Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 62
Found at i:403958 original size:20 final size:21
Alignment explanation
Indices: 403924--403964 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
403914 TAAAAAGGGT
403924 GAAAAAGAACAAAAA-AAAAA
1 GAAAAAGAACAAAAAGAAAAA
**
403944 GAAAAAGAATGAAAAGAAAAA
1 GAAAAAGAACAAAAAGAAAAA
403965 AATATTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (21 bp):
GAAAAAGAACAAAAAGAAAAA
Found at i:408574 original size:23 final size:22
Alignment explanation
Indices: 408548--408597 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
408538 ACATTCTAGG
408548 TTTCACCATTAGATCTCTCTATC
1 TTTCACCATT-GATCTCTCTATC
* * *
408571 TTTCCACTATTTATCTCTTTATC
1 TTT-CACCATTGATCTCTCTATC
408594 TTTC
1 TTTC
408598 CATCATCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 16 0.70
24 6 0.26
ACGTcount: A:0.18, C:0.28, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTCACCATTGATCTCTCTATC
Found at i:410682 original size:22 final size:22
Alignment explanation
Indices: 410657--410699 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
410647 ACATTAAACT
*
410657 ATAAATTGACCTATTTATAATA
1 ATAAATTAACCTATTTATAATA
* *
410679 ATAAATTAATCTATTTCTAAT
1 ATAAATTAACCTATTTATAAT
410700 CTTATTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAAATTAACCTATTTATAATA
Found at i:411677 original size:3 final size:3
Alignment explanation
Indices: 411671--411705 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
411661 TTATCGTTAT
*
411671 TTA TTA TTA TTA TTA TTT TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
411706 CATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:411697 original size:17 final size:18
Alignment explanation
Indices: 411670--411704 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
411660 TTTATCGTTA
411670 TTTATTATTATTATTATT
1 TTTATTATTATTATTATT
411688 TTTA-TATTATTATTATT
1 TTTATTATTATTATTATT
411705 ACATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTATTATTATTATT
Found at i:412182 original size:14 final size:14
Alignment explanation
Indices: 412163--412189 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
412153 TCGGGAGGCC
412163 AGAGAAAAAAAAAA
1 AGAGAAAAAAAAAA
412177 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
412190 TATATTCGAG
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAAAAAA
Found at i:419054 original size:32 final size:30
Alignment explanation
Indices: 419012--419079 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 30
419002 CTCACAAATC
419012 AACATACATACATCAATACAAACATATATCA
1 AACATACATACATCAATACAAACATATAT-A
* *
419043 ATACATACATACATCAATACATACCTATATA
1 A-ACATACATACATCAATACAAACATATATA
419074 AACATA
1 AACATA
419080 AAATTTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 5 0.15
31 3 0.09
32 26 0.76
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (30 bp):
AACATACATACATCAATACAAACATATATA
Found at i:419064 original size:16 final size:16
Alignment explanation
Indices: 419013--419066 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
419003 TCACAAATCA
419013 ACATACATACATCAAT
1 ACATACATACATCAAT
* *
419029 ACAAACATATATCAAT
1 ACATACATACATCAAT
419045 ACATACATACATCAAT
1 ACATACATACATCAAT
419061 ACATAC
1 ACATAC
419067 CTATATAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
ACATACATACATCAAT
Found at i:419634 original size:101 final size:104
Alignment explanation
Indices: 419513--419705 Score: 286
Period size: 101 Copynumber: 1.9 Consensus size: 104
419503 TTGAGACAAA
419513 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTT-CCTTTGAGATACAAA-TT-GAATTTG
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTG
419575 ATTCAC-TTAAAACAAAATTAATCTCACCTTAGATGTTGT
66 ATTCACATT-AAACAAAATTAATCTCACCTTAGATGTTGT
* * * *
419614 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTG
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTG
* * *
419679 TTTCACATTAAACAAAGTTGATCTCAC
66 ATTCACATTAAACAAAATTAATCTCAC
419706 TTGAGATCGT
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
101 35 0.43
102 14 0.17
103 2 0.02
104 28 0.35
105 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (104 bp):
TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTG
ATTCACATTAAACAAAATTAATCTCACCTTAGATGTTGT
Found at i:419729 original size:102 final size:100
Alignment explanation
Indices: 419520--419748 Score: 259
Period size: 102 Copynumber: 2.3 Consensus size: 100
419510 AAATTCTCTT
*
419520 AAAACAAACTTCGTCTCGCTTGAGACATTTTCCTTTGAGATACAAATTGAATTTGATTCACTTAA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCTTTGAGATACAAATTGAATTTGATTCACTTAA
* * **
419585 AACAAAATTAATCTCACCTTAGATGTTGTTTCTTTT
66 AACAAAATTAATCTCACCTTAGA-GTCGTTTCCTCA
* * *
419621 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTT-CCTTTGAGATACAAA-TT-GAATTTGATTCAC-
* *
419686 TT-AAACAAAGTTGATCTCA-CTT-GAGATCGTTTCCTCA
62 TTAAAACAAAATTAATCTCACCTTAGAG-TCGTTTCCTCA
**
419723 AAAACAAACTTT-GTCTCATTTGAGAC
1 AAAACAAA-TTTCGTCTCGCTTGAGAC
419749 TATATCTTAA
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
101 30 0.27
102 43 0.39
103 8 0.07
104 27 0.25
105 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (100 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCTTTGAGATACAAATTGAATTTGATTCACTTAA
AACAAAATTAATCTCACCTTAGAGTCGTTTCCTCA
Found at i:420259 original size:15 final size:15
Alignment explanation
Indices: 420236--420279 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
420226 TTTTGAGTCG
*
420236 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
420251 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
420266 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
420280 AGATCTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:421031 original size:3 final size:3
Alignment explanation
Indices: 421020--421062 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
421010 TTTTTTATCG
421020 TTA TT- TTA TTA TTA TTA TTA TTA TT- TATA TTA TATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA TTA TTA T
421063 ACATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 3 0.08
3 29 0.81
4 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:422157 original size:15 final size:15
Alignment explanation
Indices: 422134--422164 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
422124 CATTATATTT
*
422134 TCCTTTTTATATTAG
1 TCCTATTTATATTAG
422149 TCCTATTTATATTAG
1 TCCTATTTATATTAG
422164 T
1 T
422165 ATTTTGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (15 bp):
TCCTATTTATATTAG
Found at i:424291 original size:2 final size:2
Alignment explanation
Indices: 424284--424309 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
424274 GGCTTATCGG
424284 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
424310 TTAATTTTTA
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:424757 original size:16 final size:15
Alignment explanation
Indices: 424736--424778 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
424726 CATACTTATC
*
424736 ATTTTTTTAAATAATT
1 ATTTTTTTAAATAA-A
424752 ATTTTTTT-AATAAA
1 ATTTTTTTAAATAAA
424766 ATTTTTATTAAAT
1 ATTTTT-TTAAAT
424779 CCTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTTAAATAAA
Found at i:425319 original size:22 final size:22
Alignment explanation
Indices: 425291--425333 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
425281 ATTCAACACA
425291 AAAAGATTAATTAAATAATAAT
1 AAAAGATTAATTAAATAATAAT
425313 AAAAGATTAATTAAATAATAA
1 AAAAGATTAATTAAATAATAA
425334 CAATCAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
AAAAGATTAATTAAATAATAAT
Found at i:427074 original size:25 final size:25
Alignment explanation
Indices: 427022--427078 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
427012 AAATTTTATG
*
427022 TTAGATGATATGAACTAATAAAATT
1 TTAGAGGATATGAACTAATAAAATT
*
427047 TTAGAGGATGATGAACTTATAAAA-T
1 TTAGAGGAT-ATGAACTAATAAAATT
427072 TTAGAGG
1 TTAGAGG
427079 GCAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (25 bp):
TTAGAGGATATGAACTAATAAAATT
Found at i:428310 original size:31 final size:31
Alignment explanation
Indices: 428275--428365 Score: 173
Period size: 31 Copynumber: 2.9 Consensus size: 31
428265 ACGAATGTGT
428275 GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
1 GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
*
428306 GTTGATGGTTTGGTTGGAAAGTGTGTTATGC
1 GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
428337 GTTGATAGTTTGGTTGGAAAGTGTGTTAT
1 GTTGATAGTTTGGTTGGAAAGTGTGTTAT
428366 TGGATAACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.19, C:0.02, G:0.36, T:0.43
Consensus pattern (31 bp):
GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
Found at i:431153 original size:2 final size:2
Alignment explanation
Indices: 431146--431201 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
431136 GATCTAGCCA
431146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
431188 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
431202 TTGAGGTACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:437708 original size:21 final size:21
Alignment explanation
Indices: 437683--437724 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
437673 ATGTGAACAG
*
437683 TGCTACAGTGCATCTATGCAT
1 TGCTACAGTGCATCGATGCAT
437704 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
437725 GAAAATATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:456103 original size:21 final size:21
Alignment explanation
Indices: 456077--456116 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
456067 CAGAACCCCA
*
456077 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
456098 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
456117 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:456148 original size:21 final size:23
Alignment explanation
Indices: 456097--456148 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
456087 GATTCCCCTG
456097 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
456120 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
456141 TGGGGGGA
1 TGGGGGGA
456149 TTGATTAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:460002 original size:22 final size:21
Alignment explanation
Indices: 459960--459999 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
459950 GAGTTTGTTT
*
459960 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
459981 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
460000 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:463121 original size:18 final size:18
Alignment explanation
Indices: 463098--463132 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
463088 AAAGGTTTGC
*
463098 GATGAGTAGCACAAAACT
1 GATGAGCAGCACAAAACT
*
463116 GATGAGCAGCGCAAAAC
1 GATGAGCAGCACAAAAC
463133 CAGTGAGCAC
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:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (18 bp):
GATGAGCAGCACAAAACT
Found at i:472937 original size:18 final size:18
Alignment explanation
Indices: 472911--473001 Score: 93
Period size: 18 Copynumber: 5.2 Consensus size: 18
472901 ACCGGTCAAA
472911 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* * *
472929 ACACGACCCGACCCTTTT
1 ACCCGACCCGACCCGTTG
472947 ACCC-A----ACCCGTTG
1 ACCCGACCCGACCCGTTG
472960 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
472978 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
472999 ACC
1 ACC
473002 GTTGACCGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
13 10 0.17
14 1 0.02
17 1 0.02
18 35 0.59
21 12 0.20
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:472950 original size:13 final size:13
Alignment explanation
Indices: 472933--472995 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
472923 CCGTTGACAC
*
472933 GACCCGACCCTTT
1 GACCCGACCCGTT
* *
472946 TACCCAACCCGTT
1 GACCCGACCCGTT
472959 GACCCGACCCGACCCGTT
1 GACCCG-----ACCCGTT
472977 GACCCGACCCGTT
1 GACCCGACCCGTT
472990 GACCCG
1 GACCCG
472996 TTGACCGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 27 0.68
18 13 0.32
ACGTcount: A:0.17, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:472980 original size:8 final size:8
Alignment explanation
Indices: 472969--473018 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
472959 GACCCGACCC
472969 GACCCGTT
1 GACCCGTT
472977 GACCC---
1 GACCCGTT
472982 GACCCGTT
1 GACCCGTT
472990 GACCCGTT
1 GACCCGTT
472998 GA-CCGTT
1 GACCCGTT
473005 GACCGGCGTT
1 GACC--CGTT
473015 GACC
1 GACC
473019 ATTGTTGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.14
7 7 0.19
8 16 0.44
10 8 0.22
ACGTcount: A:0.14, C:0.38, G:0.28, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:472993 original size:31 final size:31
Alignment explanation
Indices: 472915--472995 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
472905 GTCAAAACCC
* *
472915 GACCCGACCCGTTGACACGACCCGACCCTTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
472946 TACCCAACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
472977 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
472996 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.47, G:0.20, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:473005 original size:15 final size:16
Alignment explanation
Indices: 472985--473018 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
472975 TTGACCCGAC
472985 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
473000 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
473017 CC
1 CC
473019 ATTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:474898 original size:42 final size:43
Alignment explanation
Indices: 474805--475064 Score: 418
Period size: 42 Copynumber: 6.1 Consensus size: 43
474795 GTAAAAACGA
* * * *
474805 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
*
474849 TAAGGCTTACCCTTGTACACAGCAAAGGAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
474891 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
474933 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
474976 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
475018 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACTG
475062 TAA
1 TAA
475065 CAATAATTAA
Statistics
Matches: 203, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
42 123 0.61
43 63 0.31
44 17 0.08
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
Found at i:474980 original size:85 final size:85
Alignment explanation
Indices: 474805--475064 Score: 423
Period size: 85 Copynumber: 3.0 Consensus size: 85
474795 GTAAAAACGA
* * * * *
474805 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGTACACA
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACA
*
474870 GCAAAGGAACCT-GGGAAACTG
64 GCAAAGGAACCTGGGGGAACTG
474891 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGC
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGC
*
474956 AAAGGGACCTGGGGGAACTG
66 AAAGGAACCTGGGGGAACTG
474976 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGC
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGC
475041 AAAGGAACCTGGGGGAAACTG
66 AAAGGAACCTGGGGG-AACTG
475062 TAA
1 TAA
475065 CAATAATTAA
Statistics
Matches: 164, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
84 40 0.24
85 111 0.68
86 13 0.08
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (85 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGC
AAAGGAACCTGGGGGAACTG
Found at i:475042 original size:127 final size:129
Alignment explanation
Indices: 474805--475064 Score: 436
Period size: 127 Copynumber: 2.0 Consensus size: 129
474795 GTAAAAACGA
* * *
474805 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGTACACA
1 TAAGGTCTTACCCTTGCACACAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACA
474870 GCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACTG
66 GCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
474933 TAAGG-CTTACCCTTGCACACAGC-AAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACAC
1 TAAGGTCTTACCCTTGCACACAGCAAAAGAG-CCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
474996 AGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACT
65 AGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACT
475061 G
129 G
475062 TAA
1 TAA
475065 CAATAATTAA
Statistics
Matches: 124, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
126 5 0.04
127 102 0.82
128 5 0.04
129 12 0.10
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (129 bp):
TAAGGTCTTACCCTTGCACACAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACA
GCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
Found at i:477904 original size:18 final size:18
Alignment explanation
Indices: 477854--477907 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
477844 CGCCGGTCAA
*
477854 CGGGTCAACGGGTCAGGT
1 CGGGTCAACGGGTCGGGT
*
477872 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
477890 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
477908 TGTGACCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:484470 original size:45 final size:45
Alignment explanation
Indices: 484406--484512 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 45
484396 GTGATAACCT
** * * **
484406 TGGGACCACACCGCTTGGAGATATGCGAGACAATGCTCATGTCCA
1 TGGGACCACACCATTTGGAGATATGCGAGACAATACGCATGAACA
* * *
484451 TGGGACCACACCATTTGGAGCTATGCGAGATATTACGCATGAACA
1 TGGGACCACACCATTTGGAGATATGCGAGACAATACGCATGAACA
*
484496 TGGGGCCACACCATTTG
1 TGGGACCACACCATTTG
484513 AATTAATAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.21
Consensus pattern (45 bp):
TGGGACCACACCATTTGGAGATATGCGAGACAATACGCATGAACA
Found at i:492055 original size:25 final size:25
Alignment explanation
Indices: 492027--492074 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
492017 CTATTTAAAA
492027 TAATATACAGTAAAATT-AATTTTTT
1 TAATA-ACAGTAAAATTGAATTTTTT
* *
492052 TAATAATAGTTAAATTGAATTTT
1 TAATAACAGTAAAATTGAATTTT
492075 ATTATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (25 bp):
TAATAACAGTAAAATTGAATTTTTT
Found at i:504424 original size:20 final size:24
Alignment explanation
Indices: 504366--504441 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 24
504356 GAAAAAGATG
504366 AGTAAAAGAAAGAGAAAAAGTTAA
1 AGTAAAAGAAAGAGAAAAAGTTAA
*
504390 AGTTAAAATGAAAGAGAAAAATTAATAA
1 AG-TAAAA-GAAAGAGAAAAAGT--TAA
504418 AG-AAAGAGAAA-AGAAAAAGTTAA
1 AGTAAA-AGAAAGAGAAAAAGTTAA
504441 A
1 A
504442 AATTTAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.09
24 2 0.04
25 13 0.29
26 20 0.44
27 1 0.02
28 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (24 bp):
AGTAAAAGAAAGAGAAAAAGTTAA
Found at i:506243 original size:24 final size:24
Alignment explanation
Indices: 506199--506248 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
506189 ATAAAGAACC
*
506199 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
506223 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
506247 AA
1 AA
506249 TCATCCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:521070 original size:6 final size:6
Alignment explanation
Indices: 521061--521095 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
521051 GCATATAACA
*
521061 TATATG TATATG TATATG TATATG TATATA TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
521096 TGTGTTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:523205 original size:12 final size:12
Alignment explanation
Indices: 523185--523219 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
523175 TAAAGTTGAG
*
523185 TTGAGTTCTGTC
1 TTGAATTCTGTC
523197 TTGAATTCTGTC
1 TTGAATTCTGTC
523209 TTGAATTCTGT
1 TTGAATTCTGT
523220 ATTCAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.51
Consensus pattern (12 bp):
TTGAATTCTGTC
Found at i:525384 original size:16 final size:17
Alignment explanation
Indices: 525363--525405 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
525353 ATTTAAAAAT
525363 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
525379 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
525396 AAATATTTAA
1 AAATATTTAA
525406 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:527842 original size:30 final size:30
Alignment explanation
Indices: 527807--527870 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
527797 AGAACCGGTA
* * *
527807 GAACCGGCTGAGAACCGGCAAAACCGGGGT
1 GAACCGACTGAAAACCGACAAAACCGGGGT
*
527837 GAACCGACTGAAAACCGACAAAACCGGTGT
1 GAACCGACTGAAAACCGACAAAACCGGGGT
527867 GAAC
1 GAAC
527871 TGTCGATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.30, T:0.08
Consensus pattern (30 bp):
GAACCGACTGAAAACCGACAAAACCGGGGT
Found at i:530011 original size:26 final size:26
Alignment explanation
Indices: 529975--530032 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
529965 TTTTTCTGGT
529975 GAGGTAGAGGTGGTCAGATTTATCTC
1 GAGGTAGAGGTGGTCAGATTTATCTC
*
530001 GAGGTAGAGGTGGTCGGATTTATCTC
1 GAGGTAGAGGTGGTCAGATTTATCTC
530027 GAGGTA
1 GAGGTA
530033 AACTTCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.38, T:0.29
Consensus pattern (26 bp):
GAGGTAGAGGTGGTCAGATTTATCTC
Found at i:533518 original size:91 final size:91
Alignment explanation
Indices: 533388--533569 Score: 337
Period size: 91 Copynumber: 2.0 Consensus size: 91
533378 GAATCGAGCT
*
533388 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
533453 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGATCC
* *
533479 AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCGTTGGATGAGTTGTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
533544 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGATCC
533570 CTCGAGTGAG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCC
Found at i:533657 original size:230 final size:230
Alignment explanation
Indices: 533249--533708 Score: 692
Period size: 230 Copynumber: 2.0 Consensus size: 230
533239 GAAACAAGTT
* * *
533249 AAGGCTGAACAAGTTCTTCTCATTATGAACTTATTCTCTCTTATCGGATAAGTTCTTCTCATTAT
1 AAGGCTGAACAAGTTCTTCTCATTATCAACTTATTCTCCCTCATCGGATAAGTTCTTCTCATTAT
* *
533314 GAACTTTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGCAATG
66 GAACTCTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATG
**
533379 AATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCT
131 AATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCT
*
533444 TCTCATTATGAACTCTCCACTG-GAAATGTTGATCC
196 TCTCATTATGAACTCTCCACTGAG-AATGTTCATCC
* * * * * *
533479 AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCGTTGGATGAGTTGTTCTCATTAT
1 AAGGCTGAACAAGTTCTTCTCATTATCAACTTATTCTCCCTCATCGGATAAGTTCTTCTCATTAT
*
533544 GAACTCTCCACTG-GAAATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGA
66 GAACTCTCCACTGAG-AATGTTGATCCCTCGAGTGAGGTG-TTGCTGATTCAACTCCATATACAA
* * *
533608 TGAATCGATCT-ATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAGTT
129 TGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTT
* *
533672 CTTTTCATTATGAACTTTCCACTGAGAATGTTCATCC
194 CTTCTCATTATGAACTCTCCACTGAGAATGTTCATCC
533709 CTCGAGTGAG
Statistics
Matches: 207, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
229 1 0.00
230 173 0.84
231 33 0.16
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (230 bp):
AAGGCTGAACAAGTTCTTCTCATTATCAACTTATTCTCCCTCATCGGATAAGTTCTTCTCATTAT
GAACTCTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATG
AATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCT
TCTCATTATGAACTCTCCACTGAGAATGTTCATCC
Found at i:533764 original size:139 final size:140
Alignment explanation
Indices: 533479--533847 Score: 609
Period size: 139 Copynumber: 2.6 Consensus size: 140
533469 ATGTTGATCC
* *
533479 AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCGTTGGATGAGTTGTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
533544 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGAT
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGAT
*
533609 GAATCGATCT
131 GAATCGAGCT
* ** *
533619 -ATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAGTTCTTTTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
533683 GAACTTTCCACT-GAGAATGTTCATCCCTCGAGTGAGGTG-TTGCTGATTCAACTCCATATACGA
66 GAACTCTCCACTGGA-AATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGA
533746 TGAATCGAGCT
130 TGAATCGAGCT
* *
533757 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
533822 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGATCC
533848 AAGGTTGAAC
Statistics
Matches: 209, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
138 36 0.17
139 171 0.82
140 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36
Consensus pattern (140 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGAT
GAATCGAGCT
Found at i:533857 original size:230 final size:230
Alignment explanation
Indices: 533621--534071 Score: 753
Period size: 230 Copynumber: 2.0 Consensus size: 230
533611 ATCGATCTAT
*
533621 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAGTTCTTT-TCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAATT-TTTCTCATTATGA
* *
533685 ACTTTCCACT-GAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGA
65 ACTCTCCACTAGA-AATATTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGA
*
533749 ATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAGTTCTT
129 ATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATTGGATGAGTTCTT
533814 CTCATTATGAACTCTCCACTGGAAATGTTGATCCAAG
194 CTCATTATGAACTCTCCACTGGAAATGTTGATCCAAG
* **
533851 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGATGAATTTTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAATTTTTCTCATTATGAA
* **
533916 CTCTCCACTAGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAAT
66 CTCTCCACTAGAAATATTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAAT
* * *
533981 CGAGCTAATGTTGAATAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATGAGTTCTTCT
131 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATTGGATGAGTTCTTCT
534046 CATTATGAACTCTCCACTGGAAATGT
196 CATTATGAACTCTCCACTGGAAATGT
534072 ATATTGGTTC
Statistics
Matches: 206, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
229 3 0.01
230 201 0.98
231 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (230 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAATTTTTCTCATTATGAA
CTCTCCACTAGAAATATTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAAT
CGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCATCATTGGATGAGTTCTTCT
CATTATGAACTCTCCACTGGAAATGTTGATCCAAG
Found at i:533895 original size:91 final size:91
Alignment explanation
Indices: 533757--533938 Score: 301
Period size: 91 Copynumber: 2.0 Consensus size: 91
533747 GAATCGAGCT
*
533757 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAATTCTTCTCATTAT
* *
533822 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTAGAAATATTGATCC
* * * *
533848 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGATGAATTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAATTCTTCTCATTAT
533913 GAACTCTCCACTAGAAATATTGATCC
66 GAACTCTCCACTAGAAATATTGATCC
533939 CTCGAGTGAG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAATTCTTCTCATTAT
GAACTCTCCACTAGAAATATTGATCC
Found at i:533938 original size:369 final size:369
Alignment explanation
Indices: 533254--534064 Score: 1390
Period size: 369 Copynumber: 2.2 Consensus size: 369
533244 AAGTTAAGGC
* * * *
533254 TGAACAAGTTCTTCTCATTATGAACTTATTCTCTCTTATCGGATAAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
* *
533319 TTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGCAATGAATCG
66 TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATGAATCG
*
533384 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCA
131 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAGTTCTTCTCA
533449 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAACTTCTT
196 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAACTTCTT
* * *
533514 CTCCCTCGTTGGATGAGTTGTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGA
261 CTCCCTCGTTGGATGAATTGTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTGA
*
533579 GGTGTTTGCTGATTCAACTCCATATACGATGAATCGATCT-ATGT
326 GGTG-TTGCTGATTCAACTCCATATACGATGAATCGAGCTAATGT
* * *
533623 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAGTTCTTTTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
*
533688 TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAATCG
66 TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATGAATCG
533753 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAGTTCTTCTCA
131 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAGTTCTTCTCA
* *
533818 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTT
196 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAACTTCTT
*
533883 CTCCCTCGTTGGATGAATTTTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTGA
261 CTCCCTCGTTGGATGAATTGTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTGA
**
533948 GGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTAATGT
326 GGTGTTGCTGATTCAACTCCATATACGATGAATCGAGCTAATGT
* * *
533992 TGAATAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
*
534057 CTCCACTG
66 TTCCACTG
534065 GAAATGTATA
Statistics
Matches: 414, Mismatches: 27, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
368 32 0.08
369 382 0.92
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (369 bp):
TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATGAATCG
AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATCATTGGATGAGTTCTTCTCA
TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAACTTCTT
CTCCCTCGTTGGATGAATTGTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTGA
GGTGTTGCTGATTCAACTCCATATACGATGAATCGAGCTAATGT
Found at i:535128 original size:227 final size:230
Alignment explanation
Indices: 534730--535179 Score: 737
Period size: 227 Copynumber: 2.0 Consensus size: 230
534720 GAACTGATAT
534730 ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
1 ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
*
534795 AGAAGAGCTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
66 AGAAGAACTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
*
534860 GAGGGATCAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAA
131 GAGGGATCAACATTTACAGTGGAAAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAA
534925 TTCATAATGAGAAGAACTTGTTCAACCTTGGATCA
196 TTCATAATGAGAAGAACTTGTTCAACCTTGGATCA
* * *
534960 ACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCATTGA-GG-G-AGAAGTTCATAATG
1 ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
* * * * * *
535022 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGGATCAGCAACACCTCACTC
66 AGAAGAACTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
*
535087 GAGGGATCAACATTCT-CAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAA
131 GAGGGATCAACATT-TACAGTGGAAAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAA
* *
535151 GTTCATAATGAGAAGAACTTTTTCAACCT
195 ATTCATAATGAGAAGAACTTGTTCAACCT
535180 AGCTCGATTC
Statistics
Matches: 205, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
227 158 0.77
228 2 0.01
229 2 0.01
230 43 0.21
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (230 bp):
ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
AGAAGAACTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
GAGGGATCAACATTTACAGTGGAAAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAA
TTCATAATGAGAAGAACTTGTTCAACCTTGGATCA
Found at i:535234 original size:138 final size:136
Alignment explanation
Indices: 534954--535317 Score: 563
Period size: 138 Copynumber: 2.6 Consensus size: 136
534944 GTTCAACCTT
*
534954 GGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCATTGA-GG-G-AGAAGTTC
1 GGATCAACATTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCCA-CGAGGGAGAAGAAGTTC
*
535016 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGGATCAGCAACACC
64 ATAATGAGAAGAACTTGTTCAACC-TAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACC
535081 TCACTCGAG
128 TCACTCGAG
*
535090 GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
1 GGATCAACATT-TCAGTGGAGAGTTCATAATGAGAAGAACTCATCC-ACGAGGGAGAAGAAGTTC
* *
535155 ATAATGAGAAGAACTTTTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATTAGCAACACCT
64 ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
535220 CACTCGAG
129 CACTCGAG
* * *
535228 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
1 GGATCAACATTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCC-ACGAGGGAGAAGAAGTTC
*
535293 ATAATGAGTAGAACTTGTTCAACCT
64 ATAATGAGAAGAACTTGTTCAACCT
535318 TGGATCAACA
Statistics
Matches: 210, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
136 44 0.21
137 6 0.03
138 129 0.61
139 31 0.15
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (136 bp):
GGATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCACGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCA
CTCGAG
Found at i:535384 original size:91 final size:91
Alignment explanation
Indices: 535228--535409 Score: 310
Period size: 91 Copynumber: 2.0 Consensus size: 91
535218 CTCACTCGAG
535228 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
1 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
*
535293 ATAATGAGTAGAACTTGTTCAACCTT
66 ATAATGAGAAGAACTTGTTCAACCTT
* *** *
535319 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCATTGAGGGAGAAAATGTTC
1 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
535384 ATAATGAGAAGAACTTGTTCAACCTT
66 ATAATGAGAAGAACTTGTTCAACCTT
535410 AGCTCGATTC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.26
Consensus pattern (91 bp):
GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
ATAATGAGAAGAACTTGTTCAACCTT
Found at i:535492 original size:230 final size:229
Alignment explanation
Indices: 535090--535548 Score: 728
Period size: 230 Copynumber: 2.0 Consensus size: 229
535080 CTCACTCGAG
535090 GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
1 GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
* *
535155 ATAATGAGAAGAACTTTTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATTAGCAACACCT
66 ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
* *
535220 CACTCGAGGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGA
131 CACTCGAGGGATCAACATTTCCAGTGGAAAGTTCATAATGAGAACAACTCATCCAACAAGAGAGA
*
535285 AAAAGTTCATAATGAGTAGAACTTGTTCAACCTT
196 AAAAGTTCATAATGAGAAGAACTTGTTCAACCTT
* * *
535319 GGATCAACATT-TCCAGTGGAGAGTTCATAATGAGAATAACTCATCC-ATTGAGGGAGAA-AATG
1 GGATCAACATTCT-CAGTGGAAAGTTCATAATGAGAAGAACTCATCCGA-CGAGGGAGAAGAA-G
535381 TTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAAC
63 TTCATAATGAGAAGAACTTGTTCAACC-TAGCTCGATTCATCGCATATGGAGTTGAATCAGCAAC
* * **
535446 ACCTCACTCGAGGGATCAACA-TTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGATGAG
127 ACCTCACTCGAGGGATCAACATTTC-CAGTGGAAAGTTCATAATGAGAACAACTCATCCAACAAG
*
535510 AGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
191 AGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTT
535549 AACTTGTTTC
Statistics
Matches: 212, Mismatches: 13, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
228 4 0.02
229 81 0.38
230 127 0.60
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (229 bp):
GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
CACTCGAGGGATCAACATTTCCAGTGGAAAGTTCATAATGAGAACAACTCATCCAACAAGAGAGA
AAAAGTTCATAATGAGAAGAACTTGTTCAACCTT
Found at i:538084 original size:2 final size:2
Alignment explanation
Indices: 538073--538101 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
538063 AATTCGAATA
538073 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
538102 GGATGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:544382 original size:20 final size:20
Alignment explanation
Indices: 544339--544379 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
544329 AGACCATAGT
* *
544339 ATTTTAGAGTTTTAAATTGA
1 ATTTTAGAATTTTAAAGTGA
544359 ATTTTACGAATTTTAAAGTGA
1 ATTTTA-GAATTTTAAAGTGA
544380 TTTATGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTTAGAATTTTAAAGTGA
Found at i:556643 original size:19 final size:19
Alignment explanation
Indices: 556621--556667 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
556611 GGAGAAAGAA
556621 ATGATTTTGGGATTTTGGG
1 ATGATTTTGGGATTTTGGG
556640 ATGATTTTGGGATTTTGGG
1 ATGATTTTGGGATTTTGGG
556659 ATGATTTTG
1 ATGATTTTG
556668 AAGCTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (19 bp):
ATGATTTTGGGATTTTGGG
Found at i:556647 original size:11 final size:11
Alignment explanation
Indices: 556631--556667 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
556621 ATGATTTTGG
556631 GATTTTGGGAT
1 GATTTTGGGAT
556642 GATTTT-GG--
1 GATTTTGGGAT
556650 GATTTTGGGAT
1 GATTTTGGGAT
556661 GATTTTG
1 GATTTTG
556668 AAGCTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 2 0.09
11 13 0.57
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (11 bp):
GATTTTGGGAT
Found at i:561991 original size:6 final size:6
Alignment explanation
Indices: 561976--562014 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
561966 CAGGACCGCT
* * *
561976 TCCCCA TCCCCG TCCCCG TCCCCT TCCCCG TCCTCG TCC
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCC
562015 AAGACCTGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.64, G:0.10, T:0.23
Consensus pattern (6 bp):
TCCCCG
Found at i:562003 original size:18 final size:18
Alignment explanation
Indices: 561976--562014 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
561966 CAGGACCGCT
561976 TCCCCATCCCCGTCCCCG
1 TCCCCATCCCCGTCCCCG
* *
561994 TCCCCTTCCCCGTCCTCG
1 TCCCCATCCCCGTCCCCG
562012 TCC
1 TCC
562015 AAGACCTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.64, G:0.10, T:0.23
Consensus pattern (18 bp):
TCCCCATCCCCGTCCCCG
Found at i:563306 original size:15 final size:15
Alignment explanation
Indices: 563286--563316 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
563276 ATTTCCTTTA
563286 GCGGCTAAAGGAAAT
1 GCGGCTAAAGGAAAT
563301 GCGGCTAAAGGAAAT
1 GCGGCTAAAGGAAAT
563316 G
1 G
563317 TGGGATTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.35, T:0.13
Consensus pattern (15 bp):
GCGGCTAAAGGAAAT
Found at i:563397 original size:59 final size:60
Alignment explanation
Indices: 563305--563444 Score: 257
Period size: 59 Copynumber: 2.4 Consensus size: 60
563295 GGAAATGCGG
563305 CTAAAGGAAATGTGGGATTGTGGGATTACAAGACCTTAACACTCAAAAGATTTTAGT-GA
1 CTAAAGGAAATGTGGGATTGTGGGATTACAAGACCTTAACACTCAAAAGATTTTAGTGGA
*
563364 CTAAAGGAAATGTGGGATTGTGGGATTACAAGACCTTAACACTCAAAAGCTTTTAGTGGA
1 CTAAAGGAAATGTGGGATTGTGGGATTACAAGACCTTAACACTCAAAAGATTTTAGTGGA
563424 -TAAAGGAAATGTGGGATTGTG
1 CTAAAGGAAATGTGGGATTGTG
563445 CTTATACTGC
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
59 77 0.97
60 2 0.03
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (60 bp):
CTAAAGGAAATGTGGGATTGTGGGATTACAAGACCTTAACACTCAAAAGATTTTAGTGGA
Found at i:568035 original size:21 final size:21
Alignment explanation
Indices: 568010--568065 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
568000 TACATATATC
* *
568010 ATCATCTATTTTCTTAGCATT
1 ATCATCTATATTATTAGCATT
* *
568031 ATCATATATATTATTATCATT
1 ATCATCTATATTATTAGCATT
568052 ATC-TCTATCATTAT
1 ATCATCTAT-ATTAT
568066 CATCAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCATCTATATTATTAGCATT
Found at i:568070 original size:21 final size:21
Alignment explanation
Indices: 568027--568070 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
568017 ATTTTCTTAG
*
568027 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
568048 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
568069 CA
1 CA
568071 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:568552 original size:149 final size:149
Alignment explanation
Indices: 568282--568730 Score: 762
Period size: 149 Copynumber: 3.0 Consensus size: 149
568272 CCGAAGTGCA
*
568282 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
* *
568347 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAAGGACCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
568412 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
*
568431 CGTAGAATTGCACCTTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
568496 CATATACATATACTAAGGACCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAAGGACCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
568561 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
568580 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
* * * * * *
568645 CATATACATATACTAAGGACC-AGTATGTGCCTCA-AAGACCTCATAAATGTTCCAAAG-A-ATA
66 CATATACATATACTAAGGACCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
* *
568706 CATATGTCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
568725 CGTAGA
1 CGTAGA
568731 CCCTCGACTC
Statistics
Matches: 287, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
145 26 0.09
146 1 0.00
147 19 0.07
148 11 0.04
149 230 0.80
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAAGGACCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:570200 original size:64 final size:62
Alignment explanation
Indices: 570070--570227 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 62
570060 TAATGAAGGT
* * * *
570070 ATGCATCGATGCACACC-ATGCATCGATGCATAAATCCTATTTGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
570132 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
570196 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
570228 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
62 16 0.19
64 56 0.67
65 8 0.10
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:577377 original size:16 final size:17
Alignment explanation
Indices: 577346--577380 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
577336 AATTCAATGT
577346 TATAAAGTAATGACTAG
1 TATAAAGTAATGACTAG
*
577363 TATAAAGT-TTGACTAG
1 TATAAAGTAATGACTAG
577379 TA
1 TA
577381 AGATCTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (17 bp):
TATAAAGTAATGACTAG
Found at i:580881 original size:164 final size:163
Alignment explanation
Indices: 580624--581134 Score: 569
Period size: 182 Copynumber: 3.0 Consensus size: 163
580614 AAGTTATAGC
* * * * * *
580624 ACTTATAAAGTGTCGATACTTTAAAAAAATATATCGATCTACAACAATATAACATGTAAAAATAT
1 ACTTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATAT
* * * *
580689 GATAAAACAT-GTCTCAAAATTGACAAAACCAGTAAAACGATACCAGATATGTTGAAAGTGTCGA
66 GATAAAAC-TGGTCTCAAAAATGACAAAACC-GGAAAAAGTTACC-GATATGTTGAAAGTGTCGA
*
580753 TAATTTAATATAAGTATCAACACTTTCTGAAATTAA
128 TAATTTAATATAAGTATCGACACTTTCTGAAATTAA
*
580789 AC-TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACATGTAAAAATAT
1 ACTTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATAT
* *
580853 GATAAAACTGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATATTGAAAGTTTCGATA
66 GATAAAACTGGTCTCAAAAATGACAAAACCGGAAAAAGTTACC-GATATGTTGAAAGTGTCGATA
* *
580918 ATTTAATGTTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATA
130 ATTTAATATAAGTATCGACACTTTC------T------G-A-AA-TTA-A
* * * * * *
580968 GCGCTTAAAAAGTGTCGACACTTTATTAAAATGTATCGATCCTTACCAATATAACAGGTAAATAT
1 --ACTTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAT
*
581033 ATGATAAAA-TAGGTCTCAAAAATGACAAAATCGGAAAAAGTTACCGAATATGTTGAAAGTGTCG
64 ATGATAAAACT-GGTCTCAAAAATGACAAAACCGGAAAAAGTTACCG-ATATGTTGAAAGTGTCG
*
581097 ATAATTTAATATAAGTATCGACACTTTCTGAATTTAA
127 ATAATTTAATATAAGTATCGACACTTTCTGAAATTAA
581134 A
1 A
581135 AGAGAAGTAG
Statistics
Matches: 294, Mismatches: 30, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
163 52 0.18
164 82 0.28
165 2 0.01
166 1 0.00
167 3 0.01
168 1 0.00
169 2 0.01
170 1 0.00
175 1 0.00
176 2 0.01
177 2 0.01
178 3 0.01
179 1 0.00
181 3 0.01
182 138 0.47
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (163 bp):
ACTTAAAAAGTGTCGACACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATAT
GATAAAACTGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGATATGTTGAAAGTGTCGATAA
TTTAATATAAGTATCGACACTTTCTGAAATTAA
Found at i:581100 original size:182 final size:181
Alignment explanation
Indices: 580791--581289 Score: 766
Period size: 182 Copynumber: 2.7 Consensus size: 181
580781 GAAATTAAAC
*
580791 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* *
580856 AAAACTGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATATTGAAAGTTTCGATAATT
66 AAAA-TGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
* *
580921 TAATGTTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
130 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
* * * *
580973 TAAAAAGTGTCGACACTTTATTAAAATGTATCGATCCTTACCAATATAACAGGTAAATATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* *
581038 AAAATAGGTCTCAAAAATGACAAAATCGGAAAAAGTTACCGAATATGTTGAAAGTGTCGATAATT
66 AAAAT-GGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
*
581103 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGTAGTTATAGCGCT
130 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
* * *
581155 TAAAAAGTCTCGACACTTTATGAAAATATATCGATCCAAAACAATATAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* * * * * *
581220 AAAATCGGTCTC-AAAATGACAAAACCGGTAAATAGATATCGGATATGTTGAAAGTGACAATACT
66 AAAAT-GGTCTCAAAAATGACAAAACCGG-AAAAAGTTACCGGATATGTTGAAAGTGTCGATAAT
581284 TTAATA
129 TTAATA
581290 AGTACGCGTA
Statistics
Matches: 287, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
181 16 0.06
182 271 0.94
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (181 bp):
TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
AAAATGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATTT
AATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCT
Found at i:581678 original size:18 final size:19
Alignment explanation
Indices: 581655--581699 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
581645 TAGTTAATAT
581655 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
581673 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
581692 TTTTAGGT
1 TTATAGGT
581700 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:583849 original size:198 final size:195
Alignment explanation
Indices: 583326--583984 Score: 736
Period size: 198 Copynumber: 3.3 Consensus size: 195
583316 TTTCAAAAAG
** * *
583326 TATCGA-CCCAAAAACATCGAAA-CAAATAATTATAATGTAATATTTAAATTAACAATGTAACCA
1 TATCGATCCCAAAAACATCGAAACCAAA-AATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * * *
583389 ATATACATATACCGGTTAATTATAAAACAGGTCAACATAAAGTATCGACACTTTTTAAGTTTGTG
65 GTATAAATATACCGGTTTATGAGAAAATAGGTCAA-ATAAAGTATCGACACTTTAT-AGTTTGTG
* * * * * * *
583454 TCAATACTTTTTTCCA-AAAGAAAGCACAAAC-AGGTTCACGCATAAAGTGTCGATACATTTAAA
128 TCGATACTTTTTTCCATAATGAATGC-CCAACGAGGTGCAAGAATAAAGTGTCGATACATTTAAA
583517 ATTA
192 ATTA
* * * *
583521 TATCGATCACAAAAACATCGAAACCGATAATTATAATGTAATAGGTCAATTTACAATGTAACCGG
1 TATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAACCGG
* * * *
583586 TTTAAATTTACCGGATTTATGAGAAAATAGGTCAGAATAAAGTATCGACACTTGTGTAATTTGTG
66 TATAAATATACCGG-TTTATGAGAAAATAGGTCA-AATAAAGTATCGACACTT-TATAGTTTGTG
* *
583651 TCGATACATTTTGTCCATAATGAATGCCCAACGAGGTGCAAGAATAACGTGTCGATACATTTAAA
128 TCGATAC-TTTTTTCCATAATGAATGCCCAACGAGGTGCAAGAATAAAGTGTCGATACATTTAAA
*
583716 ATTG
192 ATTA
* * *
583720 TATCGATCCCAAAAACATCGAAA-CAAAAATTACAATGTTATAGGTAAATTTACAATGTACCCGG
1 TATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAACCGG
*
583784 TATAAATATACCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCGACACCTTTATAGTTTGTG
66 TATAAATATACCGG-TTTATGAGAAAATAGGTC-AAATAAAGTATCGACA-CTTTATAGTTTGTG
* *
583849 TTGATACTTTTTTCCAGAATGAATTAGGAATGTCCAACGAGGTGCAA-ACATAAAGTGTCGATAC
128 TCGATACTTTTTTCC---AT-AA-T--GAATGCCCAACGAGGTGCAAGA-ATAAAGTGTCGATAC
583913 ATTTAAAATTA
185 ATTTAAAATTA
* * * * * *
583924 TATCGATCCAAAAAACAACGAAATCAATAATTATAATGTAATTGGTAAATTTGCAATGTAA
1 TATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAA
583985 TTGGTAAATT
Statistics
Matches: 391, Mismatches: 54, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
195 6 0.02
196 57 0.15
197 54 0.14
198 109 0.28
199 64 0.16
200 2 0.01
201 2 0.01
202 1 0.00
203 1 0.00
204 64 0.16
205 31 0.08
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (195 bp):
TATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAACCGG
TATAAATATACCGGTTTATGAGAAAATAGGTCAAATAAAGTATCGACACTTTATAGTTTGTGTCG
ATACTTTTTTCCATAATGAATGCCCAACGAGGTGCAAGAATAAAGTGTCGATACATTTAAAATTA
Found at i:583983 original size:20 final size:20
Alignment explanation
Indices: 583958--584001 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
583948 CAATAATTAT
583958 AATGTAATTGGTAAATTTGC
1 AATGTAATTGGTAAATTTGC
583978 AATGTAATTGGTAAATTTGC
1 AATGTAATTGGTAAATTTGC
583998 AATG
1 AATG
584002 CCAAGAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
AATGTAATTGGTAAATTTGC
Found at i:585736 original size:171 final size:166
Alignment explanation
Indices: 585459--585869 Score: 558
Period size: 171 Copynumber: 2.5 Consensus size: 166
585449 AAACATGAAC
* * * *
585459 AATAAAATCAACGTAAAAG-ATTAAAAAATATATTGAAACATTGTATTTATGTAAAATCCCAAAT
1 AATAGAATTAACGTAAAAGAATAAAAAAATATATTAAAACATTGTATTTATGTAAAATCCCAAAT
* *** * *
585523 ATCACTCTTTTTTTATTTTTTTATTGAATTACTAAATTTTGAGTATATTGATAAGGCACT-TTGT
66 ATCATTCTTTTAAAATTGTTTTATTGAATTACTAAATTTTGAGTATAGTGATAAGGCA-TGTTGT
* *
585587 TGATATTATTAAGAGAGATAATTACGAAACTCCTAAT
130 TCATATTATTAAGAGAGATAATTACGAAACTCCGAAT
* *
585624 AATAGAATTAACTTAAAAGAATAAAAAATATATATTAAAACATTGTATTTATGTAAAATCTCAAA
1 AATAGAATTAACGTAAAAGAATAAAAAA-ATATATTAAAACATTGTATTTATGTAAAATCCCAAA
*
585689 TATCATTCTTTTAAAAAAAATTGTTTTATTGAATTACTAAATTTTGAGTATAGTGATAAGGTATG
65 TATCATTCTTTT----AAAATTGTTTTATTGAATTACTAAATTTTGAGTATAGTGATAAGGCATG
585754 TTGTTCATATTATTAAGAGAGATAATTACGAAACTCCGAAT
126 TTGTTCATATTATTAAGAGAGATAATTACGAAACTCCGAAT
* * * * *
585795 AATAGAATTAACGTAAAAAAACAAAGAAA-ATATTAAAATATTATATTTATGTAAAATCCCAAAT
1 AATAGAATTAACGTAAAAGAATAAAAAAATATATTAAAACATTGTATTTATGTAAAATCCCAAAT
*
585859 ATCATTATTTT
66 ATCATTCTTTT
585870 TCCGAAGAAA
Statistics
Matches: 216, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
165 16 0.07
166 7 0.03
167 45 0.21
169 42 0.19
170 2 0.01
171 104 0.48
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (166 bp):
AATAGAATTAACGTAAAAGAATAAAAAAATATATTAAAACATTGTATTTATGTAAAATCCCAAAT
ATCATTCTTTTAAAATTGTTTTATTGAATTACTAAATTTTGAGTATAGTGATAAGGCATGTTGTT
CATATTATTAAGAGAGATAATTACGAAACTCCGAAT
Found at i:593300 original size:45 final size:45
Alignment explanation
Indices: 593250--593340 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
593240 TAATTTAGTT
*
593250 TTACAGCTCAATTTCGGTTAAACAAATCAATATTTTCTAATTAAA
1 TTACAGCTCAATTTCGGTTAAACAAATCAATATATTCTAATTAAA
* *
593295 TTACAGCTCAATTTTGGTTAGACAAATCAATATATTCTAATTAAA
1 TTACAGCTCAATTTCGGTTAAACAAATCAATATATTCTAATTAAA
593340 T
1 T
593341 CGATTAGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (45 bp):
TTACAGCTCAATTTCGGTTAAACAAATCAATATATTCTAATTAAA
Found at i:601016 original size:43 final size:43
Alignment explanation
Indices: 600945--601056 Score: 174
Period size: 43 Copynumber: 2.6 Consensus size: 43
600935 TCATATATCA
600945 GTTGTTTTCCTTTTTTGGCC-TTTTTTGGC-GAGATTAAGGTT
1 GTTGTTTTCCTTTTTTGGCCTTTTTTTGGCAGAGATTAAGGTT
*
600986 GTTGTATTTCTTTTTTTGGCCTTTTTTTGGCAGAGATTAAGGTT
1 GTTGT-TTTCCTTTTTTGGCCTTTTTTTGGCAGAGATTAAGGTT
* *
601030 GTCGTTTTCCTTTTTTGGCTTTTTTTT
1 GTTGTTTTCCTTTTTTGGCCTTTTTTT
601057 ATTGAGACCC
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
41 5 0.08
42 14 0.22
43 29 0.45
44 16 0.25
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (43 bp):
GTTGTTTTCCTTTTTTGGCCTTTTTTTGGCAGAGATTAAGGTT
Found at i:601169 original size:21 final size:19
Alignment explanation
Indices: 601143--601186 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
601133 CGATGGATAA
*
601143 ATATTATATTATAATAATTAC
1 ATATTAT-TTATAA-AAATAC
*
601164 ATATTATTTTTAAAAATAC
1 ATATTATTTATAAAAATAC
601183 ATAT
1 ATAT
601187 ATGATCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 5 0.24
21 7 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTATTTATAAAAATAC
Found at i:611420 original size:13 final size:13
Alignment explanation
Indices: 611385--611426 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
611375 CACTCATTTT
611385 TTAA-TATT-TTA
1 TTAATTATTATTA
*
611396 TT-ATTCTTATTA
1 TTAATTATTATTA
611408 TTAATTATTATTA
1 TTAATTATTATTA
611421 TTAATT
1 TTAATT
611427 TACATGCAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 5 0.19
12 5 0.19
13 15 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATTATTATTA
Found at i:612869 original size:28 final size:28
Alignment explanation
Indices: 612788--612869 Score: 67
Period size: 30 Copynumber: 2.8 Consensus size: 28
612778 GTGTTTATAT
** *
612788 ATATATATATGCTATATATAGTATGTGA
1 ATATATATATTATATATATATTATGTGA
*
612816 ATATATATCTATTTTATTATCCATATTATGT-A
1 ATATATA--TATTATA-TAT--ATATTATGTGA
612848 ATATATATATTATAGTATATAT
1 ATATATATATTATA-TATATAT
612870 GCATAACATG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
28 11 0.25
30 14 0.32
31 3 0.07
32 8 0.18
33 8 0.18
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (28 bp):
ATATATATATTATATATATATTATGTGA
Found at i:620360 original size:34 final size:33
Alignment explanation
Indices: 620322--620411 Score: 144
Period size: 34 Copynumber: 2.7 Consensus size: 33
620312 TCGGGTCATC
620322 AGTAAGTCTTCCGAGCATGATGATCAAATCCATT
1 AGTAAGTCTTCCGAGCATGATGATCAAATCCA-T
*
620356 AGTAAGTCTTCTGAGCATGATGATCAAATCCAT
1 AGTAAGTCTTCCGAGCATGATGATCAAATCCAT
*
620389 ATGTAAGTCTTTCGAGCATGATG
1 A-GTAAGTCTTCCGAGCATGATG
620412 CTTAAATCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 2 0.04
34 50 0.96
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (33 bp):
AGTAAGTCTTCCGAGCATGATGATCAAATCCAT
Found at i:620520 original size:79 final size:80
Alignment explanation
Indices: 620380--620547 Score: 198
Period size: 79 Copynumber: 2.1 Consensus size: 80
620370 GCATGATGAT
* * * * * **
620380 CAAATCCAT-ATGTAAGTCTTTCGAGCATGATGCTTAAATCTTTTGGGCCATCTTAAACCTTCAT
1 CAAATCCATCATGTAAGTATTCCGAGCATGACGATTAAATCCTCCGGGCCATCTTAAACCTTCA-
**
620444 C-GAAGTGTAGTGAAG
65 CAGAAGAATAGTGAAG
* * *
620459 CAAATCCATCA-GTAAGTATTCCGAGCATGACGATTAAGTCCTCCGGGCCATTTTAAGCCTTCAC
1 CAAATCCATCATGTAAGTATTCCGAGCATGACGATTAAATCCTCCGGGCCATCTTAAACCTTCAC
620523 AGAAGAATAGTGAAG
66 AGAAGAATAGTGAAG
620538 CAAATCCATC
1 CAAATCCATC
620548 TATCTAATAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
78 1 0.01
79 73 0.97
80 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (80 bp):
CAAATCCATCATGTAAGTATTCCGAGCATGACGATTAAATCCTCCGGGCCATCTTAAACCTTCAC
AGAAGAATAGTGAAG
Found at i:620749 original size:111 final size:111
Alignment explanation
Indices: 620549--621088 Score: 767
Period size: 111 Copynumber: 4.9 Consensus size: 111
620539 AAATCCATCT
* * * * *
620549 ATCTAATATTCTCTTCAGAAGAAGTGGAACAGATCACTCT-TTTCAAGATTTGATACTCCCTGAG
1 ATCTGATATTC-CCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
* * *
620613 TAACAGCGGAACAAGTCTACCCTGATTCAATAAATCAACTTTCCCAA
65 TGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * * * *
620660 ATCTGATATTCCCTCAGAGGAAGTGGAATAAATCCCTCTCTTTTAAGATTTGATATTCCCTGAGC
1 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
* * *
620725 GACAGTGGAACAAGTCTACACTGATTCAATGGATCAACTTTCCCAG
66 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * *
620771 ATCTGATATTCCCTCAGAAGAAACGAAACAAATCCCTCTCTTTCAAGATTTGATAGTCCCTGAGT
1 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
620836 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
66 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * *
620882 ATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCTTCTCTTTCATGATTTGATATTCCTTGAGT
1 ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
*
620947 GACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTCCCAG
66 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * * *
620993 ATCTGATATTCCCTTCAGAAGAAGCAGAACAGATTCTTATCTTCCAAGATTTGATATTCCCTGAG
1 ATCTGATATTCCC-TCAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
*
621058 TGACAGCGGAACAAGTCTACACTGATTCAAT
65 TGACAGCGGAACAAGTCTACCCTGATTCAAT
621089 CTTCCCTGAA
Statistics
Matches: 384, Mismatches: 43, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
110 23 0.06
111 287 0.75
112 74 0.19
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (111 bp):
ATCTGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
Found at i:621306 original size:3 final size:3
Alignment explanation
Indices: 621296--621333 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
621286 TTTTTTTTAA
621296 TAT T-T TAT TAT TAT TAT TAT TAT TAAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA
621334 ATTTACATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:621326 original size:13 final size:13
Alignment explanation
Indices: 621300--621336 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
621290 TTTTAATATT
621300 TTATTATT-ATTA
1 TTATTATTAATTA
621312 TTATTATTAATTA
1 TTATTATTAATTA
621325 TTATTATTAATT
1 TTATTATTAATT
621337 TACATGCAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:622853 original size:2 final size:2
Alignment explanation
Indices: 622846--622882 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
622836 TTAAATACGA
622846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
622883 ATTTACGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:626326 original size:21 final size:22
Alignment explanation
Indices: 626290--626360 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
626280 TTGGTACAGA
* *
626290 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
626312 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
626335 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATTCCCCCTTGAAG
626356 GGGAA
1 GGGAA
626361 TTGATACCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.20
22 14 0.31
23 22 0.49
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:626370 original size:21 final size:22
Alignment explanation
Indices: 626290--626370 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 22
626280 TTGGTACAGA
*
626290 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
626312 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
626335 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
**
626356 GGGAATTGATACCCC
1 GGGAACCGATACCCC
626371 TTGGAGGTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.31
22 14 0.27
23 22 0.42
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:627981 original size:18 final size:18
Alignment explanation
Indices: 627946--627984 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
627936 GGAGCAGCAC
*
627946 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
627964 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
627982 GAG
1 GAG
627985 TATCAAATGC
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:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:629776 original size:16 final size:17
Alignment explanation
Indices: 629748--629781 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
629738 TGTATCGCCA
629748 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
629765 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
629781 A
1 A
629782 TGTGAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:648872 original size:164 final size:164
Alignment explanation
Indices: 648621--649280 Score: 585
Period size: 182 Copynumber: 3.8 Consensus size: 164
648611 TAGCGCCTAT
* * * * *
648621 AAAGTGTCGATACTTTAAAAAAATATATCGA-TCTACAACAATATAACATGTAAAAATATGATAA
1 AAAGTGTCGACACTTTATAAAAATGTATCGATTC-ATAACAATATAACAGGTAAAAATATGATAA
* * *
648685 AACAT-GTCTCAAAATTGACAAAACCAGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATT
65 AAC-TGGTCTCAAAAATGACAAAACCAG-AAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
648749 TAATATAAGTATCGACACTTTCTGAAATTAAAC-TAA
128 TAATATAAGTATCGACACTTTCTGAAATTAAACTTAA
*
648785 AAAGTGTCGACACTTTATGAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGATAAA
** *
648850 ACTGGTCTCAAAAATGACAAAACTGGAAAAAGTTACCGGATATGTTGAAAGTTTCGATAATTTAA
66 ACTGGTCTCAAAAATGACAAAACCAGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATTTAA
* * * *
648915 TGTTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAT
131 TATAAGTATCGACACTTTC------T------G-A-AA-TTA-A--ACTTAA
* * * * * *
648967 AAAGTGCCGACACTTTATTAAAATGTATCGATCCTTACCAATATAACAGGTAAATATATGATAAA
1 AAAGTGTCGACACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGATAAA
* * *
649032 ACAGGTCTCAAAAATGACAAAACCAGAAAAATTTATCGGATATGTTGAAAGTGTCGATAATTTAA
66 ACTGGTCTCAAAAATGACAAAACCAGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATTTAA
* *
649097 TATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAG
131 TATAAGTATCGACACTTTC------T------G-A-AA-TTA-A--ACTTAA
* *
649149 AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGATAAA
* * * ** *
649214 ACCGGTCTC-AAAATGACAAAACC-GATAAATAGATATCATATATGTTGAAAGT-TACGATACTT
66 ACTGGTCTCAAAAATGACAAAACCAGA-AAA-AGTTACCGGATATGTTGAAAGTGT-CGATAATT
649276 TAATA
128 TAATA
649281 AGTACGCGTA
Statistics
Matches: 430, Mismatches: 42, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
163 54 0.13
164 77 0.18
165 2 0.00
169 1 0.00
175 1 0.00
176 1 0.00
177 2 0.00
178 3 0.01
179 1 0.00
180 2 0.00
181 19 0.04
182 267 0.62
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (164 bp):
AAAGTGTCGACACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGATAAA
ACTGGTCTCAAAAATGACAAAACCAGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATTTAA
TATAAGTATCGACACTTTCTGAAATTAAACTTAA
Found at i:649107 original size:182 final size:180
Alignment explanation
Indices: 648785--649280 Score: 760
Period size: 182 Copynumber: 2.7 Consensus size: 180
648775 ATTAAACTAA
*
648785 AAAGTGTCGACACTTTATGAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * *
648850 ACTGGTCTCAAAAATGACAAAACTGGAAAAAGTTACCGGATATGTTGAAAGTTTCGATAATTTAA
66 ACAGGTCTCAAAAATGACAAAAC-CGAAAAAGTTATCGGATATGTTGAAAG-TTCGATAATTTAA
* * *
648915 TGTTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAT
129 TATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAG
* * * * *
648967 AAAGTGCCGACACTTTATTAAAATGTATCGATCCTTACCAATATAACAGGTAAATATATGATAAA
1 AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
*
649032 ACAGGTCTCAAAAATGACAAAACCAGAAAAATTTATCGGATATGTTGAAAGTGTCGATAATTTAA
66 ACAGGTCTCAAAAATGACAAAACC-GAAAAAGTTATCGGATATGTTGAAAGT-TCGATAATTTAA
649097 TATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAG
129 TATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAG
649149 AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * ** *
649214 ACCGGTCTC-AAAATGACAAAACCGATAAATAGATATCATATATGTTGAAAGTTACGATACTTTA
66 ACAGGTCTCAAAAATGACAAAACCGA-AAA-AGTTATCGGATATGTTGAAAGTT-CGATAATTTA
649278 ATA
128 ATA
649281 AGTACGCGTA
Statistics
Matches: 285, Mismatches: 24, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
180 2 0.01
181 19 0.07
182 264 0.93
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (180 bp):
AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
ACAGGTCTCAAAAATGACAAAACCGAAAAAGTTATCGGATATGTTGAAAGTTCGATAATTTAATA
TAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAG
Found at i:649691 original size:18 final size:19
Alignment explanation
Indices: 649668--649712 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
649658 TAGTTAATAT
649668 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
649686 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
649705 TTTTAGGT
1 TTATAGGT
649713 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:649998 original size:18 final size:17
Alignment explanation
Indices: 649962--650002 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
649952 GTTGAAATGG
649962 TAAATGGATTAAAACTT
1 TAAATGGATTAAAACTT
* *
649979 TAAATTGATTAAAAATTT
1 TAAATGGATT-AAAACTT
649997 TAAATG
1 TAAATG
650003 TTGACAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (17 bp):
TAAATGGATTAAAACTT
Found at i:651816 original size:197 final size:194
Alignment explanation
Indices: 651329--651983 Score: 732
Period size: 197 Copynumber: 3.3 Consensus size: 194
651319 TTTTCAAAAA
** *
651329 GTATCGA-CCCAAAAACATCGAAA-CAAATAATTATAATGTAATATTTAAATTAACAATGTAACC
1 GTATCGATCCCAAAAACATCGAAACCAAA-AATTATAATGTAATAGGTAAATTTACAATGTAACC
* * * * * * *
651392 AGTATACATATACCGGTTAATTATAAAACAGGTCA-ACATAAAGTATCGACACTTCTTAAGTTTG
65 GGTATAAATATACCGTTTTATGAGAAAATAGGTCATA-ATAAAGTATCGACACTT-TTAA-TTTG
* * * * *
651456 TGTCGATACTTTTTCCA-AAAGAAAGCACAAAC-AGGTTCACGCATAAAGTGTCGATACATTTAA
127 TGTCGATACTTTTTCCATAATGAATGC-CCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAA
651519 AATT
191 AATT
* * * * * *
651523 ATATCGATCACAAAAACATCGAAACCGATAATTATAATGTAATAGGTCAATTTACAATGTAGCCG
1 GTATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
651588 GTTTAAATTTACCGGTTTTATGAGAAAATAGGTCATAATAAAGTATCGACACTTGTGTAATTTGT
66 GTATAAATATACC-GTTTTATGAGAAAATAGGTCATAATAAAGTATCGACACTT-T-TAATTTGT
* *
651653 GTCGATACATTTTGTCCATAATGAATGCCCAACGAGGTGCAAGAATAACGTGTCGATACATTTAA
128 GTCGATAC-TTTT-TCCATAATGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAA
651718 AATT
191 AATT
* * *
651722 GTATCGATCCCAAAAA-ATCGAAA-CAAAAATTACAATGTTATAGGTAAATTTACAATGTACCCG
1 GTATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
651785 GTATAAATATACCGATTTTATGAGAAAATAGGTC-TAAATAATGTATCGACACCTTTATAGTTTG
66 GTATAAATATACCG-TTTTATGAGAAAATAGGTCAT-AATAAAGTATCGACA-CTTT-TAATTTG
* *
651849 TGTTGATACTTTTTTCCAGAATGAATTAGGAATGCCCAACGAGGTGCAAGCATAAAGTGTAGATA
127 TGTCGATAC-TTTTTCC---AT-AA-T--GAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATA
651914 CATTTAAAATT
184 CATTTAAAATT
* * * *
651925 GTATCAATCCAAAAAACAACGAAACCAATAATTATAATGTAATAGGTAAATTTACAATG
1 GTATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATG
651984 CCAAGAACAT
Statistics
Matches: 390, Mismatches: 50, Indels: 31
0.83 0.11 0.07
Matches are distributed among these distances:
194 6 0.02
195 55 0.14
196 54 0.14
197 105 0.27
198 18 0.05
199 54 0.14
200 2 0.01
201 1 0.00
203 58 0.15
204 6 0.02
205 31 0.08
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (194 bp):
GTATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAATTTACAATGTAACCG
GTATAAATATACCGTTTTATGAGAAAATAGGTCATAATAAAGTATCGACACTTTTAATTTGTGTC
GATACTTTTTCCATAATGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATT
Found at i:653695 original size:167 final size:167
Alignment explanation
Indices: 653476--653815 Score: 497
Period size: 170 Copynumber: 2.0 Consensus size: 167
653466 AAAATCAACG
* * * **
653476 TAAAAGATTAAAAAATATATTGAAACATTGTATTTATGTAAAATCCCAAATATCACTCTTTT-TT
1 TAAAAGATAAAAAAATATATTAAAACATAGTATTTATGTAAAATCCCAAATATCACTCTTTTAAA
*
653540 AAATT-TTTTATTGAATTACTAAATTTTGAGTATACTGATAAGACACT-TTGTTGATATTATTAA
66 AAATTGTTTTATTGAATTACTAAATTTTGAGTATACTGATAAGACA-TGTTGTTCATATTATTAA
* *
653603 GAGAGATAATTACGAAACTCCTAATAATAGAATTAACT
130 GAGAGATAATTACGAAACTCCGAATAATAGAATTAACA
* *
653641 TAAAAGAATAAAAAATATATATTAAAACATAGTATTTATGTAAAATCTCAAATATCATTCTTTTA
1 TAAAAG-ATAAAAAA-ATATATTAAAACATAGTATTTATGTAAAATCCCAAATATCACTCTTTT-
* **
653706 AAAAAATTGTTTTATTGAATTACTAAATTTTGAGTATAGTGATAAGGTATGTTGTTCATATTATT
63 AAAAAATTGTTTTATTGAATTACTAAATTTTGAGTATACTGATAAGACATGTTGTTCATATTATT
*
653771 AAGAGAGATAATTATGAAACTCCGAATAATAGAATTAACA
128 AAGAGAGATAATTACGAAACTCCGAATAATAGAATTAACA
653811 TAAAA
1 TAAAA
653816 AAACAATGAA
Statistics
Matches: 155, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
165 6 0.04
166 7 0.05
167 44 0.28
169 6 0.04
170 92 0.59
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (167 bp):
TAAAAGATAAAAAAATATATTAAAACATAGTATTTATGTAAAATCCCAAATATCACTCTTTTAAA
AAATTGTTTTATTGAATTACTAAATTTTGAGTATACTGATAAGACATGTTGTTCATATTATTAAG
AGAGATAATTACGAAACTCCGAATAATAGAATTAACA
Found at i:675673 original size:16 final size:15
Alignment explanation
Indices: 675652--675690 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
675642 ATAGCCTCTA
*
675652 AATCATTCAGCATCTT
1 AATCATTCAGC-GCTT
*
675668 AATCATTTAGCGCTT
1 AATCATTCAGCGCTT
675683 AATCATTC
1 AATCATTC
675691 TGAAGTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (15 bp):
AATCATTCAGCGCTT
Found at i:678197 original size:16 final size:17
Alignment explanation
Indices: 678172--678214 Score: 79
Period size: 16 Copynumber: 2.6 Consensus size: 17
678162 AAATTTGAAA
678172 TTTATATGTTCAATTTT
1 TTTATATGTTCAATTTT
678189 TTT-TATGTTCAATTTT
1 TTTATATGTTCAATTTT
678205 TTTATATGTT
1 TTTATATGTT
678215 AAAAAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (17 bp):
TTTATATGTTCAATTTT
Found at i:679879 original size:6 final size:6
Alignment explanation
Indices: 679870--680472 Score: 650
Period size: 6 Copynumber: 101.8 Consensus size: 6
679860 TGCATAAGCA
* * * ** * *
679870 TATACG TATACG TATACG TATATG TATACA TATATG TATACG TATACG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * ** *
679918 TATATG TATACG TATACG TATACG TATATG TATACA TATATG TATACG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * * *
679966 TATATG TATA-G TATACG TATACG TATATG TATGTA TACGTATG TATACG
1 TATATG TATATG TATATG TATATG TATATG TATATG TA--TATG TATATG
* * * * *
680015 TATATTA TATATG TATACG --TATG TATATA CATATAA TATATG TATATG
1 TATA-TG TATATG TATATG TATATG TATATG TATAT-G TATATG TATATG
*
680063 TATATG TATATG TATACG TATATG TATATG TATATG TATA-G TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * *
680110 TATATA TGTATA T-TATG TATATG TATATG TATACG TATATG T-TATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * *
680156 TATACG TATATG TATATG --TACG TATAAG TA-GTG TATATG --TATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* *
680199 TATACG TATATG TATATG TATACG TACGTATG TATATG TAT-TG T-TATG
1 TATATG TATATG TATATG TATATG TA--TATG TATATG TATATG TATATG
680247 TATA-G TATATG TATATG TATATG TATCGTATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TA---TATG TATATG TATATG TATATG
*
680297 TATATG TATATG GATATG TATATG TATATAG TATAATG TATATG -ATATG
1 TATATG TATATG TATATG TATATG TATAT-G TAT-ATG TATATG TATATG
680346 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
680394 TATATG TATATG TATCT- TATATG TATATG TATATG TATATG ---ATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
680438 TATATG TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
680473 ATATTGTGTT
Statistics
Matches: 515, Mismatches: 52, Indels: 60
0.82 0.08 0.10
Matches are distributed among these distances:
3 3 0.01
4 11 0.02
5 42 0.08
6 425 0.83
7 17 0.03
8 11 0.02
9 6 0.01
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.45
Consensus pattern (6 bp):
TATATG
Found at i:693678 original size:45 final size:45
Alignment explanation
Indices: 693613--693703 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
693603 TATATAATCG
*
693613 ATTTAATTAGAATATATTGATTTGTCTAACCAAAATTGAGCTGTA
1 ATTTAATTAGAAAATATTGATTTGTCTAACCAAAATTGAGCTGTA
* *
693658 ATTTAATTAGAAAA-ATTTGATTTGTTTAACCGAAATTGAGCTGTA
1 ATTTAATTAGAAAATA-TTGATTTGTCTAACCAAAATTGAGCTGTA
693703 A
1 A
693704 AACTAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (45 bp):
ATTTAATTAGAAAATATTGATTTGTCTAACCAAAATTGAGCTGTA
Found at i:696814 original size:24 final size:23
Alignment explanation
Indices: 696783--696833 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
696773 TATATTAATA
696783 TTTAATTTT-ATATCTCTTAAATT
1 TTTAATTTTCATAT-TCTTAAATT
*
696806 TTTATATTTTCGTATTCTTAAATT
1 TTTA-ATTTTCATATTCTTAAATT
696830 TTTA
1 TTTA
696834 CATTCCATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 18 0.72
25 3 0.12
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTAATTTTCATATTCTTAAATT
Found at i:703191 original size:3 final size:3
Alignment explanation
Indices: 703183--703215 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
703173 GAGGTAAAGA
703183 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
703216 TATGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:704998 original size:28 final size:28
Alignment explanation
Indices: 704906--705003 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
704896 TGGATGCTTT
* * *
704906 TTATTTTAATTTGTAAAAAATATAGGGTA
1 TTATTGTAATTTATAAAAATTATA-GGTA
* * * ** *
704935 TTATTGTAATTT-GAAAAATGCAGACCTT
1 TTATTGTAATTTATAAAAAT-TATAGGTA
704963 TTCA-TGTAATTTATAAAAATTATAGGTA
1 TT-ATTGTAATTTATAAAAATTATAGGTA
704991 TTATTGTAATTTA
1 TTATTGTAATTTA
705004 GAGAAGTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
27 1 0.02
28 30 0.59
29 20 0.39
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (28 bp):
TTATTGTAATTTATAAAAATTATAGGTA
Found at i:705050 original size:29 final size:28
Alignment explanation
Indices: 704967--705066 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
704957 GACCTTTTCA
* *
704967 TGTAATTTATAAAAATTATAGGTA-TTAT
1 TGTAATTTATAAAAGTT-TTGGTATTTAT
* * * *
704995 TGTAATTTAGAGAAGTTTT-TTCTTTTAT
1 TGTAATTTATAAAAGTTTTGGT-ATTTAT
705023 TGTAATTTATAAATAGTTTTGGTATTTAT
1 TGTAATTTATAAA-AGTTTTGGTATTTAT
*
705052 TGTAATATTAAAAAA
1 TGTAAT-TTATAAAA
705067 TTGACTTCTA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 29 0.52
29 18 0.32
30 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (28 bp):
TGTAATTTATAAAAGTTTTGGTATTTAT
Found at i:711202 original size:19 final size:19
Alignment explanation
Indices: 711149--711205 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 19
711139 TATATATATA
*
711149 TACAAAGACCAAATTCGAT
1 TACAAAGACCAAATTCGAG
*
711168 TAAAGAAAATGACCAAATTCGAG
1 T--A-CAAA-GACCAAATTCGAG
711191 TACAAAGACCAAATT
1 TACAAAGACCAAATT
711206 TACAACATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 10 0.32
20 3 0.10
21 2 0.06
22 3 0.10
23 13 0.42
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (19 bp):
TACAAAGACCAAATTCGAG
Found at i:712746 original size:12 final size:12
Alignment explanation
Indices: 712729--712753 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
712719 CGAAAATTAG
712729 AAAATTTAAATT
1 AAAATTTAAATT
712741 AAAATTTAAATT
1 AAAATTTAAATT
712753 A
1 A
712754 CTCAATTCGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:714240 original size:9 final size:9
Alignment explanation
Indices: 714226--714285 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
714216 CTGAAAAAAC
714226 AAAATAAAT
1 AAAATAAAT
714235 AAAATAAAT
1 AAAATAAAT
**
714244 AAAACGAAT
1 AAAATAAAT
714253 AATAA-AAAT
1 AA-AATAAAT
*
714262 AAAA-AAAA
1 AAAATAAAT
* *
714270 AAAAAAAAA
1 AAAATAAAT
714279 AAAATAA
1 AAAATAA
714286 TTATATATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
8 9 0.20
9 33 0.75
10 2 0.05
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (9 bp):
AAAATAAAT
Found at i:714285 original size:31 final size:31
Alignment explanation
Indices: 714226--714286 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
714216 CTGAAAAAAC
* * * **
714226 AAAATAAATAAAATAAATAAAACGAATAATA
1 AAAATAAAAAAAAAAAAAAAAAAAAATAATA
714257 AAAATAAAAAAAAAAAAAAAAAAAAATAAT
1 AAAATAAAAAAAAAAAAAAAAAAAAATAAT
714287 TATATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.15
Consensus pattern (31 bp):
AAAATAAAAAAAAAAAAAAAAAAAAATAATA
Found at i:714414 original size:2 final size:2
Alignment explanation
Indices: 714399--714463 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
714389 TTTCAAAGAT
*
714399 TA TA TA T- TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
714440 TA TA TT TG TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
714464 AAACAAAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:715185 original size:165 final size:162
Alignment explanation
Indices: 715029--716038 Score: 1059
Period size: 165 Copynumber: 6.1 Consensus size: 162
715019 CTTTGCCTTG
* *
715029 AGCTATGCTGTAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCAAAGGTC-TTTGGCAGAT
1 AGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGCAGAT
* * * *
715093 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGA
65 AACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGA
* * *
715158 AGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTG
130 AGGTC-TTTGGTC-CAGATAACCCTTCTCGACTTA
* * * * * * ***
715193 AGTTATGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGCAGA
1 AGCTATGCTGCAAATGATG-TGCCTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGCAGA
*
715257 TAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAATCGAACTC
64 TAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAATCGAACTC
* * * *
715321 AAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTA
128 GAAGGTC-TTTGGT-CCAGATAACCCTTCTCGACTTA
* * * *
715358 AGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
1 AGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTC-TT--TTGGCA
* * * * * *
715423 GATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
62 GATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAAC
** *
715488 TCGGGGGTCTTTGG--CAGATAGCCCTTCTCGACTTA
126 TCGAAGGTCTTTGGTCCAGATAACCCTTCTCGACTTA
*
715523 AGCTATGCTGCAAATGATGTGCCGTTGAGCTGAACGTAGTCGAACTCAAAGGTCTTTGGTTGGCA
1 AGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TT--TTGGCA
* * * * *
715588 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
62 GATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAAC
*
715653 TCGAAGGTCTTTGG--CAGATAGCCCTTCTCGACTTA
126 TCGAAGGTCTTTGGTCCAGATAACCCTTCTCGACTTA
* *
715688 AGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAACGGTCTTTTGTTGCCA
1 AGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG--G-CA
* * * * * * * * *
715753 GACAACCCTTCTAGACTTAAGTTGTACTACAAATTATATACCTTGGAGCTGAGCGTAGTCGAACT
62 GATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACT
*
715818 CGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
127 CGAAGGTCTTTGG-T-CCAGATAACCCTTCTCGACTTA
* ** * * *
715856 AGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGGCAGA
1 AGCTATGCTGCAAATGATGTG-CCT-TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGCAGA
* * *
715920 TAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTC
64 TAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAATCGAACTC
* * *
715984 -AACGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTA
128 GAA-GGTC-TTTGGT-CCAGATAACCCTTCTCGACTTA
* *
716021 AGTTGTGCTGCAAATGAT
1 AGCTATGCTGCAAATGAT
716039 TTGTTTTTAA
Statistics
Matches: 735, Mismatches: 87, Indels: 47
0.85 0.10 0.05
Matches are distributed among these distances:
162 3 0.00
164 85 0.12
165 493 0.67
166 13 0.02
168 91 0.12
169 50 0.07
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (162 bp):
AGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGCAGATA
ACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAA
GGTCTTTGGTCCAGATAACCCTTCTCGACTTA
Found at i:715474 original size:249 final size:245
Alignment explanation
Indices: 715007--715959 Score: 1200
Period size: 249 Copynumber: 3.8 Consensus size: 245
714997 ATTTTATTGA
* * * * * *
715007 CAGATAGCCCTTCTTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGTTGAGCGTAGTCGA
1 CAGATAGCCCTTC-TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
715072 ACTCAAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
65 ACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
* * * * * * *
715133 TGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTA
130 TAGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGG---CAGATAACCCTTCTCGACTTAAGCTA
* * *
715198 TGCTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
191 TACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
*
715253 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAATCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGA
* * * * * *
715317 ACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCT
65 ACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
* *
715382 TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
130 TAGAGCTGAGCGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTA
* *
715447 TGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
191 TACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* *
715502 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAACGTAGTCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGA
*
715566 ACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCC
65 ACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
* * *
715631 TCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
130 TAG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATAC
* * * * ***
715696 TGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAACGGTCTTTTGTTG
194 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG--G
* * * * * * * * *
715750 CCAGACAACCCTTCTAGACTTAAGTTGTACTACAAATTATATACCTTGGAGCTGAGCGTAGTCGA
1 -CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
715815 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCC
65 ACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CC
* * * *
715880 TCAAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
129 TTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATAC
715945 TGCAAATGATGTGCC
194 TGCAAATGATGTGCC
715960 GTTGAGCTGA
Statistics
Matches: 632, Mismatches: 60, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
245 74 0.12
246 65 0.10
247 1 0.00
248 4 0.01
249 455 0.72
250 29 0.05
252 4 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (245 bp):
CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
AGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTG
CAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
Found at i:715804 original size:414 final size:414
Alignment explanation
Indices: 715032--716038 Score: 1660
Period size: 414 Copynumber: 2.4 Consensus size: 414
715022 TGCCTTGAGC
* * * * * *
715032 TATGCTGTAAATGATGTG-CCTTGGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTGGCAGATAGC
1 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGC
*
715096 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCAAACTCGAAG
66 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTCAAAG
* * * * *
715160 GTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGC
130 GTC-TTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGC
**
715224 TGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
194 TGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
715289 GATGTGCCGTTGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGA
259 GATGTGCCGTTGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGA
* * *
715354 CTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTT
324 CTTAAGTTGTACTACAAATGATATACCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTT
715419 GGCAGATAACCCTTCTCGACTTAAGT
389 GGCAGATAACCCTTCTCGACTTAAGT
**
715445 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGC
1 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGC
* *
715510 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAACGTAGTCGAACTCAAAGG
66 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGG
* *
715575 TCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTG
131 TCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTG
715640 AGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGA
196 AGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGA
* *
715705 TGTGCCGTTGAGCTGAGCGTAGTCGAACTCAACGGTCTTTTGTTGCCAGACAACCCTTCTAGACT
261 TGTGCCGTTGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACT
* *
715770 TAAGTTGTACTACAAATTATATACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
326 TAAGTTGTACTACAAATGATATACCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
715835 CAGATAACCCTTCTCGACTTAAGT
391 CAGATAACCCTTCTCGACTTAAGT
* *
715859 TATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGC
1 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGC
* *
715924 CCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAACGG
66 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGG
* * * *
715989 TCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGAT
131 TCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
716039 TTGTTTTTAA
Statistics
Matches: 551, Mismatches: 40, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
413 23 0.04
414 526 0.95
415 2 0.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (414 bp):
TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGC
CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGG
TCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTG
AGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGA
TGTGCCGTTGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACT
TAAGTTGTACTACAAATGATATACCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
CAGATAACCCTTCTCGACTTAAGT
Found at i:717227 original size:84 final size:86
Alignment explanation
Indices: 717131--717359 Score: 268
Period size: 96 Copynumber: 2.6 Consensus size: 86
717121 GGCTAGCTAA
717131 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCCCAATAT-GTA-AA-CACCT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCCCAATATAGTATAATCACCT
*
717193 TTATCAGGCTAGCTGAAATCTT
66 TTATCAGGCTAGCTG-AATATT
*
717215 ATCCATAAAGCCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAGC-C---C---A--ATATAGT
717279 ATAATCACCTTTATCAGGCTAGCTGAATATT
56 ATAATCACCTTTATCAGGCTAGCTGAATATT
* * * *
717310 ATCCATAAAGCTGAGGCGTTTTAACCAATTGCTTTAGAGGGACAACCCAA
1 ATCCATAAAGCCGGGGCG-TTTAACCAATTGCTCTAGAGGGACAGCCCAA
717360 GCTTTATTGT
Statistics
Matches: 123, Mismatches: 7, Indels: 27
0.78 0.04 0.17
Matches are distributed among these distances:
83 1 0.01
84 43 0.35
85 1 0.01
88 1 0.01
89 1 0.01
91 1 0.01
92 1 0.01
93 3 0.02
94 3 0.02
95 24 0.20
96 44 0.36
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (86 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCCCAATATAGTATAATCACCT
TTATCAGGCTAGCTGAATATT
Found at i:717352 original size:96 final size:95
Alignment explanation
Indices: 717179--717378 Score: 303
Period size: 96 Copynumber: 2.1 Consensus size: 95
717169 GGACAGCCCA
* * * *
717179 ATATGTAAACACCTTTATCAGGCTAGCTGAAATCTTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATATATAATCACCTTTATCAGGCTAGCTGAAATATTATCCATAAAGCCGAGGCGTTTAACCAATT
* *
717244 GCCTTAGAGGGACAGCTCAAGCTTTATTGT
66 GCCTTAGAGGGACAACCCAAGCTTTATTGT
*
717274 ATAGTATAATCACCTTTATCAGGCTAGCTG-AATATTATCCATAAAGCTGAGGCGTTTTAACCAA
1 ATA-TATAATCACCTTTATCAGGCTAGCTGAAATATTATCCATAAAGCCGAGGCG-TTTAACCAA
*
717338 TTGCTTTAGAGGGACAACCCAAGCTTTATTGT
64 TTGCCTTAGAGGGACAACCCAAGCTTTATTGT
717370 ATATATAAT
1 ATATATAAT
717379 AGTATAATCT
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
95 30 0.32
96 65 0.68
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (95 bp):
ATATATAATCACCTTTATCAGGCTAGCTGAAATATTATCCATAAAGCCGAGGCGTTTAACCAATT
GCCTTAGAGGGACAACCCAAGCTTTATTGT
Found at i:722199 original size:6 final size:6
Alignment explanation
Indices: 722188--722221 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
722178 TAAAACGAAT
*
722188 AATAAA AATAAA AA-AAA AATAAT AATAAA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAA
722222 TTATATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:722208 original size:20 final size:22
Alignment explanation
Indices: 722170--722221 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
722160 CTGAAAAAAC
*
722170 AAAATAAATAAAACGAATAATA
1 AAAATAAATAAAACAAATAATA
* *
722192 AAAATAAAAAAAAAATAATAATA
1 AAAATAAATAAAACA-AATAATA
722215 AAAATAA
1 AAAATAA
722222 TTATATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAATAAATAAAACAAATAATA
Found at i:722266 original size:38 final size:38
Alignment explanation
Indices: 722220--722306 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 38
722210 TAATAAAAAT
*
722220 AATTATATATTATATATATATTT-AAAAATGATTTC-AA
1 AATTATATAATATATATAT-TTTCAAAAATGATTTCGAA
* *
722257 AATCTATATAATATATTTATTTTCGAAAACTGATTTCTGAA
1 AAT-TATATAATATATATATTTTC-AAAAATGATTTC-GAA
722298 AATTATATA
1 AATTATATA
722307 CCATATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 6 0.14
38 14 0.33
39 11 0.26
40 6 0.14
41 5 0.12
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (38 bp):
AATTATATAATATATATATTTTCAAAAATGATTTCGAA
Found at i:722348 original size:2 final size:2
Alignment explanation
Indices: 722332--722366 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
722322 ACCTTTTCAA
722332 AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
722367 AAACAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:725252 original size:17 final size:18
Alignment explanation
Indices: 725219--725252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
725209 CCGTTATTAG
725219 TGAACCGATCAGAACCGC
1 TGAACCGATCAGAACCGC
*
725237 TGAACCGTTC-GAACCG
1 TGAACCGATCAGAACCG
725253 GACCGACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (18 bp):
TGAACCGATCAGAACCGC
Found at i:729016 original size:36 final size:38
Alignment explanation
Indices: 728966--729043 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
728956 TATAATAATA
728966 TAAATTGTAAAATATTTATAT-ATTTTCTTTAAAAAAT
1 TAAATTGTAAAATATTTATATAATTTTCTTTAAAAAAT
* * *
729003 TAAATT-TATAATATTTATATAATTTTTTTTATAAAAT
1 TAAATTGTAAAATATTTATATAATTTTCTTTAAAAAAT
729040 TAAA
1 TAAA
729044 AATATAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 13 0.35
37 24 0.65
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
TAAATTGTAAAATATTTATATAATTTTCTTTAAAAAAT
Found at i:729440 original size:11 final size:11
Alignment explanation
Indices: 729424--729449 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
729414 AACAAACACC
729424 CCTTAATTATG
1 CCTTAATTATG
729435 CCTTAATTATG
1 CCTTAATTATG
729446 CCTT
1 CCTT
729450 TTACCAATCT
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (11 bp):
CCTTAATTATG
Found at i:740413 original size:6 final size:6
Alignment explanation
Indices: 740395--740450 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
740385 TTGACCAGAG
* * *
740395 TTGACT GTTGACT TTGACT ATTGAC- CTGACT TTGACA TTGACCG TTGACT
1 TTGACT -TTGACT TTGACT -TTGACT TTGACT TTGACT TTGA-CT TTGACT
740445 TTGACT
1 TTGACT
740451 CAAAAAGTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
5 4 0.10
6 21 0.51
7 16 0.39
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (6 bp):
TTGACT
Found at i:740413 original size:13 final size:13
Alignment explanation
Indices: 740395--740450 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
740385 TTGACCAGAG
740395 TTGACTGTTGACT
1 TTGACTGTTGACT
*
740408 TTGACTATTGAC-
1 TTGACTGTTGACT
* *
740420 CTGACT-TTGACA
1 TTGACTGTTGACT
*
740432 TTGACCGTTGACT
1 TTGACTGTTGACT
740445 TTGACT
1 TTGACT
740451 CAAAAAGTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 5 0.14
12 9 0.26
13 21 0.60
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (13 bp):
TTGACTGTTGACT
Found at i:740442 original size:24 final size:25
Alignment explanation
Indices: 740396--740443 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
740386 TGACCAGAGT
* *
740396 TGACTGTTGACTTTGACTATTGACC
1 TGACTGTTGACATTGACCATTGACC
*
740421 TGACT-TTGACATTGACCGTTGAC
1 TGACTGTTGACATTGACCATTGAC
740444 TTTGACTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (25 bp):
TGACTGTTGACATTGACCATTGACC
Done.