA-ATATAAA-AT
3386255 ATAATATAATATTAAAAT
1 ATAATATAATA-TAAAAT
3386273 ATAATA
1 ATAATA
3386279 AGACAACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 11 0.31
19 15 0.42
20 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATATAATATAAAAT
Found at i:3386491 original size:3 final size:3
Alignment explanation
Indices: 3386483--3386515 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3386473 AAGCATAAAC
*
3386483 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3386516 CATTGGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3386638 original size:23 final size:22
Alignment explanation
Indices: 3386612--3386665 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
3386602 TGTATACACG
3386612 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
3386635 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
3386657 TAC-TAATAA
1 TACATAATAA
3386666 TGCTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:3386646 original size:3 final size:3
Alignment explanation
Indices: 3386615--3386685 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
3386605 ATACACGTAC
* * * *
3386615 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * *
3386662 ATA ATG CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3386686 CAAGGATATT
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3390186 original size:44 final size:44
Alignment explanation
Indices: 3390136--3390225 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
3390126 TTGGTGTCTG
3390136 AATTACTTTTATTTATTTGGTGCTCGAATTTGTATTTCATTATC
1 AATTACTTTTATTTATTTGGTGCTCGAATTTGTATTTCATTATC
3390180 AATTACTTTTATTTATTTGGTGCTCGAATTTGTATTTCATTATC
1 AATTACTTTTATTTATTTGGTGCTCGAATTTGTATTTCATTATC
3390224 AA
1 AA
3390226 AATTAGTACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (44 bp):
AATTACTTTTATTTATTTGGTGCTCGAATTTGTATTTCATTATC
Found at i:3392317 original size:16 final size:17
Alignment explanation
Indices: 3392291--3392329 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3392281 TTGTGTATAT
3392291 ATTTCAATAAAAATC-AA
1 ATTT-AATAAAAATCAAA
*
3392308 ATTTAATAAAGATCAAA
1 ATTTAATAAAAATCAAA
3392325 ATTTA
1 ATTTA
3392330 TGTATCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (17 bp):
ATTTAATAAAAATCAAA
Found at i:3394853 original size:16 final size:15
Alignment explanation
Indices: 3394831--3394869 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
3394821 ATACTAAAAA
3394831 TATAATTTATGAT-TT
1 TATAATTTAT-ATATT
3394846 TAATAATTTATATATT
1 T-ATAATTTATATATT
3394862 TATAATTT
1 TATAATTT
3394870 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATAATTTATATATT
Found at i:3396927 original size:16 final size:18
Alignment explanation
Indices: 3396902--3396943 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
3396892 ATGACTCCCT
*
3396902 TTTTAATTTTTG-A-AAA
1 TTTTATTTTTTGTATAAA
3396918 TTTTATTTTTTGTATAAA
1 TTTTATTTTTTGTATAAA
3396936 TTTT-TTTT
1 TTTTATTTT
3396944 AAAATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
18 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTATTTTTTGTATAAA
Found at i:3404810 original size:175 final size:176
Alignment explanation
Indices: 3404519--3404870 Score: 697
Period size: 175 Copynumber: 2.0 Consensus size: 176
3404509 AACTTGTTGT
3404519 AAGAAACTAGACACTGTTTTATCAATCAATTCCTCTGAGAGAGTTTCCAAATTAGTTAGTTTTTC
1 AAGAAACTAGACACTGTTTTATCAATCAATTCCTCTGAGAGAGTTTCCAAATTAGTTAGTTTTTC
3404584 TCTCAAAGTTGCATCTTGAATTCTCTGCCAAAAAAAAGAGCCTAAATTTAGTTCGAAGTATAC-A
66 TCTCAAAGTTGCATCTTGAATTCTCTGCCAAAAAAAAGAGCCTAAATTTAGTTCGAAGTATACAA
3404648 AAAATCAAATACATGGCAATCCTTAGTCTTATTCACAATGGTTAAA
131 AAAATCAAATACATGGCAATCCTTAGTCTTATTCACAATGGTTAAA
3404694 AAGAAACTAGACACTGTTTTATCAATCAATTCCTCTGAGAGAGTTTCCAAATTAGTTAGTTTTTC
1 AAGAAACTAGACACTGTTTTATCAATCAATTCCTCTGAGAGAGTTTCCAAATTAGTTAGTTTTTC
3404759 TCTCAAAGTTGCATCTTGAATTCTCTGCCAAAAAAAAGAGCCTAAATTTAGTTCGAAGTATACAA
66 TCTCAAAGTTGCATCTTGAATTCTCTGCCAAAAAAAAGAGCCTAAATTTAGTTCGAAGTATACAA
3404824 AAAATCAAATACATGGCAATCCTTAGTCTTATTCACAATGGTTAAA
131 AAAATCAAATACATGGCAATCCTTAGTCTTATTCACAATGGTTAAA
3404870 A
1 A
3404871 TATATGCATT
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 128 0.73
176 48 0.27
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (176 bp):
AAGAAACTAGACACTGTTTTATCAATCAATTCCTCTGAGAGAGTTTCCAAATTAGTTAGTTTTTC
TCTCAAAGTTGCATCTTGAATTCTCTGCCAAAAAAAAGAGCCTAAATTTAGTTCGAAGTATACAA
AAAATCAAATACATGGCAATCCTTAGTCTTATTCACAATGGTTAAA
Found at i:3406607 original size:2 final size:2
Alignment explanation
Indices: 3406602--3406634 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3406592 GTGAACACAC
3406602 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 A
3406635 ACTACTTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3407017 original size:79 final size:79
Alignment explanation
Indices: 3406928--3407085 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
3406918 AATTTGAAAA
3406928 AGAAATTTAAAATAAAAGAGGGATTAATTTGATATAATAAATATATAATGATTGGACTATAATAA
1 AGAAATTTAAAATAAAAGAGGGATTAATTTGATATAATAAATATATAATGATTGGACTATAATAA
3406993 TTTATTTTTACTAT
66 TTTATTTTTACTAT
3407007 AGAAATTTAAAATAAAAGAGGGATTAATTTGATATAATAAATATATAATGATTGGACTATAATAA
1 AGAAATTTAAAATAAAAGAGGGATTAATTTGATATAATAAATATATAATGATTGGACTATAATAA
3407072 TTTATTTTTACTAT
66 TTTATTTTTACTAT
3407086 TTTGGTATAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (79 bp):
AGAAATTTAAAATAAAAGAGGGATTAATTTGATATAATAAATATATAATGATTGGACTATAATAA
TTTATTTTTACTAT
Found at i:3408559 original size:22 final size:23
Alignment explanation
Indices: 3408534--3408580 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3408524 AGGTGATGAT
*
3408534 TTAATTAACATACT-TT-TTTTTA
1 TTAACTAACAT-CTCTTATTTTTA
3408556 TTAACTAACATCTCTTATTTTTA
1 TTAACTAACATCTCTTATTTTTA
3408579 TT
1 TT
3408581 GACTCCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 12 0.55
23 8 0.36
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAACTAACATCTCTTATTTTTA
Found at i:3408923 original size:86 final size:85
Alignment explanation
Indices: 3408763--3408924 Score: 306
Period size: 86 Copynumber: 1.9 Consensus size: 85
3408753 AATTAAACTA
3408763 ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAATCCTTTCATTTGTAACCCTAATAC
1 ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAATCCTTTCATTTGTAACCCTAATAC
3408828 ATCTTATATGATATATACTG
66 ATCTTATATGATATATACTG
*
3408848 ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAAATCCTTTTATTTGTAACCCTAATA
1 ATATCACTTTCTTATCATAATAAATAAAATTGT-AAAAAAAATCCTTTCATTTGTAACCCTAATA
3408913 CATCTTATATGA
65 CATCTTATATGA
3408925 GAAAATGATA
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
85 33 0.44
86 42 0.56
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (85 bp):
ATATCACTTTCTTATCATAATAAATAAAATTGTAAAAAAAATCCTTTCATTTGTAACCCTAATAC
ATCTTATATGATATATACTG
Found at i:3416644 original size:36 final size:33
Alignment explanation
Indices: 3416604--3416671 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
3416594 TTTTTTAGAA
3416604 TAAACAAACTTTTGTTAATAAAAATATTAAAAATTT
1 TAAACAAACTTTT-TTAAT-AAAA-ATTAAAAATTT
***
3416640 TAAACTTGCTTTTTTAATAAAAATTAAAAATT
1 TAAACAAACTTTTTTAATAAAAATTAAAAATT
3416672 AACAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 10 0.34
34 4 0.14
35 5 0.17
36 10 0.34
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (33 bp):
TAAACAAACTTTTTTAATAAAAATTAAAAATTT
Found at i:3425265 original size:20 final size:20
Alignment explanation
Indices: 3425226--3425266 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3425216 AATTCGAAAT
* *
3425226 GTTTAGAGTTTAGTGTTCGA
1 GTTTAGAGTTTAGAGATCGA
*
3425246 GTTTAGAGTTTGGAGATCGA
1 GTTTAGAGTTTAGAGATCGA
3425266 G
1 G
3425267 ATTCAAGGTT
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:0.22, C:0.05, G:0.34, T:0.39
Consensus pattern (20 bp):
GTTTAGAGTTTAGAGATCGA
Found at i:3428653 original size:46 final size:46
Alignment explanation
Indices: 3428583--3428755 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
3428573 TTGGGCATCA
3428583 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAATGTCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAATGTCC
* * *
3428629 GAACTCGTTGAGTTGAGTCCGAGTTCG-TGA--GATG-TAACTAGGCATCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAA-T--G--TCC
* * * *
3428676 GAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAATGTCC
3428722 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
3428756 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.29
Consensus pattern (46 bp):
GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAATGTCC
Found at i:3428735 original size:93 final size:93
Alignment explanation
Indices: 3428576--3428748 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
3428566 GGGATATTTG
* * * *
3428576 GGCATCAGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCAGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3428641 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
3428669 GGCATCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCAGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3428734 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
3428749 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (93 bp):
GGCATCAGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:3431420 original size:20 final size:20
Alignment explanation
Indices: 3431395--3431455 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
3431385 GACGAGCTAG
3431395 GCAATACTATTCTGCATCTA
1 GCAATACTATTCTGCATCTA
3431415 GC-A-A-TA--CT-CAT-TA
1 GCAATACTATTCTGCATCTA
3431428 GGCAATACTATTCTGCATCTA
1 -GCAATACTATTCTGCATCTA
3431449 GCAATAC
1 GCAATAC
3431456 ATCATCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
13 2 0.06
14 5 0.15
15 3 0.09
16 1 0.03
17 4 0.12
18 1 0.03
19 3 0.09
20 12 0.36
21 2 0.06
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (20 bp):
GCAATACTATTCTGCATCTA
Found at i:3431435 original size:34 final size:35
Alignment explanation
Indices: 3431392--3431460 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
3431382 AAGGACGAGC
3431392 TAGGCAATACTATTCTGCATCTAGCAATAC-TCAT
1 TAGGCAATACTATTCTGCATCTAGCAATACATCAT
3431426 TAGGCAATACTATTCTGCATCTAGCAATACATCAT
1 TAGGCAATACTATTCTGCATCTAGCAATACATCAT
3431461 CCAAAGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (35 bp):
TAGGCAATACTATTCTGCATCTAGCAATACATCAT
Found at i:3443563 original size:14 final size:14
Alignment explanation
Indices: 3443544--3443570 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3443534 GAGCTAGTAC
3443544 GGTTGAAATGGAAT
1 GGTTGAAATGGAAT
3443558 GGTTGAAATGGAA
1 GGTTGAAATGGAA
3443571 ATGAAATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (14 bp):
GGTTGAAATGGAAT
Found at i:3444008 original size:20 final size:21
Alignment explanation
Indices: 3443971--3444009 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3443961 TTTCTTTCTT
* *
3443971 TTATTTTTTAATATTATTAGA
1 TTATTTTATAATAGTATTAGA
3443992 TTATTTTATAA-AGTATTA
1 TTATTTTATAATAGTATTA
3444010 TTGTAGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TTATTTTATAATAGTATTAGA
Found at i:3446041 original size:14 final size:14
Alignment explanation
Indices: 3446017--3446054 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
3446007 ATAATAAAAC
3446017 AGAATGAAAATATACA
1 AGAA-GAAAATA-ACA
3446033 A-AAGAAAATAACA
1 AGAAGAAAATAACA
3446046 AGAAGAAAA
1 AGAAGAAAA
3446055 AATTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 14 0.67
15 2 0.10
16 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.13, T:0.11
Consensus pattern (14 bp):
AGAAGAAAATAACA
Found at i:3449217 original size:15 final size:15
Alignment explanation
Indices: 3449197--3449230 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3449187 AGAGTTTGAG
3449197 AAGTACTGTATTATA
1 AAGTACTGTATTATA
3449212 AAGTACTGTATTATA
1 AAGTACTGTATTATA
3449227 AAGT
1 AAGT
3449231 GTAGTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (15 bp):
AAGTACTGTATTATA
Found at i:3454001 original size:31 final size:31
Alignment explanation
Indices: 3453948--3454023 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
3453938 TGGACTGTTT
* *
3453948 AAAATTTTTTAATAGTTTAGTGATTTAAATA
1 AAAATTTTTAAATAGTTCAGTGATTTAAATA
*
3453979 AAAACTTTTAAATAGTTCAGTGATTTAAATA
1 AAAATTTTTAAATAGTTCAGTGATTTAAATA
*
3454010 AAATTTTTTAAATA
1 AAAATTTTTAAATA
3454024 ATTTAATGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (31 bp):
AAAATTTTTAAATAGTTCAGTGATTTAAATA
Found at i:3455060 original size:41 final size:42
Alignment explanation
Indices: 3455015--3455096 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 42
3455005 CAACTGTATT
*
3455015 GAATTA-AAGTGCAGATATTTTATAATTTAACCAAAT-AAATC
1 GAATTAGAAG-GCAGATACTTTATAATTTAACCAAATGAAATC
* * * *
3455056 GAATTAGAAGGGATATACTTTATGATTTAATCAAATGAAAT
1 GAATTAGAAGGCAGATACTTTATAATTTAACCAAATGAAAT
3455097 TGAAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 27 0.79
42 7 0.21
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (42 bp):
GAATTAGAAGGCAGATACTTTATAATTTAACCAAATGAAATC
Found at i:3460754 original size:5 final size:5
Alignment explanation
Indices: 3460744--3460771 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3460734 ATATCAGCCT
3460744 CCCCA CCCCA CCCCA CCCCA CCCCA CCC
1 CCCCA CCCCA CCCCA CCCCA CCCCA CCC
3460772 ACACATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCCA
Found at i:3468911 original size:31 final size:31
Alignment explanation
Indices: 3468876--3468936 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3468866 ATAAAATGAT
**
3468876 TATTGAACTATTCAAATTTTTTTATTTAAAC
1 TATTGAACTATTCAAAAATTTTTATTTAAAC
*
3468907 TATTGAACTATTTAAAAATTTTTATTTAAA
1 TATTGAACTATTCAAAAATTTTTATTTAAA
3468937 GTACTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (31 bp):
TATTGAACTATTCAAAAATTTTTATTTAAAC
Found at i:3472600 original size:30 final size:30
Alignment explanation
Indices: 3472554--3472677 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
3472544 TTTTATTATG
*
3472554 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
3472585 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3472615 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
3472645 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3472675 CCA
1 CCA
3472678 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:3472609 original size:15 final size:15
Alignment explanation
Indices: 3472564--3472671 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
3472554 CCAATATCTC
3472564 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3472579 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3472594 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3472609 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3472624 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
3472639 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
3472654 GATACCCATATCTTT
1 GATACCCATATCTTT
3472669 GAT
1 GAT
3472672 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:3477291 original size:30 final size:30
Alignment explanation
Indices: 3477245--3477368 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
3477235 TTTTATTATG
*
3477245 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
3477276 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
3477306 CTAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
3477336 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
3477366 CCA
1 CCA
3477369 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:3477300 original size:15 final size:15
Alignment explanation
Indices: 3477255--3477362 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
3477245 CCAATATCTC
3477255 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
3477270 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
3477285 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
3477300 GACTTTCTA-ATATTT
1 GA-TACCCATATCTTT
3477315 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
3477330 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
3477345 GATACCCATATCTTT
1 GATACCCATATCTTT
3477360 GAT
1 GAT
3477363 TTTCCATAAA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
14 11 0.17
15 43 0.66
16 11 0.17
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:3483854 original size:15 final size:15
Alignment explanation
Indices: 3483813--3483859 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3483803 CCTATTTCGT
3483813 AATATATCAAAAAGA
1 AATATATCAAAAAGA
* *
3483828 ATTATGACCAAAAAGA
1 AATAT-ATCAAAAAGA
*
3483844 AATCTATCAAAAAGA
1 AATATATCAAAAAGA
3483859 A
1 A
3483860 TTCAAATAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.19
Consensus pattern (15 bp):
AATATATCAAAAAGA
Found at i:3497978 original size:18 final size:18
Alignment explanation
Indices: 3497955--3498014 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
3497945 TTTTAGAATT
3497955 ATTTTTGAAATTTTTATA
1 ATTTTTGAAATTTTTATA
* **
3497973 ATTTTTTAAA-TAATATA
1 ATTTTTGAAATTTTTATA
* *
3497990 AATTGTGAAATTTTTATAA
1 ATTTTTGAAATTTTTAT-A
3498009 ATTTTT
1 ATTTTT
3498015 ATAATTATTT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
17 12 0.40
18 13 0.43
19 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
ATTTTTGAAATTTTTATA
Found at i:3498012 original size:10 final size:10
Alignment explanation
Indices: 3497935--3498032 Score: 50
Period size: 9 Copynumber: 10.2 Consensus size: 10
3497925 TTTAACTTTC
*
3497935 TTTATATATT
1 TTTATAAATT
3497945 TTT-TAGAATT
1 TTTATA-AATT
*
3497955 ATTTTTGAAATT
1 -TTTAT-AAATT
3497967 TTTAT-AATT
1 TTTATAAATT
3497976 TTT-TAAA-T
1 TTTATAAATT
**
3497984 AATATAAA-T
1 TTTATAAATT
* *
3497993 TGT-GAAATT
1 TTTATAAATT
3498002 TTTATAAATT
1 TTTATAAATT
3498012 TTTAT-AATT
1 TTTATAAATT
3498021 ATTT-TAAATT
1 -TTTATAAATT
3498031 TT
1 TT
3498033 AAAAATTATT
Statistics
Matches: 69, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
8 6 0.09
9 27 0.39
10 23 0.33
11 7 0.10
12 5 0.07
13 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (10 bp):
TTTATAAATT
Found at i:3498028 original size:19 final size:19
Alignment explanation
Indices: 3498006--3498054 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
3497996 GAAATTTTTA
3498006 TAAATTTTTATAATTATTT
1 TAAATTTTTATAATTATTT
* *
3498025 TAAATTTTAAAAATTATTT
1 TAAATTTTTATAATTATTT
* *
3498044 TTATTTTTTAT
1 TAAATTTTTAT
3498055 TTTTAGAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TAAATTTTTATAATTATTT
Found at i:3498068 original size:15 final size:15
Alignment explanation
Indices: 3498048--3498082 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3498038 TTATTTTTAT
3498048 TTTTTATTTTTAG-AA
1 TTTTTATTTTT-GTAA
3498063 TTTTTATTTTTGTAA
1 TTTTTATTTTTGTAA
3498078 TTTTT
1 TTTTT
3498083 GTTCAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTTGTAA
Found at i:3498231 original size:23 final size:23
Alignment explanation
Indices: 3498198--3498248 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3498188 AATTTGAAAA
* *
3498198 TTGAATTACTT-ATTCGAATTGAC
1 TTGAATAACTTGATTCG-ATTAAC
*
3498221 TTGAATAACTTGATTTGATTAAC
1 TTGAATAACTTGATTCGATTAAC
3498244 TTGAA
1 TTGAA
3498249 ATTCAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (23 bp):
TTGAATAACTTGATTCGATTAAC
Found at i:3499778 original size:25 final size:25
Alignment explanation
Indices: 3499744--3499792 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3499734 CGTTAACTCG
3499744 ACTCGATTTGACTC-AAAAACATTTT
1 ACTCGATTTGACTCGAAAAA-ATTTT
*
3499769 ACTCGATTTGATTCGAAAAAATTT
1 ACTCGATTTGACTCGAAAAAATTT
3499793 CAAGTTGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (25 bp):
ACTCGATTTGACTCGAAAAAATTTT
Found at i:3505927 original size:47 final size:47
Alignment explanation
Indices: 3505835--3505930 Score: 117
Period size: 47 Copynumber: 2.0 Consensus size: 47
3505825 AAAATATAAG
* * *
3505835 ATAATTGAGTGATAAAAAATAATTTAAATGATAATTTTGTTATTTTT
1 ATAATTAAGTGATAAAAAATAATTTAAATGATAATTATGTAATTTTT
3505882 ATAATTAAGTGA-AAAAATATAA-TTAAATGAGT-ATTAATGTAATTTTT
1 ATAATTAAGTGATAAAAA-ATAATTTAAATGA-TAATT-ATGTAATTTTT
3505929 AT
1 AT
3505931 TTTTTTATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
46 16 0.37
47 27 0.63
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (47 bp):
ATAATTAAGTGATAAAAAATAATTTAAATGATAATTATGTAATTTTT
Found at i:3515100 original size:18 final size:19
Alignment explanation
Indices: 3515077--3515119 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3515067 TCGAAAGAGA
*
3515077 AAAAAACT-CAAAAAAAAT
1 AAAAAACTCCAAAAAAAAG
*
3515095 AAAAAA-TCCACAAAAAAG
1 AAAAAACTCCAAAAAAAAG
3515113 AAAAAAC
1 AAAAAAC
3515120 ACAAGAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.77, C:0.14, G:0.02, T:0.07
Consensus pattern (19 bp):
AAAAAACTCCAAAAAAAAG
Found at i:3529645 original size:36 final size:35
Alignment explanation
Indices: 3529580--3529650 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
3529570 TTTAATCTTT
* *
3529580 GATTCAATATATAATTTTTCTTTAAAAAAATACAAA
1 GATTCAATAAACAATTTTTCTTTAAAAAAA-ACAAA
3529616 GATTCAATAAACAA-TTTT-TTTAATTAAAAAACAAA
1 GATTCAATAAACAATTTTTCTTTAA--AAAAAACAAA
3529651 ATACAATTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 5 0.16
35 9 0.29
36 17 0.55
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (35 bp):
GATTCAATAAACAATTTTTCTTTAAAAAAAACAAA
Found at i:3531461 original size:24 final size:20
Alignment explanation
Indices: 3531443--3531483 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3531433 TTTGAATAAG
3531443 AAATGGTGAAGGATTTTGAA
1 AAATGGTGAAGGATTTTGAA
3531463 AAATGGTGAAGGATTTT-AA
1 AAATGGTGAAGGATTTTGAA
3531482 AA
1 AA
3531484 GGAGAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (20 bp):
AAATGGTGAAGGATTTTGAA
Found at i:3540842 original size:25 final size:25
Alignment explanation
Indices: 3540796--3540843 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3540786 TGAAGATTAT
* * *
3540796 TCATCATTCAAACATTTCTACTTAC
1 TCATCATACAAACATATATACTTAC
*
3540821 TCATCATACACACATATATACTT
1 TCATCATACAAACATATATACTT
3540844 GTTCATCGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (25 bp):
TCATCATACAAACATATATACTTAC
Found at i:3541117 original size:51 final size:51
Alignment explanation
Indices: 3541062--3541161 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
3541052 CTACCACATA
*
3541062 ACATGTAA-CACATCCATAATGAACTCGGACCTCTCAACGAGCTTGGATGTT
1 ACATG-AATCACATCCATAATGAACTCGAACCTCTCAACGAGCTTGGATGTT
* *
3541113 ACATGAATCGCATCCATTATGAACTCGAACCTCTCAACGAGCTTGGATG
1 ACATGAATCACATCCATAATGAACTCGAACCTCTCAACGAGCTTGGATG
3541162 CTCGCATCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.04
51 43 0.96
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (51 bp):
ACATGAATCACATCCATAATGAACTCGAACCTCTCAACGAGCTTGGATGTT
Found at i:3555992 original size:44 final size:45
Alignment explanation
Indices: 3555936--3556026 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 45
3555926 ACTAAATAAA
* * *
3555936 ATCTCTCTCTTAAAGTGTAACGTTGTACATAG-AAAAAAATATAC
1 ATCTCTCTCTTAAAATGTAACATTGTACAAAGAAAAAAAATATAC
*
3555980 ATCTCTCTCTTAAAATGTTACATTGTACAAAGAAAAAAAATATAC
1 ATCTCTCTCTTAAAATGTAACATTGTACAAAGAAAAAAAATATAC
3556025 AT
1 AT
3556027 ATAATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 28 0.67
45 14 0.33
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (45 bp):
ATCTCTCTCTTAAAATGTAACATTGTACAAAGAAAAAAAATATAC
Found at i:3559414 original size:2 final size:2
Alignment explanation
Indices: 3559407--3559440 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3559397 TCATGGGCTC
3559407 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3559441 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3563166 original size:22 final size:21
Alignment explanation
Indices: 3563138--3563179 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3563128 ATTTTATCAT
*
3563138 TTTAATCGTTAATTATTTTTAG
1 TTTAATCATTAATT-TTTTTAG
3563160 TTTAATCATTAATTTTTTTA
1 TTTAATCATTAATTTTTTTA
3563180 AAATAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTAATCATTAATTTTTTTAG
Found at i:3563692 original size:13 final size:13
Alignment explanation
Indices: 3563674--3563699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3563664 TTACAAGTAT
3563674 AATGAAAATTTTA
1 AATGAAAATTTTA
3563687 AATGAAAATTTTA
1 AATGAAAATTTTA
3563700 GGTTAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AATGAAAATTTTA
Found at i:3565346 original size:17 final size:17
Alignment explanation
Indices: 3565311--3565349 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3565301 CTTTAGAATT
*
3565311 TTTTTAAAAAGTTATAA
1 TTTTTAAAAAATTATAA
3565328 TTTTTAAAAAA-TATAA
1 TTTTTAAAAAATTATAA
*
3565344 ATTTTA
1 TTTTTA
3565350 GATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTTTAAAAAATTATAA
Found at i:3569801 original size:24 final size:24
Alignment explanation
Indices: 3569759--3569808 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
3569749 TCATCAACAG
* * *
3569759 ATTTTACTACCATCGAAACCATCC
1 ATTTTACTACCACCAAAACCAACC
*
3569783 ATTTTACTATCACCAAAACCAACC
1 ATTTTACTACCACCAAAACCAACC
3569807 AT
1 AT
3569809 CCTTATCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.32, G:0.02, T:0.28
Consensus pattern (24 bp):
ATTTTACTACCACCAAAACCAACC
Found at i:3573408 original size:23 final size:24
Alignment explanation
Indices: 3573382--3573444 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 24
3573372 TATTATATTG
**
3573382 ATTAAAAAATATATT-TTTTAAAT
1 ATTAAAAAATATATTATTAAAAAT
* * *
3573405 ATTATATATTATATTAATTAAAAAT
1 ATTAAAAAATATATT-ATTAAAAAT
3573430 ATTAAAAAATCATAT
1 ATTAAAAAAT-ATAT
3573445 ATAATATATA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
23 12 0.41
25 13 0.45
26 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTAAAAAATATATTATTAAAAAT
Found at i:3583848 original size:3 final size:3
Alignment explanation
Indices: 3583840--3583882 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3583830 CCCTTTCATC
3583840 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3583883 TTATATTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:3588096 original size:30 final size:28
Alignment explanation
Indices: 3588035--3588102 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
3588025 AAAAACCTAC
* *
3588035 ATTAATTTTCTATAATGAAAGTTAAATA
1 ATTACTTTTCTATAATGAAAGATAAATA
* *
3588063 ATTACTTTTCATATAATTAAGAGATAATTA
1 ATTACTTTTC-TATAATGAA-AGATAAATA
3588093 ATTACCTTTT
1 ATTA-CTTTT
3588103 TCTGTACCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 9 0.27
29 8 0.24
30 11 0.33
31 5 0.15
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (28 bp):
ATTACTTTTCTATAATGAAAGATAAATA
Found at i:3588574 original size:15 final size:14
Alignment explanation
Indices: 3588547--3588582 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
3588537 AGATAATAGA
3588547 AAATAAATAAAAAG
1 AAATAAATAAAAAG
*
3588561 AAATAAAGTTAAAAG
1 AAATAAA-TAAAAAG
3588576 AAATAAA
1 AAATAAA
3588583 AGAATTGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (14 bp):
AAATAAATAAAAAG
Found at i:3590034 original size:34 final size:35
Alignment explanation
Indices: 3589996--3590062 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3589986 CTGTAAAATG
3589996 TTTTCCGTAAAATGAATT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
* *
3590030 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTT
3590063 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
Found at i:3591437 original size:27 final size:27
Alignment explanation
Indices: 3591407--3591476 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
3591397 AATAATCAAT
*
3591407 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
3591434 TCAATATCTAACCAATTCAAGACATATA
1 TCAATATCCAA-CAATTCAAAACATATA
*
3591462 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
3591477 CTAAAATCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:3595746 original size:6 final size:6
Alignment explanation
Indices: 3595735--3595765 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3595725 AATATTTCCC
*
3595735 ACAGAA ACAGAA ACAGAA ACAAAA ACAGAA A
1 ACAGAA ACAGAA ACAGAA ACAGAA ACAGAA A
3595766 ATACAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.71, C:0.16, G:0.13, T:0.00
Consensus pattern (6 bp):
ACAGAA
Found at i:3597611 original size:106 final size:111
Alignment explanation
Indices: 3597488--3597715 Score: 270
Period size: 112 Copynumber: 2.1 Consensus size: 111
3597478 TAGAGATATA
* * * *
3597488 AAAAAAAAAATTGGTGCTGACCA-GTAGATGGCTGGCACCAGGT-ATTTTTTGTGTCCCAA-GCC
1 AAAAAAAAAATTGGTGCTGACCATGTA-ATAGCTGGCACCAGGTAATTTTTCGAGTCCCAAGGCA
* *
3597550 A-A-TTTTTTTTACTTTGGAACACTGATGGCTGGCACCAGTGAATTT
65 ATATTTTTTTTTACTTTGGAACACTGATGGCCGGCACCAGGGAATTT
* * *
3597595 AAAAAAAAAA-TGGTGCTGACCATGTAATAGCTGGCACTAGGTACATTTTTCGAGTCCTAAGGTA
1 AAAAAAAAAATTGGTGCTGACCATGTAATAGCTGGCACCAGGTA-ATTTTTCGAGTCCCAAGGCA
* * *
3597659 ATATTTTTTTTTTACTTTGGGACACTGATTGCCGGCACCAGGGTATTT
65 ATA-TTTTTTTTTACTTTGGAACACTGATGGCCGGCACCAGGGAATTT
*
3597707 TAAAAAAAA
1 AAAAAAAAA
3597716 TTTTGGGTGC
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
106 26 0.26
107 13 0.13
108 13 0.13
109 2 0.02
110 1 0.01
112 46 0.46
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (111 bp):
AAAAAAAAAATTGGTGCTGACCATGTAATAGCTGGCACCAGGTAATTTTTCGAGTCCCAAGGCAA
TATTTTTTTTTACTTTGGAACACTGATGGCCGGCACCAGGGAATTT
Found at i:3597790 original size:44 final size:44
Alignment explanation
Indices: 3597735--3597823 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
3597725 CTGGCCATTT
3597735 AATGGCCGACACCAAGTACATTTAAAAAAGAATTGGTGTTGGCC
1 AATGGCCGACACCAAGTACATTTAAAAAAGAATTGGTGTTGGCC
3597779 AATGGCCGACACCAAGTACATTTAAAAAAGAATTGGTGTTGGCC
1 AATGGCCGACACCAAGTACATTTAAAAAAGAATTGGTGTTGGCC
3597823 A
1 A
3597824 GTAGATGGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (44 bp):
AATGGCCGACACCAAGTACATTTAAAAAAGAATTGGTGTTGGCC
Found at i:3598718 original size:21 final size:21
Alignment explanation
Indices: 3598694--3598743 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3598684 ACCATAGAAG
*
3598694 ATGGTGATGAAGGGTCTGATA
1 ATGGTGATGAAGGGTCTAATA
3598715 ATGGTGATGAAGGGTCTAATA
1 ATGGTGATGAAGGGTCTAATA
3598736 ATGGTGAT
1 ATGGTGAT
3598744 CAGTCCCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (21 bp):
ATGGTGATGAAGGGTCTAATA
Found at i:3599293 original size:90 final size:90
Alignment explanation
Indices: 3599199--3599428 Score: 327
Period size: 90 Copynumber: 2.6 Consensus size: 90
3599189 TATGGATTAA
* * * *
3599199 ATTAAATTTACATATACAAAAAAATACGAACATTCTAATAAATTAATACACGAAAATATAAAAAC
1 ATTAAATTTACAAATATAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAC
*
3599264 GAAACCTTAAATCATAAACAAGTAC
66 GAAACCTTAAATCATAAACAACTAC
* * * *
3599289 ATTAAGTATACAAATATAAAAAAATACAAACATTCTAAGAAATTAATATACGAAAATATAAAAAT
1 ATTAAATTTACAAATATAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAC
* *
3599354 GAAACCTTAAATCCTAGACAACTAC
66 GAAACCTTAAATCATAAACAACTAC
* *
3599379 ATTAAATTTACAGATATAAAAAAATACAAAAATTCTAAAGAAA-TAATACA
1 ATTAAATTTACAAATATAAAAAAATACAAACATTCT-AAGAAATTAATACA
3599429 ATTATTTTGA
Statistics
Matches: 123, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
90 117 0.95
91 6 0.05
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.25
Consensus pattern (90 bp):
ATTAAATTTACAAATATAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAC
GAAACCTTAAATCATAAACAACTAC
Found at i:3608780 original size:19 final size:20
Alignment explanation
Indices: 3608756--3608797 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3608746 GACAACCTCT
3608756 AAATATAAA-AAAATTTTAA
1 AAATATAAATAAAATTTTAA
* *
3608775 AAATATAAATTAATTTTTAA
1 AAATATAAATAAAATTTTAA
3608795 AAA
1 AAA
3608798 AATATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATAAATAAAATTTTAA
Found at i:3608864 original size:32 final size:32
Alignment explanation
Indices: 3608804--3608865 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
3608794 AAAAAATATA
**
3608804 ATTTTTTAGACAAATTCAAGTATTAATTAGGT
1 ATTTTTTAGACAAATTCAAGTACCAATTAGGT
* * *
3608836 ATTTTTTGGACAAATTTAGGTACCAATTAG
1 ATTTTTTAGACAAATTCAAGTACCAATTAG
3608866 ATACTTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (32 bp):
ATTTTTTAGACAAATTCAAGTACCAATTAGGT
Found at i:3620878 original size:16 final size:16
Alignment explanation
Indices: 3620867--3620897 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3620857 GTTTTTTTAT
*
3620867 ATTTATTATTTTTAAA
1 ATTTAATATTTTTAAA
3620883 ATTTAATATTTTTAA
1 ATTTAATATTTTTAA
3620898 TAAATCATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAATATTTTTAAA
Found at i:3628535 original size:12 final size:12
Alignment explanation
Indices: 3628518--3628558 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3628508 GATTGATTTT
3628518 TTTTTTTTACAA
1 TTTTTTTTACAA
* **
3628530 TTTTTTATATTA
1 TTTTTTTTACAA
3628542 TTTTTTTTACAA
1 TTTTTTTTACAA
3628554 TTTTT
1 TTTTT
3628559 AATAATGTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTTTTACAA
Found at i:3628638 original size:18 final size:19
Alignment explanation
Indices: 3628615--3628654 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3628605 TTATTCTAGA
3628615 TTATATATATTTGA-ATTT
1 TTATATATATTTGATATTT
* *
3628633 TTATATATTTTTTATATTT
1 TTATATATATTTGATATTT
3628652 TTA
1 TTA
3628655 AATGTGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATATATATTTGATATTT
Found at i:3629613 original size:17 final size:17
Alignment explanation
Indices: 3629591--3629625 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3629581 AAATTAAGCG
*
3629591 CTTCAAACTTATATTTA
1 CTTCAAACATATATTTA
*
3629608 CTTCAACCATATATTTA
1 CTTCAAACATATATTTA
3629625 C
1 C
3629626 CTTAGATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (17 bp):
CTTCAAACATATATTTA
Found at i:3631541 original size:23 final size:23
Alignment explanation
Indices: 3631514--3631558 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3631504 TACAAAGTAG
3631514 TTTTAATAATTTGTAATTTAGAT
1 TTTTAATAATTTGTAATTTAGAT
* *
3631537 TTTTAGTAATTTTTAATTTAGA
1 TTTTAATAATTTGTAATTTAGA
3631559 AAATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (23 bp):
TTTTAATAATTTGTAATTTAGAT
Found at i:3652006 original size:30 final size:31
Alignment explanation
Indices: 3651955--3652013 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
3651945 AAAAGTTAAA
* *
3651955 CTTTTAAAATTTTTGAAAATTTTCATTAATT
1 CTTTTAAAAATTTTGAAAATTTTAATTAATT
3651986 CTTTTAAAAATTTT-AAAATTTTAATTAA
1 CTTTTAAAAATTTTGAAAATTTTAATTAA
3652014 GCCCTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (31 bp):
CTTTTAAAAATTTTGAAAATTTTAATTAATT
Found at i:3656862 original size:29 final size:32
Alignment explanation
Indices: 3656809--3656870 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
3656799 AAAAGAATTT
*
3656809 TAAAAAATAAAAAAAGTCTAAATA-TTCAAAAA
1 TAAAAAAT-AAAAAAGTATAAATATTTCAAAAA
3656841 TAAAAAAT-AAAAA-TATAAATATTTCAAAAA
1 TAAAAAATAAAAAAGTATAAATATTTCAAAAA
3656871 GAATATTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.25
30 13 0.46
32 8 0.29
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (32 bp):
TAAAAAATAAAAAAGTATAAATATTTCAAAAA
Found at i:3657243 original size:41 final size:41
Alignment explanation
Indices: 3657164--3657268 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 41
3657154 ACCCTAATAT
* *
3657164 AAACATTAAAATA-ATATTAAAATAATTGTATAAAAAATTTA
1 AAACAATAAAATATATATTAAAATAATTGAATAAAAAA-TTA
* **
3657205 AATA-AATAAAATATATA-TAAAATTATTGAATATTAAATTA
1 AA-ACAATAAAATATATATTAAAATAATTGAATAAAAAATTA
* *
3657245 AAACAATACAAATATTTTTTAAAA
1 AAACAATA-AAATATATATTAAAA
3657269 AATAATATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
39 1 0.02
40 9 0.17
41 33 0.63
42 9 0.17
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (41 bp):
AAACAATAAAATATATATTAAAATAATTGAATAAAAAATTA
Found at i:3659293 original size:39 final size:39
Alignment explanation
Indices: 3659239--3659317 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3659229 GCTTTCTAAT
3659239 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
1 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
3659278 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
1 TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
3659317 T
1 T
3659318 TCAAATGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (39 bp):
TACAGGCTTATTTACAGATGTGCAATGGACAATGAATCA
Found at i:3664120 original size:29 final size:30
Alignment explanation
Indices: 3664067--3664146 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
3664057 ATATTAAAAT
* *
3664067 TATATATGAATTATGATTTAATGTGCAATTA
1 TATATATAAATTTTGATTT-ATGTGCAATTA
* *
3664098 TATATATAAATTTTGATTT-TGTGTAATTT
1 TATATATAAATTTTGATTTATGTGCAATTA
*
3664127 TATATTTAAAATTTTGATTT
1 TATATAT-AAATTTTGATTT
3664147 GATTCCATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.33
30 12 0.28
31 17 0.40
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (30 bp):
TATATATAAATTTTGATTTATGTGCAATTA
Found at i:3664372 original size:29 final size:30
Alignment explanation
Indices: 3664333--3664398 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
3664323 TAGAATTTTT
3664333 TATATATAATTAT-ATCAAATTAAAATTTA
1 TATATATAATTATAATCAAATTAAAATTTA
* *
3664362 TATATTTAATTATACATTAAATTAAAATTTA
1 TATATATAATTATA-ATCAAATTAAAATTTA
3664393 TATATA
1 TATATA
3664399 ATTTTAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 12 0.38
31 20 0.62
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
TATATATAATTATAATCAAATTAAAATTTA
Found at i:3676227 original size:43 final size:46
Alignment explanation
Indices: 3676177--3676262 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
3676167 AGATTAATTA
* *
3676177 AGTGATCAAATT-AA-AAAATTGATAATTGGGT-GAAAAAAAAAGT
1 AGTGATCAAATTGAAGAAAATTAATAATTGAGTAGAAAAAAAAAGT
*
3676220 AGTGATCAAATTGAAGCAAATTAATAATTGAGTAGAAAAAAAA
1 AGTGATCAAATTGAAGAAAATTAATAATTGAGTAGAAAAAAAA
3676263 GACAATATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 12 0.32
44 2 0.05
45 14 0.38
46 9 0.24
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.24
Consensus pattern (46 bp):
AGTGATCAAATTGAAGAAAATTAATAATTGAGTAGAAAAAAAAAGT
Found at i:3683315 original size:36 final size:36
Alignment explanation
Indices: 3683268--3683338 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
3683258 GAATGTGTGT
3683268 TTCTGTTATTGTCTATGGTTCCTAGAACTTTTCTGC
1 TTCTGTTATTGTCTATGGTTCCTAGAACTTTTCTGC
*
3683304 TTCTGTTATTGTCTATGGTTCCTAGAGCTTTTCTG
1 TTCTGTTATTGTCTATGGTTCCTAGAACTTTTCTG
3683339 TAATTTGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.51
Consensus pattern (36 bp):
TTCTGTTATTGTCTATGGTTCCTAGAACTTTTCTGC
Found at i:3688691 original size:29 final size:32
Alignment explanation
Indices: 3688657--3688717 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 32
3688647 AAGTTTATAT
3688657 TTTAGTCACTA-AT-GTT-TCAATTG-TAATAA
1 TTTAGTCAC-AGATAGTTATCAATTGATAATAA
3688686 TTTAGTCACAGATAGTTATCAATTGATAATAA
1 TTTAGTCACAGATAGTTATCAATTGATAATAA
3688718 GTTGGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 1 0.04
29 11 0.39
30 3 0.11
31 7 0.25
32 6 0.21
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (32 bp):
TTTAGTCACAGATAGTTATCAATTGATAATAA
Found at i:3690675 original size:10 final size:10
Alignment explanation
Indices: 3690657--3690699 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
3690647 TAAAAATTGA
3690657 AAAATTATAT
1 AAAATTATAT
*
3690667 AAAAGTATAT
1 AAAATTATAT
3690677 AAAATTATA-
1 AAAATTATAT
*
3690686 AATATATATAT
1 AAAAT-TATAT
3690697 AAA
1 AAA
3690700 TACATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 4 0.15
10 21 0.78
11 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATTATAT
Found at i:3690680 original size:28 final size:28
Alignment explanation
Indices: 3690649--3690708 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
3690639 ATTATTTTTA
*
3690649 AAAATTGAAAAAT-TATATA-AAAGTATAT
1 AAAATT-AAAAATATATATATAAA-TACAT
*
3690677 AAAATTATAAATATATATATAAATACAT
1 AAAATTAAAAATATATATATAAATACAT
3690705 AAAA
1 AAAA
3690709 AAAATTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
28 20 0.71
29 3 0.11
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAATTAAAAATATATATATAAATACAT
Found at i:3691667 original size:15 final size:15
Alignment explanation
Indices: 3691647--3691699 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3691637 CAGCAAGGAG
*
3691647 AAGAAAATAAAGAGA
1 AAGAAAAGAAAGAGA
*
3691662 AAGAAAGGAGAAGAG-
1 AAGAAAAGA-AAGAGA
3691677 AAGAAAAAGAAAGAGA
1 AAG-AAAAGAAAGAGA
*
3691693 AGGAAAA
1 AAGAAAA
3691700 AAGAAGGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (15 bp):
AAGAAAAGAAAGAGA
Found at i:3691669 original size:25 final size:26
Alignment explanation
Indices: 3691641--3691696 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
3691631 AATCAGCAGC
* *
3691641 AAGGAGAAGAAAATAAAGAGAAAGA-
1 AAGGAGAAGAAAAGAAAAAGAAAGAG
*
3691666 AAGGAGAAGAGAAGAAAAAGAAAGAG
1 AAGGAGAAGAAAAGAAAAAGAAAGAG
3691692 AAGGA
1 AAGGA
3691697 AAAAAGAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (26 bp):
AAGGAGAAGAAAAGAAAAAGAAAGAG
Found at i:3691680 original size:21 final size:20
Alignment explanation
Indices: 3691656--3691694 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3691646 GAAGAAAATA
*
3691656 AAGAGAAAGAAAGGAGAAGAG
1 AAGAAAAAGAAA-GAGAAGAG
3691677 AAGAAAAAGAAAGAGAAG
1 AAGAAAAAGAAAGAGAAG
3691695 GAAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAAGAGAAGAG
Found at i:3691705 original size:31 final size:30
Alignment explanation
Indices: 3691644--3691705 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
3691634 CAGCAGCAAG
* **
3691644 GAGAAGAAAATAAAGAGAAAGAAAGGAGAA
1 GAGAAGAAAAGAAAGAGAAAGAAAAAAGAA
*
3691674 GAGAAGAAAAAGAAAGAGAAGGAAAAAAGAA
1 GAGAAG-AAAAGAAAGAGAAAGAAAAAAGAA
3691705 G
1 G
3691706 GTATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (30 bp):
GAGAAGAAAAGAAAGAGAAAGAAAAAAGAA
Found at i:3691853 original size:26 final size:26
Alignment explanation
Indices: 3691798--3691855 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3691788 GTTGTTAGTT
* * *
3691798 ATTAATATTGTCAGTAAAAAACCCTT
1 ATTATTATTGTCAGTAAAAAACCATA
* *
3691824 ATTATTATTGTTAGTAAAAAATCATA
1 ATTATTATTGTCAGTAAAAAACCATA
3691850 ATTATT
1 ATTATT
3691856 GTTAGTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (26 bp):
ATTATTATTGTCAGTAAAAAACCATA
Found at i:3695760 original size:17 final size:17
Alignment explanation
Indices: 3695738--3695776 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
3695728 CGGTAATAGT
3695738 ATGTTCCAATTTA-ATTA
1 ATGTTCCAA-TTAGATTA
3695755 ATGTTCCAATTAGATTA
1 ATGTTCCAATTAGATTA
3695772 ATGTT
1 ATGTT
3695777 GTAATGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (17 bp):
ATGTTCCAATTAGATTA
Found at i:3697359 original size:7 final size:8
Alignment explanation
Indices: 3697347--3697380 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
3697337 ATAATAAAAT
3697347 ATAT-AAA
1 ATATCAAA
3697354 ATAT-AAA
1 ATATCAAA
3697361 ATATCAAA
1 ATATCAAA
3697369 ATATCAAA
1 ATATCAAA
3697377 ATAT
1 ATAT
3697381 TAGAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATCAAA
Found at i:3697363 original size:24 final size:24
Alignment explanation
Indices: 3697336--3697391 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
3697326 TAATGATGTG
*
3697336 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
*
3697360 AAT-ATCAAAATATCAAAATATTAG
1 AATAAT-AAAATATCAAAATATTAA
3697384 AATAATAA
1 AATAATAA
3697392 TAATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 8 0.30
24 17 0.63
25 2 0.07
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:3697387 original size:16 final size:15
Alignment explanation
Indices: 3697340--3697387 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
3697330 GATGTGAATA
3697340 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
*
3697356 ATAAAATATCAAAAT
1 ATAAAATATTAAAAT
*
3697371 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
3697387 A
1 A
3697388 ATAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3697634 original size:28 final size:27
Alignment explanation
Indices: 3697595--3697654 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
3697585 TATAGTTAAG
* *
3697595 ATATATACATAAGATAACATGTAAATAT
1 ATATATAAATAAGATAACAT-TAAAGAT
* *
3697623 ATATATAAATAATATAATATTAAAGAT
1 ATATATAAATAAGATAACATTAAAGAT
3697650 ATATA
1 ATATA
3697655 CATAAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (27 bp):
ATATATAAATAAGATAACATTAAAGAT
Found at i:3697659 original size:25 final size:25
Alignment explanation
Indices: 3697536--3697756 Score: 122
Period size: 25 Copynumber: 9.0 Consensus size: 25
3697526 TAAATACGTG
* *
3697536 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
3697561 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
3697586 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
3697608 ATAACATGTAAATATATATATAAATAAT
1 ATAATAT-T-AA-AGATATATACATAAT
*
3697636 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * * *
3697661 ATAGTATAAAATATATATATACGTAAT
1 ATAATAT-TAA-AGATATATACATAAT
* *
3697688 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
3697711 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
3697733 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
3697756 A
1 A
3697757 ACAAAAAAGG
Statistics
Matches: 152, Mismatches: 30, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 28 0.18
24 8 0.05
25 43 0.28
26 5 0.03
27 19 0.12
28 18 0.12
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:3698280 original size:30 final size:30
Alignment explanation
Indices: 3698243--3698387 Score: 236
Period size: 30 Copynumber: 4.8 Consensus size: 30
3698233 TAGGTACAAG
*
3698243 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* * *
3698273 TAGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
3698303 TGGTGGTGGACAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
3698333 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
3698363 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
3698388 TGAGAAAAGT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 105 1.00
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:3699185 original size:14 final size:15
Alignment explanation
Indices: 3699145--3699187 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3699135 TGAAAAATAT
*
3699145 AAATTGAAAAAAACAG
1 AAATT-AAAAAGACAG
*
3699161 AAATTGAAAAGA-AG
1 AAATTAAAAAGACAG
3699175 AAATTAAAAAGAC
1 AAATTAAAAAGAC
3699188 CTCAGCATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 13 0.57
15 5 0.22
16 5 0.22
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (15 bp):
AAATTAAAAAGACAG
Found at i:3699297 original size:73 final size:75
Alignment explanation
Indices: 3699202--3699651 Score: 340
Period size: 76 Copynumber: 5.8 Consensus size: 75
3699192 GCATGTGAGT
* * *
3699202 CGAGACTCAACTCACCTCTCGCAATATGAGTT-A-ATTTTTGACAAACAGAAATTGAAATTACCT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAATACCT
3699265 CAGCGTGTCC
66 CAGCGTGTCC
* * *
3699275 CGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAA-TTGAAAATACC
3699340 TCAGCGTGTCC
65 TCAGCGTGTCC
* * * *
3699351 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATTGAAGAACAGA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTG-A-AA-A-T
** * * *
3699416 AATTGAAAAGACCTCAG-CA
62 ACCT---CAG-CGT--GTCC
* * * * * * * *
3699435 TGTGAGC-CGAGGCTCAACTCAC-C-CT-CGCAATATG-TGTTAATTTTTGACAAACAGAAATTG
1 CGAG-GCTC-A-ACTCACCTCTCGCAATATG-AGT-TGAT-TT--TTTT-GACAAACAGAAATTG
* *
3699495 AAATTACCTCAGCATGTCC
57 AAAATACCTCAGCGTGTCC
* * * * *
3699514 CGAGGCTCAACTCACCTTTCGCAATATGAGTTAATTTTTTTGAAAAATAGAAATTTAAAAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAA-TTGAAAATACC
3699579 TCAGCGTGTCC
65 TCAGCGTGTCC
* * *
3699590 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAAATTGAAAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGACAAACAGAAATTGAAAA
3699652 ACAGAAATTG
Statistics
Matches: 289, Mismatches: 57, Indels: 58
0.72 0.14 0.14
Matches are distributed among these distances:
73 30 0.10
74 1 0.00
75 28 0.10
76 123 0.43
77 15 0.05
78 24 0.08
79 10 0.03
80 3 0.01
81 2 0.01
82 2 0.01
83 3 0.01
84 11 0.04
85 9 0.03
86 10 0.03
87 5 0.02
88 13 0.04
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (75 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAATACCT
CAGCGTGTCC
Found at i:3699414 original size:14 final size:14
Alignment explanation
Indices: 3699395--3699422 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3699385 TTTTTTTTAC
3699395 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3699409 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3699423 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:3699467 original size:90 final size:88
Alignment explanation
Indices: 3699314--3699497 Score: 230
Period size: 90 Copynumber: 2.1 Consensus size: 88
3699304 GTTGATTTTT
* *
3699314 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
* * *
3699379 AGTTGATTTTTTTTACGAACAGAAA
66 AGTT-A-ATTTTTGACAAACAGAAA
* *
3699404 TTGAAGAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACC-CTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
*
3699466 ATGTGTTAATTTTTGACAAACAGAAA
63 ATGAGTTAATTTTTGACAAACAGAAA
3699492 TTGAAA
1 TTGAAA
3699498 TTACCTCAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 20 0.24
89 15 0.18
90 27 0.33
91 18 0.22
92 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (88 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTGACAAACAGAAA
Found at i:3699527 original size:163 final size:165
Alignment explanation
Indices: 3699245--3699867 Score: 460
Period size: 166 Copynumber: 3.9 Consensus size: 165
3699235 ATTTTTGACA
** * *
3699245 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAAGACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * *
3699310 TTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
66 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAA
*
3699375 TATGAGTTGATTTTTTTTACGAACAGAAATTGAAG
131 TATGAGTTAATTTTTTTTACGAACAGAAATTGAAG
* *
3699410 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACC-CTCGCAATATGTGTT-
1 AACAGAAATTGAAAAGACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * * *
3699473 A-ATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTTTCGC
64 ATATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGC
3699536 AATATGAGTTAA-TTTTTTT--G-A-A-AAA-T--AG
129 AATATGAGTTAATTTTTTTTACGAACAGAAATTGAAG
* * * * *
3699564 ---A-AATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAAGACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* * * *
3699625 TTTTTTTTTACGAACAGAAATTGAAAAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCCGAGGC
65 ----TATTT-----------TTGAAAAACAGAAATTTAAAAATACCTCAGCATGT--CCCGAGGC
*
3699689 TCAACTCACCTCTCGCAATATGAGTTGA---TTTTT--G-AC---------A-
113 TCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTACGAACAGAAATTGAAG
** * **
3699726 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG--
1 AACAGAAATTGAAAAGACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * * * *
3699789 A-TTTT-AAAAACAGAAA-TTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGC
66 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCATGT--CCCGAGGCTCAACTCACCTCTCGC
*
3699851 AATATGAGCTAATTTTT
129 AATATGAGTTAATTTTT
3699868 GATGAACATA
Statistics
Matches: 388, Mismatches: 39, Indels: 78
0.77 0.08 0.15
Matches are distributed among these distances:
146 63 0.16
147 2 0.01
148 19 0.05
149 16 0.04
150 17 0.04
151 1 0.00
154 2 0.01
156 4 0.01
157 3 0.01
158 3 0.01
159 1 0.00
160 1 0.00
162 7 0.02
163 51 0.13
164 16 0.04
165 24 0.06
166 67 0.17
167 58 0.15
169 33 0.09
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (165 bp):
AACAGAAATTGAAAAGACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTAATTTTTTTTACGAACAGAAATTGAAG
Found at i:3699576 original size:239 final size:239
Alignment explanation
Indices: 3699156--3699867 Score: 1150
Period size: 239 Copynumber: 3.0 Consensus size: 239
3699146 AATTGAAAAA
* * * *
3699156 AACAGAAATTGAAAAGAAGAAATTAAAAAGACCTCAGCATGTGAGTCGAGACTCAACTCACCTCT
1 AACAGAAATTGAAAA-CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
3699221 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
65 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
3699286 TCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC
130 TCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC
3699351 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
195 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
3699396 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACC-CT
1 AACAGAAATTGAA-AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
* *
3699460 CGCAATATGTGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCATGTCCCGAGGCTCAAC
65 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
* *
3699525 TCACCTTTCGCAATATGAGTTAATTTTTTTGAAAAATAGAAATTTAAAAATACCTCAGCGTGTCC
130 TCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC
3699590 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACG
195 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTACG
3699637 AACAGAAATTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
1 AACAGAAATTG-AAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
* **
3699702 CGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAAC
65 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
* *
3699767 TCACCTCTCGCAATATGAGTTGA---TTTT-AAAAACAGAAA-TTGAAAATACCTCAGCGTGTGA
130 TCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT--
* * * *
3699827 GCC-AAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTT
193 -CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
3699868 GATGAACATA
Statistics
Matches: 443, Mismatches: 21, Indels: 19
0.92 0.04 0.04
Matches are distributed among these distances:
237 24 0.05
238 10 0.02
239 195 0.44
240 57 0.13
241 72 0.16
242 85 0.19
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (239 bp):
AACAGAAATTGAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTC
GCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACT
CACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCT
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
Found at i:3699656 original size:14 final size:14
Alignment explanation
Indices: 3699637--3699665 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3699627 TTTTTTTACG
3699637 AACAGAAATTGAAA
1 AACAGAAATTGAAA
3699651 AACAGAAATTGAAA
1 AACAGAAATTGAAA
3699665 A
1 A
3699666 GACCTCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:3699711 original size:93 final size:92
Alignment explanation
Indices: 3699553--3699721 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 92
3699543 GTTAATTTTT
* * *
3699553 TTGAAAAATAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
3699618 AGTTGATTTTTTTTTTACGAACAGAAA
66 AGTTGATTTTTTTTTTACGAACAGAAA
*
3699645 TTGAAAAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
3699708 ATGAGTTGATTTTT
63 ATGAGTTGATTTTT
3699722 GACAAACAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
91 14 0.20
92 13 0.19
93 41 0.59
94 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (92 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTTTTTACGAACAGAAA
Found at i:3699779 original size:73 final size:74
Alignment explanation
Indices: 3699645--3699956 Score: 366
Period size: 75 Copynumber: 4.2 Consensus size: 74
3699635 CGAACAGAAA
* * *
3699645 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGC-CGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGC--GTGTGCTAGAGGCTCAACTCACCTCTCGCAATA
3699709 TGAGTTGATTT
64 TGAGTTGATTT
* * *
3699720 TTGACAAACAGAAATTGAAATTACCTCAGCGTGT-CTTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTGCTAGAGGCTCAACTCACCTCTCGCAATATG
3699784 AGTTGA-TT
66 AGTTGATTT
* *
3699792 TT-AAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCA-AGGCTCAACTCACCTCTTGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--GCTAGAGGCTCAACTCACCTCTCGCAATA
* *
3699855 TGAGCTAATTT
64 TGAGTTGATTT
** * * *
3699866 TTGATGAACATAAATT-AAAACCACCTCAGCGTGTCCTGAGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAA-TACCTCAGCGTGTGCT-AGAGGCTCAACTCACCTCTCGCAATA
3699930 TGAGTTGATTTT
64 TGAGTTGA-TTT
* *
3699942 TTTAAAATCAGAAAT
1 TTGAAAAACAGAAAT
3699957 AAAAACATCA
Statistics
Matches: 201, Mismatches: 26, Indels: 19
0.82 0.11 0.08
Matches are distributed among these distances:
71 29 0.14
72 5 0.02
73 66 0.33
74 10 0.05
75 78 0.39
76 13 0.06
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTGCTAGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTT
Found at i:3708145 original size:12 final size:12
Alignment explanation
Indices: 3708125--3708160 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3708115 TGGGATATGC
*
3708125 AATGTATGAATG
1 AATGCATGAATG
3708137 AATGCATGAATG
1 AATGCATGAATG
3708149 AATGCATGAATG
1 AATGCATGAATG
3708161 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:3709708 original size:16 final size:15
Alignment explanation
Indices: 3709687--3709734 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3709677 GATGTGAATA
3709687 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
3709703 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
3709718 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
3709734 A
1 A
3709735 ATAATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3709710 original size:24 final size:24
Alignment explanation
Indices: 3709683--3709738 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3709673 TAATGATGTG
*
3709683 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
3709707 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
3709731 AATAATAA
1 AATAATAA
3709739 TTAATATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:3709717 original size:8 final size:8
Alignment explanation
Indices: 3709683--3709734 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3709673 TAATGATGTG
*
3709683 AATAATAA
1 AATATTAA
3709691 AATATATAA
1 AATAT-TAA
3709700 AATA-TAA
1 AATATTAA
3709707 AATATTAA
1 AATATTAA
*
3709715 AATATCAA
1 AATATTAA
*
3709723 AATATTAG
1 AATATTAA
3709731 AATA
1 AATA
3709735 ATAATTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:3709911 original size:25 final size:25
Alignment explanation
Indices: 3709883--3709931 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3709873 CGTGATAATA
**
3709883 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATACATACATAATATAGTG
3709908 TTAAAAATACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
3709932 TAAGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:3709972 original size:25 final size:25
Alignment explanation
Indices: 3709933--3709997 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
3709923 TAATATAGTT
3709933 AAGATATATACATAAGATAACATGTA
1 AAGATATATACATAAGATAACAT-TA
* * *
3709959 AA-ATATATATATAATATAATATTA
1 AAGATATATACATAAGATAACATTA
3709983 AAGATATATACATAA
1 AAGATATATACATAA
3709998 AATAGTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.12
25 28 0.82
26 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (25 bp):
AAGATATATACATAAGATAACATTA
Found at i:3710023 original size:22 final size:22
Alignment explanation
Indices: 3709963--3710023 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
3709953 CATGTAAAAT
*
3709963 ATATATATAATATAATATTAAAG
1 ATATATAT-ATATAATAGTAAAG
* *
3709986 ATATATACATAAAATAGTATAA-
1 ATATATATATATAATAGTA-AAG
*
3710008 ATATATATATGTAATA
1 ATATATATATATAATA
3710024 TAGAATTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (22 bp):
ATATATATATATAATAGTAAAG
Found at i:3710091 original size:45 final size:48
Alignment explanation
Indices: 3709877--3710091 Score: 160
Period size: 47 Copynumber: 4.5 Consensus size: 48
3709867 TAAATACGTG
* * * *
3709877 ATAATATTAA-AAATATGTACATAATATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAGAAATA--TACATAATATAGT-ATAAAGATATATATATAAT
* * * * *
3709927 AT-A-GTTAAGATATATACATAAGATAACATGTAAA-ATATATATATAAT
1 ATAATATTAAGAAATATACATAATAT-A-GTATAAAGATATATATATAAT
* * * *
3709974 ATAATATTAAAGATATATACATAAAATAGTATAAATATATATATGTAAT
1 ATAATATT-AAGAAATATACATAATATAGTATAAAGATATATATATAAT
* * *
3710023 ATAGA-ATTTA-AAATATACCTAATATATTA-AAAGA-ATATATATAAT
1 ATA-ATATTAAGAAATATACATAATATAGTATAAAGATATATATATAAT
3710068 ATAATATTAAGAAATATA-ATAATA
1 ATAATATTAAGAAATATACATAATA
3710092 ACAAAAAAGG
Statistics
Matches: 134, Mismatches: 21, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
44 1 0.01
45 22 0.16
46 11 0.08
47 37 0.28
48 16 0.12
49 27 0.20
50 20 0.15
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (48 bp):
ATAATATTAAGAAATATACATAATATAGTATAAAGATATATATATAAT
Found at i:3710656 original size:31 final size:30
Alignment explanation
Indices: 3710579--3710755 Score: 282
Period size: 30 Copynumber: 5.8 Consensus size: 30
3710569 TAGGTACAAG
* * *
3710579 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
3710609 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
3710639 TGGTGGTGGAAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGG-AAAAAGAGTGGCTAGTGGAGT
3710670 TGGTGGTGGAAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGG-AAAAAGAGTGGCTAGTGGAGT
* *
3710701 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
*
3710731 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGT
3710756 TGAGAAAAGT
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
30 79 0.56
31 61 0.44
ACGTcount: A:0.24, C:0.03, G:0.48, T:0.24
Consensus pattern (30 bp):
TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:3710673 original size:61 final size:60
Alignment explanation
Indices: 3710579--3710755 Score: 282
Period size: 61 Copynumber: 2.9 Consensus size: 60
3710569 TAGGTACAAG
* * *
3710579 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
3710639 TGGTGGTGGAAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGG-AAAAAGAGTGGCTAGTGGAGTTGGTGGTGG-AAAAAGAGTGGCTAGTGGAGT
* * *
3710701 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
3710756 TGAGAAAAGT
Statistics
Matches: 109, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
60 24 0.22
61 55 0.50
62 30 0.28
ACGTcount: A:0.24, C:0.03, G:0.48, T:0.24
Consensus pattern (60 bp):
TGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:3712724 original size:148 final size:145
Alignment explanation
Indices: 3712539--3713497 Score: 637
Period size: 151 Copynumber: 6.6 Consensus size: 145
3712529 TATTACCACT
*
3712539 TTATTCGTATTTTTTACTTTCGTATATTATTTCTTAAAATATATTATTTACGTATTTTATTTTTT
1 TTATTCGTATTTTTTACTTTCGTATATTATTTTTTAAAATATATTATTTAC-TATTTTATTTTTT
* *
3712604 TATATTATTTTAGCAAAAATTGTTTCAAATGTACTTAAGTGTTTTTTATATTAATTT-AATAAAT
65 TATATTATTTTAGTAAAAA-TGTTTCAAATGTACTTAAGTATTTTTTATATT-ATTTAAATAAAT
* *
3712668 AACCTTGACTTTGGCACC
128 AACCCTGACTTTAGCACC
* * * * * * *
3712686 TTGTTCGTATTTTTTAATTTTTGGATTTTATTTTTTAAAATATATTATTTTCATATTTTATTTCT
1 TTATTCGTATTTTTT-ACTTTCGTATATTATTTTTTAAAATATATTATTTAC-TATTTTATTTTT
* * *
3712751 TTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTATTTAAGTATTTTTTATATTTTTTA
64 TTATATTATTTTAGTA-AAAATGTTTCAAATG-------TACTTAAGTATTTTTTATATTATTTA
* * *
3712816 AATAAATAACCCTGATTTTATCACT
121 AATAAATAACCCTGACTTTAGCACC
* *
3712841 TTATTCGTATTTTTTACTTTCGTATATTATTTTTT-AAATTTAATA-TTA-T-TTTCATATTTTT
1 TTATTCGTATTTTTTACTTTCGTATATTATTTTTTAAAATATATTATTTACTATTT--TATTTTT
* *
3712902 TTATATTATTTTAGTAAAAAATGTTTCAAATGTATTATTTAAGTATTTTTTATA-TA-TTACCAC
64 TTATATTATTTTAGT-AAAAATGTTTCAAATG---TACTTAAGTATTTTTTATATTATTTA--AA
* ** * ***
3712965 T--TTATTCAT-A-TTTTTTA-C
123 TAAATAACCCTGACTTTAGCACC
* * ** * * *
3712983 -T-TTCGTATATTATGTTTTC--A-A--A---TAT-A--T-T-TT-TTAAGTATTTTA-TTTTTT
1 TTATTCGTATTTTTTACTTTCGTATATTATTTTTTAAAATATATTATTTACTATTTTATTTTTTT
* * *
3713031 ATATTATTTTAGCAAAAATTGTTTCAAATGTATTACTTAAGTGTTTTCTATATTAATTT-AATAA
66 ATATTATTTTAGTAAAAA-TGTTTCAAATG---TACTTAAGTATTTTTTATATT-ATTTAAATAA
*
3713095 ATAACCCTGACTTTGGCACC
126 ATAACCCTGACTTTAGCACC
* * * * * *
3713115 TTGTTCGTATTTTTTAATTTTC-TAATTTTATTTTTTAAAATATACTATTTTCATATTTTATTTC
1 TTATTCGTATTTTTT-ACTTTCGT-ATATTATTTTTTAAAATATATTATTTAC-TATTTTATTTT
* * * * *
3713179 TTTATATTATTTTAATACATAATGTTTTAAATGTATTATTTATTTTAGTATTTTTTATATTTTTT
63 TTTATATTATTTTAGTA-AAAATGTTTCAAATG---TACTTA----AGTATTTTTTATATTATTT
* * *
3713244 AAATAAATAACCCTGATTTTATCACT
120 AAATAAATAACCCTGACTTTAGCACC
* * *
3713270 TTATTCGTATTTTTTACTTTTGTATATTATTTTTT-AAATTTAATA-TTA-T-TTTCATATTTTT
1 TTATTCGTATTTTTTACTTTCGTATATTATTTTTTAAAATATATTATTTACTATTT--TATTTTT
* *
3713331 TTATATTATTTTAGCAAAAACTGTTTCAAATGTATTATTTAAGTATTTTTTATA--ATTT-AATA
64 TTATATTATTTTAGTAAAAA-TGTTTCAAATG---TACTTAAGTATTTTTTATATTATTTAAATA
*
3713393 AATAACCCTGACTTTGGCACC
125 AATAACCCTGACTTTAGCACC
* * ** * * *
3713414 TTGTTCGTATTTTTTTATTTTCAAATTTTATTTTTTAAAATATACTATTTTCATATTTTA-TTTT
1 TTATTCGTA-TTTTTTACTTTCGTATATTATTTTTTAAAATATATTATTTAC-TATTTTATTTTT
3713478 TTATATTATTTTAGTAAAAA
64 TTATATTATTTTAGTAAAAA
3713498 ACTCGTCACC
Statistics
Matches: 642, Mismatches: 108, Indels: 124
0.73 0.12 0.14
Matches are distributed among these distances:
126 5 0.01
127 50 0.08
128 6 0.01
129 7 0.01
130 7 0.01
131 4 0.01
132 4 0.01
133 1 0.00
134 10 0.02
135 6 0.01
137 2 0.00
138 1 0.00
140 15 0.02
141 1 0.00
143 7 0.01
144 31 0.05
145 31 0.05
146 10 0.02
147 75 0.12
148 70 0.11
149 12 0.02
150 15 0.02
151 109 0.17
152 8 0.01
153 16 0.02
154 37 0.06
155 102 0.16
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.57
Consensus pattern (145 bp):
TTATTCGTATTTTTTACTTTCGTATATTATTTTTTAAAATATATTATTTACTATTTTATTTTTTT
ATATTATTTTAGTAAAAATGTTTCAAATGTACTTAAGTATTTTTTATATTATTTAAATAAATAAC
CCTGACTTTAGCACC
Found at i:3712949 original size:155 final size:153
Alignment explanation
Indices: 3712638--3712956 Score: 395
Period size: 155 Copynumber: 2.1 Consensus size: 153
3712628 TCAAATGTAC
* * * *
3712638 TTAAGTGTTTTTTATATTAATTTAATAAATAACCTTGACTTTGGCACCTTGTTCGTATTTTTTAA
1 TTAAGTATTTTTTATATTAATTTAATAAATAACCCTGACTTTAGCACCTTATTCGTATTTTTTAA
* * * *
3712703 TTTTTGGATTTTATTTTTTAAAATATATTATTTTCATATTTTATTTCTTTATATTATTTTAGTAC
66 CTTTCGGATATTATTTTTTAAAATATATTATTTTCATA--TTATTTCTTTATATTATTTTAGTAA
*
3712768 ATAATGTTTCAAATGTATTATTTAT
129 AAAATGTTTCAAATGTATTATTTAT
* * * *
3712793 TTAAGTATTTTTTATATT-TTTTAAATAAATAACCCTGATTTTATCACTTTATTCGTATTTTTT-
1 TTAAGTATTTTTTATATTAATTT-AATAAATAACCCTGACTTTAGCACCTTATTCGTATTTTTTA
* *
3712856 ACTTTCGTATATTATTTTTTAAATTTAATATTATTTTCATA-T-TTT-TTTATATTATTTTAGTA
65 ACTTTCGGATATTATTTTTTAAA-AT-ATATTATTTTCATATTATTTCTTTATATTATTTTAGTA
3712918 AAAAATGTTTCAAATG---TA-TTAT
128 AAAAATGTTTCAAATGTATTATTTAT
3712940 TTAAGTATTTTTTATAT
1 TTAAGTATTTTTTATAT
3712957 ATTACCACTT
Statistics
Matches: 146, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
147 21 0.14
148 2 0.01
151 31 0.21
152 3 0.02
153 1 0.01
154 22 0.15
155 52 0.36
156 14 0.10
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (153 bp):
TTAAGTATTTTTTATATTAATTTAATAAATAACCCTGACTTTAGCACCTTATTCGTATTTTTTAA
CTTTCGGATATTATTTTTTAAAATATATTATTTTCATATTATTTCTTTATATTATTTTAGTAAAA
AATGTTTCAAATGTATTATTTAT
Done.